SYNERGISTIC BACTERIAL COMPOSITIONS AND METHODS OF PRODUCTION AND USE THEREOF

[0001] This application is a divisional application of U.S. patent application Ser. No. 14/091,201, filed on Nov. 26, 2013, which is a continuation of International Application No. PCT/US2013/071758, filed on Nov. 25, 2013, titled “SYNERGISTIC BACTERIAL COMPOSITIONS AND METHODS OF PRODUCTION AND USE THEREOF”, which claims the benefit of U.S. Provisional Patent Application Ser. No. 61/729,518, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,519, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,520, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,521, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,522, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,524, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,515, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,517, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,525, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,526, filed Nov. 23, 2012, U.S. Provisional Patent Application Ser. No. 61/729,527, filed Nov. 23, 2012, all of which are incorporated herein by reference in their entirety for all purposes.

[0002] This application includes a Sequence Listing submitted electronically as a text file named 26469_US_CRF_sequence_listing.txt, created on Mar. 20, 2014, with a size of 2,945,024 bytes. The sequence listing is incorporated by reference.

[0003] Mammals are colonized by microbes in the gastrointestinal (GI) tract, on the skin, and in other epithelial and tissue niches such as the oral cavity, eye surface and vagina. The gastrointestinal tract harbors an abundant and diverse microbial community. It is a complex system, providing an environment or niche for a community of many different species or organisms, including diverse strains of bacteria. Hundreds of different species may form a commensal community in the GI tract in a healthy person, and this complement of organisms evolves from the time of birth to ultimately form a functionally mature microbial population by about 3 years of age. Interactions between microbial strains in these populations and between microbes and the host, e.g. the host immune system, shape the community structure, with availability of and competition for resources affecting the distribution of microbes. Such resources may be food, location and the availability of space to grow or a physical structure to which the microbe may attach. For example, host diet is involved in shaping the GI tract flora.

[0004] A healthy microbiota provides the host with multiple benefits, including colonization resistance to a broad spectrum of pathogens, essential nutrient biosynthesis and absorption, and immune stimulation that maintains a healthy gut epithelium and an appropriately controlled systemic immunity. In settings of ‘dysbiosis’ or disrupted symbiosis, microbiota functions can be lost or deranged, resulting in increased susceptibility to pathogens, altered metabolic profiles, or induction of proinflammatory signals that can result in local or systemic inflammation or autoimmunity. Thus, the intestinal microbiota plays a significant role in the pathogenesis of many diseases and disorders, including a variety of pathogenic infections of the gut. For instance, patients become more susceptible to pathogenic infections when the normal intestinal microbiota has been disturbed due to use of broad-spectrum antibiotics. Many of these diseases and disorders are chronic conditions that significantly decrease a patient's quality of life and can be ultimately fatal.

[0005] Fecal transplantation has been shown to be an effective treatment for patients suffering from severe or refractory GI infections by repopulating the gut with a diverse array of microbes that control key pathogens by creating an ecological environment inimical to their proliferation and survival. Such approaches have demonstrated significant potential to decrease host susceptibility to infection. Fecal transplantation, however, is considered to be a procedure of last resort because it has the potential to transmit infectious or allergenic agents between hosts, involves the transmission of potentially hundreds of unknown strains from donor to patient, and is difficult to perform on a mass scale. Additionally, fecal transplantation is inherently nonstandardized and different desired and/or undesired material may be transmitted in any given donation. Fecal transplantation is not approved by the FDA and is unlikely to gain approval since the product cannot be standardized and characterized according to regulatory requirements for identity, potency, purity and safety. Thus, there is a need for defined compositions that can be used to decrease susceptibility to infection and/or that facilitate restoration of a healthy gut microbiota.

[0006] Thus practitioners have a need for a much safer and reproducible treatment for disorders currently treated on an experimental (non-FDA approved) basis using fecal transplantation. In order to prepare a therapeutic with commercial potential, we have designed bacterial compositions of isolated bacterial strains with a plurality of beneficial properties based on our understanding of those bacterial strains and our analysis of the properties that would enhance the utility and commercialization of a bacterial composition.

[0007] Therefore, in response to the need for durable, efficient, and effective compositions and methods for treatment of GI diseases, in particular serious pathogenic infections, by way of restoring or enhancing microbiota functions, we address these and other shortcomings of the prior art by providing compositions and methods for treating patients.

[0008] In one aspect, provided are compositions comprising an effective amount of a bacterial composition comprising at least a first type of isolated bacterium capable of forming a spore and a second type of isolated bacterium capable of forming a spore, wherein the first type and the second type are not identical, and wherein at least one of the first type and the second type are capable of decreasing and/or inhibiting the growth and/or colonization of at least one type of pathogenic bacteria. In an embodiment, the bacterial composition comprises at least about 3, 4, 5, 6, 7, 8, 9, or 10 types of isolated bacteria. In an embodiment, the bacterial composition comprises at least about 3, 4, 5, 6, 7, 8, 9, or 10 types of isolated bacteria and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 of the isolated bacteria are capable of forming spores. In an embodiment, the bacterial composition comprises at least about 5 types of isolated bacteria and at least 2 of the isolated bacteria are capable of forming spores. In an embodiment, the bacterial composition comprises: i) at least about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more types of isolated bacteria capable of forming spores, ii) at least about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more types of isolated bacteria not known to be capable of forming spores, or iii) any combination of i) and ii). In an embodiment, the first type and the second type are present in the composition in approximately equal concentrations. In an embodiment, the first type and the second type are present in the composition in not substantially equal concentrations. In an embodiment, the first type is present in the composition in at least about 150% the concentration of the second type, or wherein the second type is present in the composition in at least about 150% the concentration of the first type. In an embodiment, the composition consists essentially of: i) between two and about twenty types of isolated bacteria, wherein at least two types of isolated bacteria are independently capable of spore formation; ii) between two and about twenty types of isolated bacteria, wherein at least two types of isolated bacteria not known to be capable of spore formation, or iii) any combination of i) and ii). In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium are selected from Table 1. In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium comprise an operational taxonomic unit (OTU) distinction. In an embodiment, the OTU distinction comprises 16S rRNA sequence similarity below about 95% identity. In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium independently comprise bacteria that comprise 16S rRNA sequence at least 95% identical to 16S rRNA sequence present in a bacterium selected from Table 3. In an embodiment, a combination of the first type and the second type are: i) cytotoxic, ii) cytostatic, iii) capable of decreasing the growth of the pathogenic bacterium, iv) capable of inhibiting the growth of the pathogenic bacterium, v) capable of decreasing the colonization of the pathogenic bacterium, vi) capable of inhibiting the colonization of the pathogenic bacterium, or vii) any combination of i)-vi). In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacteria present at a concentration at least equal to the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least about twice the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least about ten times the concentration of the combination of the first type and the second type. In an embodiment, the pathogenic bacterium is selected from the group consisting of Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella, Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia, Enterococcus, Coxiella, Corynebacterium, Clostridium, Chlamydia, Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella, Bifidobacterium, Bacillus, multi-drug resistant bacteria, Carbapenem-resistent Enterobacteriaceae (CRE), extended spectrum beta-lactam resistant Enterococci (ESBL), and vancomycin-resistant Enterococci (VRE). In an embodiment, the first type and the second type synergistically interact. In an embodiment, the first type and the second type synergistically interact to inhibit the pathogenic bacterium.

[0009] In another aspect, provided are compositions comprising an effective amount of a bacterial composition comprising at least a first type of isolated bacterium and a second type of isolated bacterium, wherein only one of the first type and the second type are capable of forming a spore, and wherein at least one of the first type and the second type are capable of decreasing the growth and/or colonization of at least one type of pathogenic bacteria.

[0010] In another aspect, provided are compositions comprising an effective amount of a bacterial composition comprising at least a first type of isolated bacterium and a second type of isolated bacterium, wherein the first type and the second type are not spores or known to be capable of forming a spore, and wherein at least one of the first type and the second type are capable of decreasing the growth and/or colonization of at least one type of pathogenic bacteria.

[0011] In an embodiment, at least one of the first type and the second type are capable of reducing the growth rate of at least one type of pathogenic bacteria. In an embodiment, at least one of the first type and the second type are cytotoxic to at least one type of pathogenic bacteria. In an embodiment, at least one of the first type and the second type are cytostatic to at least one type of pathogenic bacteria. In an embodiment, the first type and the second type are selected from Table 1. In an embodiment, the first type and the second type comprise different species. In an embodiment, the first type and the second type comprise different genera. In an embodiment, the first type and the second type comprise different families. In an embodiment, the first type and the second type comprise different orders.

[0012] In another aspect, provided are compositions comprising an effective amount of a bacterial composition comprising at least a first type of isolated bacterium and a second type of isolated bacterium, wherein: i) the first type and the second type are independently capable of forming a spore; ii) only one of the first type and the second type are capable of forming a spore or iii) neither the first type nor the second type are capable of forming a spore, wherein the first type and the second type are not identical, wherein the first type and the second type are capable of functionally populating the gastrointestinal tract of a human subject to whom the composition is administered. In an embodiment, the functional populating of the gastrointestinal tract comprises preventing a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises treating a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises reducing the severity of a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises reducing one or more symptoms of a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises preventing growth and/or colonization of the gastrointestinal tract by a pathogenic bacterium. In an embodiment, the functional populating of the gastrointestinal tract comprises reducing growth and/or colonization of the gastrointestinal tract by a pathogenic bacterium. In an embodiment, the functional populating of the gastrointestinal tract comprises reducing the number of one or more types of pathogenic bacteria in the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises increasing the number of one or more non-pathogenic bacteria in the gastrointestinal tract. In an embodiment, the bacterial composition comprises 0, 1, 2, 3 or greater than 3 types of isolated bacteria capable of forming spores. In an embodiment, the bacterial composition comprises at least about 5 types of isolated bacteria capable of forming spores. In an embodiment, the bacterial composition comprises at least about 7 types of isolated bacteria capable of forming spores. In an embodiment, the first type and the second type are present in the composition in not substantially equal concentrations. In an embodiment, the first type and the second type are present in the composition in approximately equal concentrations. In an embodiment, the first type is present in the composition in at least about 150% the concentration of the second type. In an embodiment, the second type is present in the composition in at least about 150% the concentration of the first type. In an embodiment, the composition consists essentially of between two and about ten types of isolated bacteria, wherein at least one type of isolated bacteria are independently capable of spore formation. In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium are selected from Table 1. In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium comprise an operational taxonomic unit (OTU) distinction. In an embodiment, the OTU distinction comprises 16S rRNA sequence similarity below about 95% identity. In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium independently comprise bacteria that comprise 16S rRNA sequence at least 95% identical to 16S rRNA sequence present in a bacterium selected from Table 3. In an embodiment, a combination of the first type and the second type are cytotoxic or cytostatic to the pathogenic bacterium. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacteria present at a concentration at least equal to the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least about twice the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacteria present at a concentration at least about ten times the concentration of the combination of the first type and the second type. In an embodiment, the pathogenic bacterium is selected from the group consisting of Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella, Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia, Enterococcus, Coxiella, Corynebacterium, Clostridium, Chlamydia, Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella, Bifidobacterium, Bacillus, multi-drug resistant bacteria, Carbapenem-resistent Enterobacteriaceae (CRE), extended spectrum beta-lactam resistant Enterococci (ESBL), and vancomycin-resistant Enterococci (VRE). In an embodiment, the first type and the second type synergistically interact to be cytotoxic to the pathogenic bacterium. In an embodiment, wherein the first type and the second type synergistically interact to be cytostatic to the pathogenic bacterium.

[0013] In another aspect, provided are single dose units comprising the compositions of the present invention. In an embodiment, the dose unit comprises at least 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹ or greater than 1×10¹¹ colony forming units (CFUs) of either spores or vegetative bacterial cells. In an embodiment, the dose unit comprises a pharmaceutically acceptable excipient, an enteric coating or a combination thereof. In an embodiment, the dose unit further comprises a drug selected from corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, immunosuppressive drugs, cyclosporin A, mercaptopurine, azathiopurine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anti-cholinergic drugs for rhinitis, anti-cholinergic decongestants, mast-cell stabilizers, monoclonal anti-IgE antibodies, vaccines, and combinations thereof. In an embodiment, the dose unit is formulated for oral administration, rectal administration, or the combination of oral and rectal administration, or is formulated for topical, nasal or inhalation administration.

[0014] In another aspect, provided are kits comprising in one or more containers: a first purified population of a first type of bacterial spores substantially free of viable vegetal bacterial cells; and a second purified population of a second type of bacterial spores substantially free of viable vegetal bacterial cells, wherein the first type and the second type of bacterial spores are not identical, and wherein the first type and the second type of bacterial spores, when co-localized in a target region of a gastrointestinal tract of a human subject in need thereof, are capable of functionally populating the gastrointestinal tract. In an embodiment, the first purified population and the second purified population are present in a single container. In an embodiment, the first purified population and the second purified population are present in two containers. In an embodiment, the first purified population and the second purified population are lyophilized or substantially dehydrated. In an embodiment, the kit further comprises in one or more containers an effective amount of an anti-bacterial agent, an effective amount of an anti-viral agent, an effective amount of an anti-fungal agent, an effective amount of an anti-parasitic agent, or a combination thereof in one or more containers. In an embodiment, the kit further comprises a pharmaceutically acceptable excipient or diluent.

[0015] Also provided are pharmaceutical formulations comprising an effective amount of the compositions of the invention, and further comprising an effective amount of an anti-bacterial agent, an effective amount of an anti-fungal agent, an effective amount of an anti-viral agent, an effective amount of an anti-parasitic agent.

[0016] Also provided are comestible products comprising a first purified population of a first type of bacterial spores and a second purified population of a second type of bacterial spores, wherein the first type and the second type of bacterial spores are not identical, wherein the comestible product is substantially free of viable vegetal bacterial cells, and wherein the first type and the second type of bacterial spores, when administered to a human subject in need thereof, are capable of functionally populating the gastrointestinal tract of the human subject. In an embodiment, the comestible product comprises a food or food additive, a beverage or beverage additive, or a medical food. In an embodiment, the comestible product comprises at least 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹ or greater than 1×10¹¹ colony forming units (CFUs) of viable spores. In an embodiment, the comestible product comprises a first type of bacterial spores and a second type of bacterial spores selected from Table 1, or where the first type of bacterial spores and the second type of bacterial spores independently comprise bacterial spores that comprise 16S rRNA sequence at least 95% identical to 16S rRNA sequence present in a bacterium selected from Table 3.

[0017] Also provided are methods comprising administering to a human subject in need thereof an effective amount of a bacterial composition comprising at least a first type of isolated bacterium and a second type of isolated bacterium, wherein: the first type and the second type are independently capable of forming a spore; only one of the first type and the second type are capable of forming a spore or neither the first type nor the second type are capable of forming a spore, wherein the first type and the second type are not identical, and wherein at least one of the first type and the second type exert an inhibitory effect on a pathogenic bacterium present in the gastrointestinal tract of the human subject, such that the number of pathogenic bacteria present in the gastrointestinal tract is not detectably increased or is detectably decreased over a period of time. In an embodiment, the human subject is diagnosed as having a dysbiosis of the gastrointestinal tract. In an embodiment, wherein the human subject is diagnosed as infected with a pathogenic bacterium selected from the group consisting of Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella, Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia, Enterococcus, Coxiella, Corynebacterium, Clostridium, Chlamydia, Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella, Bifidobacterium, Bacillus, multi-drug resistant bacteria, Carbapenem-resistent Enterobacteriaceae (CRE), extended spectrum beta-lactam resistant Enterococci (ESBL), and vancomycin-resistant Enterococci (VRE). In an embodiment, the bacterial composition is administered simultaneously with i) an antibiotic, ii) a prebiotic, or iii) a combination of i) and ii). In an embodiment, the bacterial composition is administered prior to administration of i) an antibiotic, ii) a prebiotic, or iii) a combination of i) and ii). In an embodiment, the bacterial composition is administered subsequent to administration of i) an antibiotic, ii) a prebiotic, or iii) a combination of i) and ii). In an embodiment, the number of pathogenic bacterium present in or excreted from the gastrointestinal tract of the human subject is detectably reduced within one month, within two weeks, or within one week of administration of the bacterial composition. In an embodiment, the number of pathogenic bacterium present in or excreted from the gastrointestinal tract of the human subject is detectably reduced within three days, two days or one day of administration of the bacterial composition. In an embodiment, the human subject is detectably free of the pathogenic bacterium within one month, two weeks, one week, three days or one day of administration of the bacterial composition. In an embodiment, the bacterial composition comprises at least about 3, 4, 5, 6, 7, 8, 9, or 10 types of isolated bacteria. In an embodiment, the bacterial composition comprises at least about 3, 4, 5, 6, 7, 8, 9, or 10 types of isolated bacteria and at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 of the isolated bacteria are capable of forming spores. In an embodiment, the bacterial composition comprises at least about 5 types of isolated bacteria and at least 2 of the isolated bacteria are capable of forming spores. In an embodiment, the bacterial composition comprises: i) at least about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more types of isolated bacteria capable of forming spores, ii) at least about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more types of isolated bacteria not known to be capable of forming spores, or iii) any combination of i) and ii). In an embodiment, the bacterial composition comprises at least about 5 types of isolated bacteria and at least 1 of the isolated bacteria are capable of forming spores. In an embodiment, the bacterial composition comprises at least about 5 types of isolated bacteria and at least 1 of the isolated bacteria is not capable of forming spores. In an embodiment, the bacterial composition comprises at least about 3, 4, 5, 6, 7, 8, 9 or 10 types of isolated bacteria, wherein i) at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 types of isolated bacteria are capable of forming spores, ii) at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 types of isolated bacteria are not capable of forming spores, or iii) any combination of i) and ii). In an embodiment, the first type and the second type are present in the composition in approximately equal concentrations. In an embodiment, the first type and the second type are present in the composition in not substantially equal concentrations. In an embodiment, the first type is present in the composition in at least about 150% the concentration of the second type, or wherein the second type is present in the composition in at least about 150% the concentration of the first type. In an embodiment, the composition consists essentially of between two and about ten types of isolated bacteria, wherein at least two types of isolated bacteria are independently capable of spore formation. In an embodiment, the composition consists essentially of between two and about ten types of isolated bacteria, wherein at least two types of isolated bacteria are not capable of spore formation. In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium are selected from Table 1. In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium comprise an operational taxonomic unit (OTU) distinction. In an embodiment, the OTU distinction comprises 16S rRNA sequence similarity below about 95% identity. In an embodiment, the first type of isolated bacterium and the second type of isolated bacterium independently comprise bacteria that comprise 16S rRNA sequence at least 95% identical to 16S rRNA sequence present in a bacterium selected from Table 3. In an embodiment, a combination of the first type and the second type are cytotoxic or cytostatic to the pathogenic bacterium. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least equal to the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least about twice the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least about ten times the concentration of the combination of the first type and the second type. In an embodiment, the pathogenic bacterium is selected from the group consisting of Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella, Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia, Enterococcus, Coxiella, Corynebacterium, Clostridium, Chlamydia, Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella, Bifidobacterium, Bacillus, multi-drug resistant bacteria, Carbapenem-resistent Enterobacteriaceae (CRE), extended spectrum beta-lactam resistant Enterococci (ESBL), and vancomycin-resistant Enterococci (VRE). In an embodiment, the first type and the second type synergistically interact to be cytotoxic to the pathogenic bacterium. In an embodiment, the first type and the second type synergistically interact to be cytostatic to the pathogenic bacterium.

[0018] Also provided are methods of functionally populating the gastrointestinal tract of a human subject, comprising administering to the subject an effective amount of a bacterial composition comprising at least a first type of isolated bacterium and a second type of isolated bacterium, wherein i) the first type and the second type are independently capable of forming a spore; ii) only one of the first type and the second type are capable of forming a spore or iii) neither the first type nor the second type are capable of forming a spore, wherein the first type and the second type are not identical, under conditions such that the first type and the second type functionally populate the gastrointestinal tract of the human subject. In an embodiment, the bacterial composition is orally administered, rectally administered, or the combination of orally and rectally administered. In an embodiment, the bacterial composition is topically or nasally administered or inhaled. In an embodiment, the first type of isolated bacteria and the second type of isolated bacteria are selected from Table 1. In an embodiment, the bacterial composition consists essentially of spores, wherein the spores comprise spores of the first type of isolated bacteria and spores of the second type of isolated bacteria. In an embodiment, the first type of isolated bacteria and the second type of isolated bacteria independently comprise bacterial spores that comprise 16S rRNA sequence at least 95% identical to 16S rRNA sequence present in a bacterium selected from Table 3. In an embodiment, the functional populating of the gastrointestinal tract comprises preventing a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises treating a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises reducing the severity of a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises reducing one or more symptoms of a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises preventing colonization of the gastrointestinal tract by a pathogenic bacterium. In an embodiment, the functional populating of the gastrointestinal tract comprises reducing colonization of the gastrointestinal tract and/or growth by a pathogenic bacterium. In an embodiment, wherein the functional populating of the gastrointestinal tract comprises reducing the number of one or more types of pathogenic bacteria in the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises increasing the number of one or more non-pathogenic bacteria in the gastrointestinal tract. In an embodiment, the bacterial composition comprises at least about 3, 5, 7 or 9 types of isolated bacteria capable of forming spores. In an embodiment, the bacterial composition comprises at least about 5 types of isolated bacteria and at least 20% of the isolated bacteria are capable of forming spores. In an embodiment, the bacterial composition comprises at least about 5 types of isolated bacteria and at least 2 of the isolated bacteria are capable of forming spores. In an embodiment, the bacterial composition comprises at least about 3, 4, 5, 6, 7, 8, 9 or 10 types of isolated bacteria, wherein i) at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 types of isolated bacteria are capable of forming spores, ii) at least 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 types of isolated bacteria are not capable of forming spores, or iii) any combination of i) and ii). In an embodiment, the first type and the second type are present in the composition in approximately equal concentrations. In an embodiment, the first type and the second type are present in the composition in not substantially equal concentrations. In an embodiment, the first type is present in the composition in at least about 150% the concentration of the second type, or wherein the second type is present in the composition in at least about 150% the concentration of the first type. In an embodiment, the composition consists essentially of between two and about ten types of isolated bacteria, wherein i) at least one type of isolated bacteria is capable of spore formation, ii) at least one type of isolated bacteria is not capable of spore formation, or iii) a combination of i) and ii). In an embodiment, a combination of the first type and the second type are inhibitory to the pathogenic bacterium. In an embodiment, the combination reduces the growth rate of the pathogenic bacterium. In an embodiment, the combination is cytostatic or cytotoxic to the pathogenic bacterium. In an embodiment, the combination is capable of inhibiting growth of the pathogenic bacterial present at a concentration at least equal to the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting growth of the pathogenic bacterial present at a concentration at least about twice the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least about ten times the concentration of the combination of the first type and the second type. In an embodiment, the pathogenic bacterium is selected from the group consisting of Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella, Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia, Enterococcus, Coxiella, Corynebacterium, Clostridium, Chlamydia, Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella, Bifidobacterium, Bacillus, multi-drug resistant bacteria, Carbapenem-resistent Enterobacteriaceae (CRE), extended spectrum beta-lactam resistant Enterococci (ESBL), and vancomycin-resistant Enterococci (VRE). In an embodiment, the first type and the second type synergistically interact to reduce or inhibit the growth of the pathogenic bacterium. In an embodiment, the first type and the second type synergistically interact to reduce or inhibit the colonization of the pathogenic bacterium. In an embodiment, the method comprises administering to the human subject a single dose unit comprising at least 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰, 1×10¹¹ or greater than 1×10¹¹ colony forming units (CFUs) of viable bacteria. In an embodiment, the dose unit comprises a bacterial population substantially in the form of spores. In an embodiment, the dose unit comprises a pharmaceutically acceptable excipient and/or an enteric coating. In an embodiment, the unit dose is formulated for oral administration, rectal administration, or the combination of oral and rectal administration. In an embodiment, the unit dose is formulated for topical or nasal administration or for inhalation.

[0019] In another aspect, provided are methods of reducing the number of pathogenic bacteria present in the gastrointestinal tract of a human subject, comprising administering to the subject an effective amount of a pharmaceutical formulation comprising an effective amount of the composition of any one of claim 1, 21, 22 or 31, and further comprising an effective amount of an anti-microbial agent, under conditions such that the number of pathogenic bacteria present in the gastrointestinal tract of the human subject is reduced within about one month of administration of the pharmaceutical formulation. In an embodiment, the number of pathogenic bacteria present in the gastrointestinal tract of the human subject is reduced within about two weeks of administration of the pharmaceutical formulation. In an embodiment, the number of pathogenic bacteria present in the gastrointestinal tract of the human subject is reduced within about one week of administration of the pharmaceutical formulation. In an embodiment, the number of pathogenic bacteria present in the gastrointestinal tract of the human subject is reduced within about three days of administration of the pharmaceutical formulation. In an embodiment, the number of pathogenic bacteria present in the gastrointestinal tract of the human subject is reduced within about one day of administration of the pharmaceutical formulation. In an embodiment, the anti-microbial agent comprises anti-bacterial agent. In an embodiment, the anti-microbial agent comprises anti-fungal agent. In an embodiment, the anti-microbial agent comprises anti-viral agent. In an embodiment, the anti-microbial agent comprises anti-parasitic agent.

[0020] In another aspect, provided are methods of preparing a comestible product, comprising combining with a comestible carrier a first purified population comprising at least a first type of isolated bacterium and a second purified population comprising at least a second type of isolated bacterium, wherein: i) the first type and the second type are independently capable of forming a spore; ii) only one of the first type and the second type are capable of forming a spore or iii) neither the first type nor the second type are capable of forming a spore, wherein the first type and the second type of bacteria are not identical, wherein the comestible product is substantially free of non-comestible materials. In an embodiment, at least one of the first purified population and the second purified population consist essentially of viable spores. In an embodiment, the first purified population and the second purified population consist essentially of viable spores. In an embodiment, the comestible product is substantially free of viable vegetal bacterial cells. In an embodiment, the viable spores, when the comestible product is consumed by a human subject in need thereof, are capable of functionally populating the gastrointestinal tract of the human subject. In an embodiment, the comestible product comprises a food or food additive. In an embodiment, the comestible product comprises a beverage or beverage additive. In an embodiment, the comestible product comprises a medical food. In an embodiment, the comestible product comprises at least 1×10⁴, 1×10⁵, 1×10⁶, 1×10⁷, 1×10⁸, 1×10⁹, 1×10¹⁰ 1×10¹¹ or greater than 1×10¹¹ colony forming units (CFUs) of viable spores. In an embodiment, spores are of a bacterium selected from Table 1. In an embodiment, the first purified population and the second purified population independently comprise bacterial spores that comprise 16S rRNA sequence at least 95% identical to 16S rRNA sequence present in a bacterium selected from Table 3.

[0021] Also provided are methods of reducing the abundance of a pathogen in the gastrointestinal tract of a patient comprising administering the composition of the invention in a therapeutically effective amount and allowing the bacterial composition to compete with the pathogen in the gastrointestinal tract of a patient.

[0022] Further provided are methods of treating diarrhea comprising administering the composition of the invention in a therapeutically effective amount and allowing the bacterial composition to reduce the diarrheal effect of a pathogen in the gastrointestinal tract of a patient. In an embodiment, the pathogen is Aeromonas hydrophila, Campylobacter fetus, Plesiomonas shigelloides, Bacillus cereus, Campylobacter jejuni, Clostridium botulinum, Clostridium difficile, Clostridium perfringens, enteroaggregative Escherichia coli, enterohemorrhagic Escherichia coli, enteroinvasive Escherichia coli, enterotoxigenic Escherichia coli (LT or ST), Escherichia coli 0157:H7, Helicobacter pylori, Lysteria monocytogenes, Plesiomonas shigelloides, Salmonella spp., Salmonella typhi, Shigella spp., Staphylococcus spp., Staphylococcus aureus, Vibrio spp., Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, Yersinia enterocolitica, multi-drug resistant bacteria, Carbapenem-resistent Enterobacteriaceae (CRE), and vancomycin-resistant Enterococci (VRE). In an embodiment, the pathogen is Clostridium difficile, Salmonella spp., pathogenic Escherichia coli, or vancomycin-resistant Enterococcus spp. In an embodiment, the pathogen is Clostridium difficile. In an embodiment, the composition is administered orally.

[0023] Also provided are therapeutic compositions comprising a first purified bacterial population capable forming spores consisting of Collinsella aerofaciens and a second purified bacterial population consisting of a species selected from Table 1 or Table 4, wherein at least one of the first type and the second type are cytotoxic or cytostatic to a pathogenic bacterium. In an embodiment, a synergistic combination of the first bacterial spore population and the second bacterial spore population are cytotoxic or cytostatic to the pathogenic bacterium. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least equal to the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least about twice the concentration of the combination of the first type and the second type. In an embodiment, the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least about ten times the concentration of the combination of the first type and the second type. In an embodiment, the pathogenic bacterium is selected from the group consisting of Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Helicobacter, Haemophilus, Francisella, Escherichia, Enterococcus, Corynebacterium, Clostridium, Chlamydia, Chlamydophila, Campylobacter, Brucella, Borrelia, and Bordetella. In an embodiment, the pathogenic bacterium is Clostridium dificile. In an embodiment, the first bacterial spore population and the second bacterial spore population synergistically interact to be cytotoxic to the pathogenic bacterium. In an embodiment, the first bacterial spore population and the second bacterial spore population synergistically interact to be cytostatic to the pathogenic bacterium. In an embodiment, the bacterial composition comprises at least about 3 types of isolated bacteria capable of forming spores. In an embodiment, the bacterial composition comprises at least about 5 types of isolated bacteria capable of forming spores. In an embodiment, the first bacterial spore population and the second bacterial spore population are present in the composition in approximately equal concentrations. In an embodiment, the composition consists essentially of between two and about ten bacterial spore populations of isolated bacteria.

[0024] In another aspect, provided are therapeutic compositions comprising a first purified bacterial spore population consisting of bacteria comprising 16S rRNA sequence at least about 97% identical to a 16S rRNA sequence present in a reference Collinsella aerofaciens OTU, and a second purified bacterial spore population consisting of bacteria comprising 16S rRNA sequence at least about 97% identical to a 16S rRNA sequence present in a reference bacterium listed in Table 1 or Table 4, wherein at least one of the first type and the second type are cytotoxic or cytostatic to a pathogenic bacterium. In an embodiment, a synergistic combination of the first type and the second type are cytotoxic or cytostatic to the pathogenic bacterium. In an embodiment, wherein the combination is capable of inhibiting proliferation of the pathogenic bacterial present at a concentration at least equal to the concentration of the combination of the first type and the second type. In an embodiment, the first type and the second type synergistically interact to be cytotoxic or cytostatic to the pathogenic bacterium. In an embodiment, the first purified bacterial spore population and the second purified bacterial spore population are capable of functionally populating the gastrointestinal tract of a human subject to whom the composition is administered. In an embodiment, the functional populating of the gastrointestinal tract comprises preventing, treating, reducing the severity of or reducing a symptom of a dysbiosis of the gastrointestinal tract. In an embodiment, the functional populating of the gastrointestinal tract comprises i) reducing the number of one or more types of pathogenic bacteria in the gastrointestinal tract; or ii) increasing the number of one or more non-pathogenic bacteria in the gastrointestinal tract. In an embodiment, the composition further comprises an effective amount of an anti-bacterial agent, an anti-fungal agent, an anti-viral agent or an anti-parasitic agent.

[0025] Also provided are methods of treating or preventing a recurrence of a Clostridium difficile infection, comprising administering to a human subject in need thereof an effective amount of the therapeutic composition of the invention under conditions such that the first purified bacterial spore population and the second purified bacterial spore population exert a cytotoxic or cytostatic effect on a pathogenic bacterium present in the gastrointestinal tract of the human subject, such that the number of Clostridium difficile bacteria present in the gastrointestinal tract is not detectably increased or is detectably decreased over a period of time. In an embodiment, the number of Clostridium difficile bacteria present in or excreted from the gastrointestinal tract of the human subject is detectably reduced within one month of administration of the bacterial composition. In an embodiment, the first purified bacterial spore population and the second purified bacterial spore population synergistically interact to be cytotoxic and/or cytostatic to the Clostridium difficile bacteria. In an embodiment, the therapeutic composition is orally administered. In an embodiment, the therapeutic composition comprises a medical food.

[0026] In another aspect, provided are kits comprising in one or more containers: a first purified population of a first type of bacteria capable of forming spores; and a second purified population of a second type of bacteria capable of forming spores, wherein the first type and the second type are not identical, and wherein the first type and the second type, when co-localized in a target region of a gastrointestinal tract of a human subject in need thereof, are capable of functionally populating the gastrointestinal tract. In an embodiment, the first purified population and the second purified population are present in a single container. In an embodiment, the kit is formulated for use as a nutritional supplement and optionally comprising a prebiotic material.

[0027] Additional objects and advantages will be set forth in part in the description which follows, and in part will be obvious from the description, or may be learned by practice of the embodiments. The objects and advantages will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims.

[0028] It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the claims.

[0029] The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several embodiments and together with the description, serve to further explain the embodiments.

[0031] Table 1 provides bacterial species and Operational Taxonomic Units (OTUs) of the bacterial compositions of the present invention, including taxonometric status and the ability of the OTU to form a viable spore as provided herein.

[0032] Table 2 provides representative combinations of the bacterial compositions of the present invention.

[0033] Table 3 provides 16S rRNA sequences of the bacterial species and Operational Taxonomic Units (OTUs) of the bacterial compositions of the present invention. Table 3 is provided in the CRF version of the Sequence Listing as SEQ ID NOS 1-1,864.

[0034] Table 4 provides taxonometric status, exemplary phylogenetic surrogacy and 16S rRNA sequences of exemplary bacterial compositions of the present invention. Table 4 is provided in the CRF version of the Sequence Listing as SEQ ID NOS 1,865-1,915.

[0035] Table 5 demonstrates the efficacy of exemplary bacterial compositions of the present invention in inhibiting a pathogenic bacterium.

[0036] Table 6 demonstrates the efficacy of exemplary bacterial compositions of the present invention in inhibiting a pathogenic bacterium.

[0037] Table 7 provides representative bacterial pathogens.

[0038] Table 8 provides representative human diseases, disorders and conditions for which the provided bacterial compositions are useful.

[0039] Table 9 provides representative human diseases, disorders and conditions for which the provided bacterial compositions are useful.

[0040] “Microbiota” refers to the communities of microbes that live in or on the patient's body, both sustainably and transiently, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses (i.e., phage)).

[0041] “Dysbiosis” refers to a state of the microbiota or microbiome of the gut or other body area, including mucosal or skin surfaces in which the normal diversity and/or function of the ecological network is disrupted. Any disruption from the preferred (e.g., ideal) state of the microbiota can be considered a dysbiosis, even if such dysbiosis does not result in a detectable decrease in health. This state of dysbiosis may be unhealthy, it may be unhealthy under only certain conditions, or it may prevent a subject from becoming healthier. Dysbiosis may be due to a decrease in diversity, the overgrowth of one or more pathogens or pathobionts, symbiotic organisms able to cause disease only when certain genetic and/or environmental conditions are present in a patient, or the shift to an ecological network that no longer provides a beneficial function to the host and therefore no longer promotes health.

[0042] A “spore” or a population of “spores” includes bacteria (or other single-celled organisms) that are generally viable, more resistant to environmental influences such as heat and bacteriocidal agents than vegetative forms of the same bacteria, and typically capable of germination and out-growth. “Spore-formers” or bacteria “capable of forming spores” are those bacteria containing the genes and other necessary abilities to produce spores under suitable environmental conditions.

[0043] The terms “pathogen”, “pathobiont” and “pathogenic” in reference to a bacterium or any other organism or entity includes any such organism or entity that is capable of causing or affecting a disease, disorder or condition of a host organism containing the organism or entity.

[0044] The term “isolated” encompasses a bacterium or other entity or substance that has been (1) separated from at least some of the components with which it was associated when initially produced (whether in nature or in an experimental setting), and/or (2) produced, prepared, purified, and/or manufactured by the hand of man. Isolated bacteria may be separated from at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or more of the other components with which they were initially associated. In some embodiments, isolated bacteria are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. As used herein, a substance is “pure” if it is substantially free of other components. The terms “purify,” “purifying” and “purified” refer to a bacterium or other material that has been separated from at least some of the components with which it was associated either when initially produced or generated (e.g., whether in nature or in an experimental setting), or during any time after its initial production. A bacterium or a bacterial population may be considered purified if it is isolated at or after production, such as from a material or environment containing the bacterium or bacterial population, and a purified bacterium or bacterial population may contain other materials up to about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, or above about 90% and still be considered “isolated.” In some embodiments, purified bacteria and bacterial populations are more than about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or more than about 99% pure. In the instance of bacterial compositions provided herein, the one or more bacterial types present in the composition can be independently purified from one or more other bacteria produced and/or present in the material or environment containing the bacterial type. Bacterial compositions and the bacterial components thereof are generally purified from residual habitat products.

[0045] “Inhibition” of a pathogen encompasses the inhibition of any desired function or activity of the bacterial compositions of the present invention. Demonstrations of pathogen inhibition, such as decrease in the growth of a pathogenic bacterium or reduction in the level of colonization of a pathogenic bacterium are provided herein and otherwise recognized by one of ordinary skill in the art. Inhibition of a pathogenic bacterium's “growth” may include inhibiting the increase in size of the pathogenic bacterium and/or inhibiting the proliferation (or multiplication) of the pathogenic bacterium. Inhibition of colonization of a pathogenic bacterium may be demonstrated by measuring the amount or burden of a pathogen before and after a treatment. An “inhibition” or the act of “inhibiting” includes the total cessation and partial reduction of one or more activities of a pathogen, such as growth, proliferation, colonization, and function.

[0046] The “colonization” of a host organism includes the non-transitory residence of a bacterium or other microscopic organism. As used herein, “reducing colonization” of a host subject's gastrointestinal tract (or any other microbiotal niche) by a pathogenic bacterium includes a reduction in the residence time of the pathogen in the gastrointestinal tract as well as a reduction in the number (or concentration) of the pathogen in the gastrointestinal tract or adhered to the luminal surface of the gastrointestinal tract. Measuring reductions of adherent pathogens may be demonstrated, e.g., by a biopsy sample, or reductions may be measured indirectly, e.g., by measuring the pathogenic burden in the stool of a mammalian host.

[0047] A “combination” of two or more bacteria includes the physical co-existence of the two bacteria, either in the same material or product or in physically connected products, as well as the temporal co-administration or co-localization of the two bacteria.

[0048] A “cytotoxic” activity or bacterium includes the ability to kill a bacterial cell, such as a pathogenic bacterial cell. A “cytostatic” activity or bacterium includes the ability to inhibit, partially or fully, growth, metabolism, and/or proliferation of a bacterial cell, such as a pathogenic bacterial cell.

[0049] To be free of “non-comestible products” means that a bacterial composition or other material provided herein does not have a substantial amount of a non-comestible product, e.g., a product or material that is inedible, harmful or otherwise undesired in a product suitable for administration, e.g., oral administration, to a human subject. Non-comestible products are often found in preparations of bacteria from the prior art.

[0050] “Microbiome” refers to the genetic content of the communities of microbes that live in and on the human body, both sustainably and transiently, including eukaryotes, archaea, bacteria, and viruses (including bacterial viruses (i.e., phage)), wherein “genetic content” includes genomic DNA, RNA such as micro RNA and ribosomal RNA, the epigenome, plasmids, and all other types of genetic information.

[0051] “Residual habitat products” refers to material derived from the habitat for microbiota within or on a human or animal. For example, microbiota live in feces in the gastrointestinal tract, on the skin itself, in saliva, mucus of the respiratory tract, or secretions of the genitourinary tract (i.e., biological matter associated with the microbial community). Substantially free of residual habitat products means that the bacterial composition no longer contains the biological matter associated with the microbial environment on or in the human or animal subject and is 100% free, 99% free, 98% free, 97% free, 96% free, or 95% free of any contaminating biological matter associated with the microbial community. Residual habitat products can include abiotic materials (including undigested food) or it can include unwanted microorganisms. Substantially free of residual habitat products may also mean that the bacterial composition contains no detectable cells from a human or animal and that only microbial cells are detectable. In one embodiment, substantially free of residual habitat products may also mean that the bacterial composition contains no detectable viral (including bacterial viruses (i.e., phage)), fungal, mycoplasmal contaminants. In another embodiment, it means that fewer than 1×10⁻²%, 1×10⁻³%, 1×10⁻⁴%, 1×10⁻⁶%, 1×10⁻⁶%, 1×10⁻⁷%, 1×10⁻⁸ of the viable cells in the bacterial composition are human or animal, as compared to microbial cells. There are multiple ways to accomplish this degree of purity, none of which are limiting. Thus, contamination may be reduced by isolating desired constituents through multiple steps of streaking to single colonies on solid media until replicate (such as, but not limited to, two) streaks from serial single colonies have shown only a single colony morphology. Alternatively, reduction of contamination can be accomplished by multiple rounds of serial dilutions to single desired cells (e.g., a dilution of 10⁻⁸ or 10⁻⁹), such as through multiple 10-fold serial dilutions. This can further be confirmed by showing that multiple isolated colonies have similar cell shapes and Gram staining behavior. Other methods for confirming adequate purity include genetic analysis (e.g. PCR, DNA sequencing), serology and antigen analysis, enzymatic and metabolic analysis, and methods using instrumentation such as flow cytometry with reagents that distinguish desired constituents from contaminants.

[0052] “Phylogenetic tree” refers to a graphical representation of the evolutionary relationships of one genetic sequence to another that is generated using a defined set of phylogenetic reconstruction algorithms (e.g. parsimony, maximum likelihood, or Bayesian). Nodes in the tree represent distinct ancestral sequences and the confidence of any node is provided by a bootstrap or Bayesian posterior probability, which measures branch uncertainty.

[0053] “Operational taxonomic unit (OTU, plural OTUs)” refers to a terminal leaf in a phylogenetic tree and is defined by a specific genetic sequence and all sequences that share sequence identity to this sequence at the level of species. A “type” or a plurality of “types” of bacteria includes an OTU or a plurality of different OTUs, and also encompasses a strain, species, genus, family or order of bacteria. The specific genetic sequence may be the 16S sequence or a portion of the 16S sequence or it may be a functionally conserved housekeeping gene found broadly across the eubacterial kingdom. OTUs share at least 95%, 96%, 97%, 98%, or 99% sequence identity. OTUs are frequently defined by comparing sequences between organisms. Sequences with less than 95% sequence identity are not considered to form part of the same OTU.

[0054] “Clade” refers to the set of OTUs or members of a phylogenetic tree downstream of a statistically valid node in a phylogenetic tree. The clade comprises a set of terminal leaves in the phylogenetic tree that is a distinct monophyletic evolutionary unit.

[0055] In microbiology, “16S sequencing” or “16S rRNA” or “16S-rRNA” or “16S” refers to sequence derived by characterizing the nucleotides that comprise the 16S ribosomal RNA gene(s). The bacterial 16S rDNA is approximately 1500 nucleotides in length and is used in reconstructing the evolutionary relationships and sequence similarity of one bacterial isolate to another using phylogenetic approaches. 16S sequences are used for phylogenetic reconstruction as they are in general highly conserved, but contain specific hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most bacteria, as well as fungi.

[0056] The “V1-V9 regions” of the 16S rRNA refers to the first through ninth hypervariable regions of the 16S rRNA gene that are used for genetic typing of bacterial samples. These regions in bacteria are defined by nucleotides 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043, 1117-1173, 1243-1294 and 1435-1465 respectively using numbering based on the E. coli system of nomenclature. Brosius et al., Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli, PNAS 75(10):4801-4805 (1978). In some embodiments, at least one of the V1, V2, V3, V4, V5, V6, V7, V8, and V9 regions are used to characterize an OTU. In one embodiment, the V1, V2, and V3 regions are used to characterize an OTU. In another embodiment, the V3, V4, and V5 regions are used to characterize an OTU. In another embodiment, the V4 region is used to characterize an OTU. A person of ordinary skill in the art can identify the specific hypervariable regions of a candidate 16S rRNA (in Table 3) by comparing the candidate sequence in question to the reference sequence and identifying the hypervariable regions based on similarity to the reference hypervariable regions.

[0057] The terms “subject” or “patient” refers to any animal subject including humans, laboratory animals (e.g., primates, rats, mice), livestock (e.g., cows, sheep, goats, pigs, turkeys, chickens), and household pets (e.g., dogs, cats, rodents, etc.). The subject or patient may be healthy, or may be suffering from an infection due to a gastrointestinal pathogen or may be at risk of developing or transmitting to others an infection due to a gastrointestinal pathogen.

[0058] The term “pathobiont” refer to specific bacterial species found in healthy hosts that may trigger immune-mediated pathology and/or disease in response to certain genetic or environmental factors. Chow et al., (2011) Curr Op Immunol. Pathobionts of the intestinal microbiota and inflammatory disease. 23: 473-80. Thus, a pathobiont is a pathogen that is mechanistically distinct from an acquired infectious organism. Thus, the term “pathogen” includes both acquired infectious organisms and pathobionts.

[0059] Provided are bacteria and combinations of bacteria of the human gut microbiota with the capacity to meaningfully provide functions of a healthy microbiota or catalyze an augmentation to the resident microbiome when administered to mammalian hosts. In particular, provided are synergistic combinations that treat, prevent, delay or reduce the symptoms of diseases, disorders and conditions associated with a dysbiosis. Representative diseases, disorders and conditions potentially associated with a dysbiosis, which are suitable for treatment with the compositions and methods as described herein, are provided in Tables 8 and 9. Without being limited to a specific mechanism, it is thought that such compositions inhibit the growth, proliferation, and/or colonization of one or a plurality of pathogenic bacteria in the dysbiotic microbiotal niche, so that a healthy, diverse and protective microbiota colonizes and populates the intestinal lumen to establish or reestablish ecological control over pathogens or potential pathogens (e.g., some bacteria are pathogenic bacteria only when present in a dysbiotic environment). Inhibition of pathogens includes those pathogens such as C. difficile, Salmonella spp., enteropathogenic E. coli, multi-drug resistant bacteria such as Klebsiella, and E. coli, Carbapenem-resistent Enterobacteriaceae (CRE), extended spectrum beta-lactam resistant Enterococci (ESBL), and vancomycin-resistant Enterococci (VRE).

[0060] The bacterial compositions provided herein are produced and the efficacy thereof in inhibiting pathogenic bacteria is demonstrated as provided in further detail herein.

[0061] In particular, in order to characterize those antagonistic relationships between gut commensals that are relevant to the dynamics of the mammalian gut habitat, provided is an in vitro microplate-based screening system that demonstrates the efficacy of those bacterial compositions, including the ability to inhibit (or antagonize) the growth of a bacterial pathogen or pathobiont, typically a gastrointestinal microorganism. These methods provide novel combinations of gut microbiota species and OTUs that are able to restore or enhance ecological control over important gut pathogens or pathobionts in vivo.

[0062] Bacterial compositions may comprise two types of bacteria (termed “binary combinations” or “binary pairs”) or greater than two types of bacteria. Bacterial compositions that comprise three types of bacteria are termed “ternary combinations”. For instance, a bacterial composition may comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, or at least 21, 22, 23, 24, 25, 26, 27, 28, 29 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or at least 40, at least 50 or greater than 50 types of bacteria, as defined by species or operational taxonomic unit (OTU), or otherwise as provided herein. In one embodiment, the composition comprises at least two types of bacteria chosen from Table 1.

[0063] In another embodiment, the number of types of bacteria present in a bacterial composition is at or below a known value. For example, in such embodiments the bacterial composition comprises 50 or fewer types of bacteria, such as 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, or 10 or fewer, or 9 or fewer types of bacteria, 8 or fewer types of bacteria, 7 or fewer types of bacteria, 6 or fewer types of bacteria, 5 or fewer types of bacteria, 4 or fewer types of bacteria, or 3 or fewer types of bacteria. In another embodiment, a bacterial composition comprises from 2 to no more than 40, from 2 to no more than 30, from 2 to no more than 20, from 2 to no more than 15, from 2 to no more than 10, or from 2 to no more than 5 types of bacteria.

[0064] In some embodiments, bacterial compositions are provided with the ability to exclude pathogenic bacteria. Exemplary bacterial compositions are demonstrated to reduce the growth rate of one pathogen, C. difficile, as provided in the Examples, wherein the ability of the bacterial compositions is demonstrated by assessing the antagonism activity of a combination of OTUs or strains towards a given pathogen using in vitro assays.

[0065] In some embodiments, bacterial compositions with the capacity to durably exclude C. difficile, are developed using a methodology for estimating an Ecological Control Factor (ECF) for constituents within the human microbiota. The ECF is determined by assessing the antagonistic activity of a given commensal strain or combination of strains towards a given pathogen using an in vitro assay, resulting in observed levels of ecological control at various concentrations of the added commensal strains. The ECF for a commensal strain or combination of strains is somewhat analogous to the longstanding minimal inhibitory concentration (MIC) assessment that is employed in the assessment of antibiotics. The ECF allows for the assessment and ranking of relative potencies of commensal strains and combinations of strains for their ability to antagonize gastrointestinal pathogens. The ECF of a commensal strain or combination of strains may be calculated by assessing the concentration of that composition that is able to mediate a given percentage of inhibition (e.g., at least 10%, 20%, 50%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%) of a target pathogen in the in vitro assay. Provided herein are combinations of strains or OTUs within the human microbiota that are able to significantly reduce the rate of gastrointestinal pathogen replication within the in vitro assay. These compositions are capable of providing a safe and effective means by which to affect the growth, replication, and disease severity of such bacterial pathogens.

[0066] Bacterial compositions may be prepared comprising at least two types of isolated bacteria, wherein a first type and a second type are independently chosen from the species or OTUs listed in Table 1 and Table 3. Certain embodiments of bacterial compositions with at least two types of isolated bacteria containing binary pairs are reflected in Table 2. Additionally, a bacterial composition may be prepared comprising at least two types of isolated bacteria, wherein a first OTU and a second OTU are independently characterized by, i.e., at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to, sequences listed in Table 3. Generally, the first bacteria and the second bacteria are not the same OTU. The sequences provided in Table 3 are full 16S sequences. Therefore, in one embodiment, the first and/or second OTUs may be characterized by the full 16S sequences listed in Table 3. In another embodiment, the first and/or second OTUs may be characterized by one or more of the variable regions of the 16S sequence (V1-V9). These regions in bacteria are defined by nucleotides 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043, 1117-1173, 1243-1294 and 1435-1465 respectively using numbering based on the E. coli system of nomenclature. (See, e.g., Brosius et al., Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli, PNAS 75(10):4801-4805 (1978)). In some embodiments, at least one of the V1, V2, V3, V4, V5, V6, V7, V8, and V9 regions are used to characterize an OTU. In one embodiment, the V1, V2, and V3 regions are used to characterize an OTU. In another embodiment, the V3, V4, and V5 regions are used to characterize an OTU. In another embodiment, the V4 region is used to characterize an OTU.

[0067] Methods for Determining 16S Sequence.

[0068] OTUs may be defined either by full 16S sequencing of the rRNA gene, by sequencing of a specific hypervariable region of this gene (i.e. V1, V2, V3, V4, V5, V6, V7, V8, or V9), or by sequencing of any combination of hypervariable regions from this gene (e.g. V1-3 or V3-5). The bacterial 16S rDNA is approximately 1500 nucleotides in length and is used in reconstructing the evolutionary relationships and sequence similarity of one bacterial isolate to another using phylogenetic approaches. 16S sequences are used for phylogenetic reconstruction as they are in general highly conserved, but contain specific hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most microbes. Using well known techniques, in order to determine the full 16S sequence or the sequence of any hypervariable region of the 16S sequence, genomic DNA is extracted from a bacterial sample, the 16S rDNA (full region or specific hypervariable regions) amplified using polymerase chain reaction (PCR), the PCR products cleaned, and nucleotide sequences delineated to determine the genetic composition of 16S gene or subdomain of the gene. If full 16S sequencing is performed, the sequencing method used may be, but is not limited to, Sanger sequencing. If one or more hypervariable regions are used, such as the V4 region, the sequencing may be, but is not limited to being, performed using the Sanger method or using a next-generation sequencing method, such as an Illumina (sequencing by synthesis) method using barcoded primers allowing for multiplex reactions.

[0069] Bacterial Compositions Exclusive of Certain Bacterial Species or Strains.

[0070] In one embodiment, the bacterial composition does not comprise at least one of Enterococcus faecalis (previously known as Streptococcus faecalis), Clostridium innocuum, Clostridium ramosum, Bacteroides ovatus, Bacteroides vulgatus, Bacteroides thetaoiotaomicron, Escherichia coli (1109 and 1108-1), Clostridum bifermentans, and Blautia producta (previously known as Peptostreptococcus productus).

[0071] In another embodiment, the bacterial composition does not comprise at least one of Acidaminococcus intestinalis, Bacteroides ovatus, two species of Bifidobacterium adolescentis, two species of Bifidobacterium longum, Collinsella aerofaciens, two species of Dorea longicatena, Escherichia coli, Eubacterium eligens, Eubacterium limosum, four species of Eubacterium rectale, Eubacterium ventriosumi, Faecalibacterium prausnitzii, Lactobacillus casei, Lactobacillus paracasei, Paracateroides distasonis, Raoultella sp., one species of Roseburia (chosen from Roseburia faecalis or Roseburia faecis), Roseburia intestinalis, two species of Ruminococcus torques, and Streptococcus mitis.

[0072] In another embodiment, the bacterial composition does not comprise at least one of Barnesiella intestinihominis; Lactobacillus reuteri; a species characterized as one of Enterococcus hirae, Enterococus faecium, or Enterococcus durans; a species characterized as one of Anaerostipes caccae or Clostridium indolis; a species characterized as one of Staphylococcus wameri or Staphylococcus pasteuri; and Adlercreutzia equolifaciens.

[0073] In another embodiment, the bacterial composition does not comprise at least one of Clostridium absonum, Clostridium argentinense, Clostridium baratii, Clostridium bifermentans, Clostridium botulinum, Clostridium butyricum, Clostridium cadaveris, Clostridium camis, Clostridium celatum, Clostridium chauvoei, Clostridium clostridioforme, Clostridium cochlearium, Clostridium difficile, Clostridium fallax, Clostridium felsineum, Clostridium ghonii, Clostridium glycolicum, Clostridium haemolyticum, Clostridium hastiforme, Clostridium histolyticum, Clostridium indolis, Clostridium innocuum, Clostridium irregulare, Clostridium limosum, Clostridium malenominatum, Clostridium novyi, Clostridium oroticum, Clostridium paraputrificum, Clostridium perfringens, Clostridium piliforme, Clostridium putrefaciens, Clostridium putrificum, Clostridium ramosum, Clostridium sardiniense, Clostridium sartagoforme, Clostridium scindens, Clostridium septicum, Clostridium sordellii, Clostridium sphenoides, Clostridium spiroforme, Clostridium sporogenes, Clostridium subterminale, Clostridium symbiosum, Clostridium tertium, Clostridium tetani, Clostridium welchii, and Clostridium villosum.

[0074] In another embodiment, the bacterial composition does not comprise at least one of Clostridium innocuum, Clostridum bifermentans, Clostridium butyricum, Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides uniformis, three strains of Escherichia coli, and Lactobacillus sp.

[0075] In another embodiment, the bacterial composition does not comprise at least one of Clostridium bifermentans, Clostridium innocuum, Clostridium butyricum, three strains of Escherichia coli, three strains of Bacteroides, and Blautia producta (previously known as Peptostreptococcus productus).

[0076] In another embodiment, the bacterial composition does not comprise at least one of Bacteroides sp., Escherichia coli, and non pathogenic Clostridia, including Clostridium innocuum, Clostridium bifermentans and Clostridium ramosum.

[0077] In another embodiment, the bacterial composition does not comprise at least one of more than one Bacteroides species, Escherichia coli and non-pathogenic Clostridia, such as Clostridium butyricum, Clostridium bifermentans and Clostridium innocuum.

[0078] In another embodiment, the bacterial composition does not comprise at least one of Bacteroides caccae, Bacteroides capillosus, Bacteroides coagulans, Bacteroides distasonis, Bacteroides eggerthii, Bacteroides forsythus, Bacteroides fragilis, Bacteroides fragilis-ryhm, Bacteroides gracilis, Bacteroides levii, Bacteroides macacae, Bacteroides merdae, Bacteroides ovatus, Bacteroides pneumosintes, Bacteroides putredinis, Bacteroides pyogenes, Bacteroides splanchnicus, Bacteroides stercoris, Bacteroides tectum, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides ureolyticus, and Bacteroides vulgatus.

[0079] In another embodiment, the bacterial composition does not comprise at least one of Bacteroides, Eubacteria, Fusobacteria, Propionibacteria, Lactobacilli, anaerobic cocci, Ruminococcus, Escherichia coli, Gemmiger, Desulfomonas, and Peptostreptococcus.

[0080] In another embodiment, the bacterial composition does not comprise at least one of Bacteroides fragilis ss. Vulgatus, Eubacterium aerofaciens, Bacteroides fragilis ss. Thetaiotaomicron, Blautia producta (previously known as Peptostreptococcus productus II), Bacteroides fragilis ss. Distasonis, Fusobacterium prausnitzii, Coprococcus eutactus, Eubacterium aerofaciens III, Blautia producta (previously known as Peptostreptococcus productus I), Ruminococcus bromii, Bifidobacterium adolescentis, Gemmiger formicilis, Bifidobacterium longum, Eubacterium siraeum, Ruminococcus torques, Eubacterium rectale III-H, Eubacterium rectale IV, Eubacterium eligens, Bacteroides eggerthii, Clostridium leptum, Bacteroides fragilis ss. A, Eubacterium biforme, Bifidobacterium infantis, Eubacterium rectale III-F, Coprococcus comes, Bacteroides capillosus, Ruminococcus albus, Eubacterium formicigenerans, Eubacterium hallii, Eubacterium ventriosum I, Fusobacterium russii, Ruminococcus obeum, Eubacterium rectale II, Clostridium ramosum I, Lactobacillus leichmanii, Ruminococcus cailidus, Butyrivibrio crossotus, Acidaminococcus fermentans, Eubacterium ventriosum, Bacteroides fragilis ss. fragilis, Bacteroides AR, Coprococcus catus, Eubacterium hadrum, Eubacterium cylindroides, Eubacterium ruminantium, Eubacterium CH-1, Staphylococcus epidermidis, Peptostreptococcus BL, Eubacterium limosum, Bacteroides praeacutus, Bacteroides L, Fusobacterium mortiferum I, Fusobacterium naviforme, Clostridium innocuum, Clostridium ramosum, Propionibacterium acnes, Ruminococcus flavefaciens, Ruminococcus AT, Peptococcus AU-1, Eubacterium AG, -AK, -AL, -AL-1, -AN; Bacteroides fragilis ss. ovatus, -ss. d, -ss. f; Bacteroides L-1, L-5; Fusobacterium nucleatum, Fusobacterium mortiferum, Escherichia coli, Streptococcus morbiliorum, Peptococcus magnus, Peptococcus G, AU-2; Streptococcus intermedius, Ruminococcus lactaris, Ruminococcus CO Gemmiger X, Coprococcus BH, -CC; Eubacterium tenue, Eubacterium ramulus, Eubacterium AE, -AG-H, -AG-M, -AJ, -BN-1; Bacteroides clostridiiformis ss. clostridliformis, Bacteroides coagulans, Bacteroides orails, Bacteroides ruminicola ss. brevis, -ss. ruminicola, Bacteroides splanchnicus, Desuifomonas pigra, Bacteroides L-4, -N-i; Fusobacterium H, Lactobacillus G, and Succinivibrio A.

[0081] Inhibition of Bacterial Pathogens.

[0082] The bacterial compositions offer a protective or therapeutic effect against infection by one or more GI pathogens of interest.

[0083] A list of exemplary bacterial pathogens is provided in Table 7.

[0084] In some embodiments, the pathogenic bacterium is selected from the group consisting of Yersinia, Vibrio, Treponema, Streptococcus, Staphylococcus, Shigella, Salmonella, Rickettsia, Orientia, Pseudomonas, Neisseria, Mycoplasma, Mycobacterium, Listeria, Leptospira, Legionella, Klebsiella, Helicobacter, Haemophilus, Francisella, Escherichia, Ehrlichia, Enterococcus, Coxiella, Corynebacterium, Clostridium, Chlamydia, Chlamydophila, Campylobacter, Burkholderia, Brucella, Borrelia, Bordetella, Bifidobacterium, Bacillus, multi-drug resistant bacteria, extended spectrum beta-lactam resistant Enterococci (ESBL), Carbapenem-resistent Enterobacteriaceae (CRE), and vancomycin-resistant Enterococci (VRE).

[0085] In some embodiments, these pathogens include, but are not limited to, Aeromonas hydrophila, Campylobacter fetus, Plesiomonas shigelloides, Bacillus cereus, Campylobacter jejuni, Clostridium botulinum, Clostridium difficile, Clostridium perfringens, enteroaggregative Escherichia coli, entero hemorrhagic Escherichia coli, enteroinvasive Escherichia coli, enterotoxigenic Escherichia coli (such as, but not limited to, LT and/or ST), Escherichia coli 0157:H7, Helicobacter pylori, Klebsiellia pneumonia, Lysteria monocytogenes, Plesiomonas shigelloides, Salmonella spp., Salmonella typhi, Salmonella paratyphi, Shigella spp., Staphylococcus spp., Staphylococcus aureus, vancomycin-resistant enterococcus spp., Vibrio spp., Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, and Yersinia enterocolitica.

[0086] In one embodiment, the pathogen of interest is at least one pathogen chosen from Clostridium difficile, Salmonella spp., pathogenic Escherichia coli, vancomycin-resistant Enterococcus spp., and extended spectrum beta-lactam resistant Enterococci (ESBL).

[0087] In Vitro Assays Substantiating Protective Effect of Bacterial Compositions.

[0088] In one embodiment, provided is an In Vitro Assay utilizing competition between the bacterial compositions or subsets thereof and C. difficile. Exemplary embodiments of this Assay are provided herein and in the Examples.

[0089] In another embodiment, provided is an In Vitro Assay utilizing 10% (wt/vol) Sterile-Filtered Feces. Provided is an in vitro assay to test for the protective effect of the bacterial compositions and to screen in vitro for combinations of microbes that inhibit the growth of a pathogen. The assay can operate in automated high-throughput or manual modes. Under either system, human or animal feces may be re-suspended in an anaerobic buffer solution, such as pre-reduced PBS or other suitable buffer, the particulate removed by centrifugation, and filter sterilized. This 10% sterile-filtered feces material serves as the base media for the in vitro assay. To test a bacterial composition, an investigator may add it to the sterile-filtered feces material for a first incubation period and then may inoculate the incubated microbial solution with the pathogen of interest for a second incubation period. The resulting titer of the pathogen may be quantified by any number of methods such as those described below, and the change in the amount of pathogen is compared to standard controls including the pathogen cultivated in the absence of the bacterial composition. The assay is conducted using at least one control. Feces from a healthy subject may be used as a positive control. As a negative control, antibiotic-treated feces or heat-treated feces may be used. Various bacterial compositions may be tested in this material and the bacterial compositions optionally compared to the positive and/or negative controls. The ability to inhibit the growth of the pathogen may be measured by plating the incubated material on C. difficile selective media and counting colonies. After competition between the bacterial composition and C. difficile, each well of the in vitro assay plate is serially diluted ten-fold six times, and plated on selective media, such as but not limited to cycloserine cefoxitin mannitol agar (CCMA) or cycloserine cefoxitin fructose agar (CCFA), and incubated. Colonies of C. difficile are then counted to calculate the concentration of viable cells in each well at the end of the competition. Colonies of C. difficile are confirmed by their characteristic diffuse colony edge morphology as well as fluorescence under UV light.

[0090] In another embodiment, the in vitro assay utilizes Antibiotic-Treated Feces. In an alternative embodiment, and instead of using 10% sterile-filtered feces, human or animal feces may be resuspended in an anaerobic buffer solution, such as pre-reduced PBS or other suitable buffer. The resuspended feces is treated with an antibiotic, such as clindamycin, or a cocktail of several antibiotics in order to reduce the ability of feces from a healthy subject to inhibit the growth of C. difficile; this material is termed the antibiotic-treated matrix. While not being bound by any mechanism, it is believed that beneficial bacteria in healthy subjects protects them from infection by competing out C. difficile. Treating feces with antibiotics kills or reduces the population of those beneficial bacteria, allowing C. difficile to grow in this assay matrix. Antibiotics in addition to clindamycin that inhibit the normal flora include ceftriaxone and piperacillin-tazobactam and may be substituted for the clindamycin. The antibiotic-treated matrix is centrifuged, the supernatant removed, and the pelleted material resuspended in filter-sterilized, diluted feces in order to remove any residual antibiotic. This washed antibiotic-treated matrix may be used in the in vitro assay described above in lieu of the 10% sterile-filtered feces.

[0091] Alternatively, the ability to inhibit the growth of the pathogen may be measured by quantitative PCR (qPCR). Standard techniques may be followed to generate a standard curve for the pathogen of interest. Genomic DNA may be extracted from samples using commercially-available kits, such as the Mo Bio Powersoil®-htp 96 Well Soil DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), the Mo Bio Powersoil® DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), or the QIAamp DNA Stool Mini Kit (QIAGEN, Valencia, Calif.) according to the manufacturer's instructions. The qPCR may be conducted using HotMasterMix (5PRIME, Gaithersburg, Md.) and primers specific for the pathogen of interest, and may be conducted on a MicroAmp® Fast Optical 96-well Reaction Plate with Barcode (0.1 mL) (Life Technologies, Grand Island, N.Y.) and performed on a BioRad C1000™ Thermal Cycler equipped with a CFX96™ Real-Time System (BioRad, Hercules, Calif.), with fluorescent readings of the FAM and ROX channels. The Cq value for each well on the FAM channel is determined by the CFX Manager™ software version 2.1. The log₁₀ (cfu/ml) of each experimental sample is calculated by inputting a given sample's Cq value into linear regression model generated from the standard curve comparing the Cq values of the standard curve wells to the known log₁₀ (cfu/ml) of those samples. The skilled artisan may employ alternative qPCR modes.

[0092] Also provided are In Vivo Assay Establishing Protective Effect of Bacterial Compositions. Provided is an in vivo mouse model to test for the protective effect of the bacterial compositions against C. difficile. In this model (based on Chen, et al., A mouse model of Clostridium difficile associated disease, Gastroenterology 135(6):1984-1992 (2008)), mice are made susceptible to C. difficile by a 7 day treatment (days −12 to −5 of experiment) with 5 to 7 antibiotics (including kanamycin, colistin, gentamycin, metronidazole and vancomycin and optionally including ampicillin and ciprofloxacin) delivered via their drinking water, followed by a single dose with Clindamycin on day −3, then challenged three days later on day 0 with 10⁴ spores of C. difficile via oral gavage (i.e., oro-gastric lavage). Bacterial compositions may be given either before (prophylactic treatment) or after (therapeutic treatment) C. difficile gavage. Further, bacterial compositions may be given after (optional) vancomycin treatment (see below) to assess their ability to prevent recurrence and thus suppress the pathogen in vivo. The outcomes assessed each day from day −1 to day 6 (or beyond, for prevention of recurrence) are weight, clinical signs, mortality and shedding of C. difficile in the feces. Weight loss, clinical signs of disease, and C. difficile shedding are typically observed without treatment. Vancomycin provided by oral gavage on days −1 to 4 protects against these outcomes and serves as a positive control. Clinical signs are subjective, and scored each day by the same experienced observer. Animals that lose greater than or equal to 25% of their body weight are euthanized and counted as infection-related mortalities. Feces are gathered from mouse cages (5 mice per cage) each day, and the shedding of C. difficile spores is detected in the feces using a selective plating assay as described for the in vitro assay above, or via qPCR for the toxin gene as described herein. The effects of test materials including 10% suspension of human feces (as a positive control), bacterial compositions, or PBS (as a negative vehicle control), are determined by introducing the test article in a 0.2 mL volume into the mice via oral gavage on day −1, one day prior to C. difficile challenge, on day 1, 2 and 3 as treatment or post-vancomycin treatment on days 5, 6, 7 and 8. Vancomycin, as discussed above, is given on days 1 to 4 as another positive control. Alternative dosing schedules and routes of administration (e.g. rectal) may be employed, including multiple doses of test article, and 10³ to 10¹³ of a given organism or composition may be delivered.

[0093] Methods for Preparing a Bacterial Composition for Administration to a Subject.

[0094] Methods for producing bacterial compositions may include three main processing steps, combined with one or more mixing steps. The steps are: organism banking, organism production, and preservation.

[0095] For banking, the strains included in the bacterial composition may be (1) isolated directly from a specimen or taken from a banked stock, (2) optionally cultured on a nutrient agar or broth that supports growth to generate viable biomass, and (3) the biomass optionally preserved in multiple aliquots in long-term storage.

[0096] In embodiments using a culturing step, the agar or broth may contain nutrients that provide essential elements and specific factors that enable growth. An example would be a medium composed of 20 g/L glucose, 10 g/L yeast extract, 10 g/L soy peptone, 2 g/L citric acid, 1.5 g/L sodium phosphate monobasic, 100 mg/L ferric ammonium citrate, 80 mg/L magnesium sulfate, 10 mg/L hemin chloride, 2 mg/L calcium chloride, 1 mg/L menadione. A variety of microbiological media and variations are well known in the art (e.g. R. M. Atlas, Handbook of Microbiological Media (2010) CRC Press). Medium can be added to the culture at the start, may be added during the culture, or may be intermittently/continuously flowed through the culture. The strains in the bacterial composition may be cultivated alone, as a subset of the bacterial composition, or as an entire collection comprising the bacterial composition. As an example, a first strain may be cultivated together with a second strain in a mixed continuous culture, at a dilution rate lower than the maximum growth rate of either cell to prevent the culture from washing out of the cultivation.

[0097] The inoculated culture is incubated under favorable conditions for a time sufficient to build biomass. For bacterial compositions for human use this is often at 37° C. temperature, pH, and other parameter with values similar to the normal human niche. The environment may be actively controlled, passively controlled (e.g., via buffers), or allowed to drift. For example, for anaerobic bacterial compositions (e.g., gut microbiota), an anoxic/reducing environment may be employed. This can be accomplished by addition of reducing agents such as cysteine to the broth, and/or stripping it of oxygen. As an example, a culture of a bacterial composition may be grown at 37° C., pH 7, in the medium above, pre-reduced with 1 g/L cysteine.HCl.

[0098] When the culture has generated sufficient biomass, it may be preserved for banking. The organisms may be placed into a chemical milieu that protects from freezing (adding ‘cryoprotectants’), drying (‘lyoprotectants’), and/or osmotic shock (‘osmoprotectants’), dispensing into multiple (optionally identical) containers to create a uniform bank, and then treating the culture for preservation. Containers are generally impermeable and have closures that assure isolation from the environment. Cryopreservation treatment is accomplished by freezing a liquid at ultra-low temperatures (e.g., at or below −80° C.). Dried preservation removes water from the culture by evaporation (in the case of spray drying or ‘cool drying’) or by sublimation (e.g., for freeze drying, spray freeze drying). Removal of water improves long-term bacterial composition storage stability at temperatures elevated above cryogenic. If the bacterial composition comprises spore forming species and results in the production of spores, the final composition may be purified by additional means such as density gradient centrifugation preserved using the techniques described above. Bacterial composition banking may be done by culturing and preserving the strains individually, or by mixing the strains together to create a combined bank. As an example of cryopreservation, a bacterial composition culture may be harvested by centrifugation to pellet the cells from the culture medium, the supernate decanted and replaced with fresh culture broth containing 15% glycerol. The culture can then be aliquoted into 1 mL cryotubes, sealed, and placed at −80° C. for long-term viability retention. This procedure achieves acceptable viability upon recovery from frozen storage.

[0099] Organism production may be conducted using similar culture steps to banking, including medium composition and culture conditions. It may be conducted at larger scales of operation, especially for clinical development or commercial production. At larger scales, there may be several subcultivations of the bacterial composition prior to the final cultivation. At the end of cultivation, the culture is harvested to enable further formulation into a dosage form for administration. This can involve concentration, removal of undesirable medium components, and/or introduction into a chemical milieu that preserves the bacterial composition and renders it acceptable for administration via the chosen route. For example, a bacterial composition may be cultivated to a concentration of 10¹⁰ CFU/mL, then concentrated 20-fold by tangential flow microfiltration; the spent medium may be exchanged by diafiltering with a preservative medium consisting of 2% gelatin, 100 mM trehalose, and 10 mM sodium phosphate buffer. The suspension can then be freeze-dried to a powder and titrated.

[0100] After drying, the powder may be blended to an appropriate potency, and mixed with other cultures and/or a filler such as microcrystalline cellulose for consistency and ease of handling, and the bacterial composition formulated as provided herein.

[0101] Formulations.

[0102] Provided are formulations for administration to humans and other subjects in need thereof. Generally the bacterial compositions are combined with additional active and/or inactive materials in order to produce a final product, which may be in single dosage unit or in a multi-dose format.

[0103] In some embodiments the composition comprises at least one carbohydrate. A “carbohydrate” refers to a sugar or polymer of sugars. The terms “saccharide,” “polysaccharide,” “carbohydrate,” and “oligosaccharide” may be used interchangeably. Most carbohydrates are aldehydes or ketones with many hydroxyl groups, usually one on each carbon atom of the molecule. Carbohydrates generally have the molecular formula C_nH_2nO_n. A carbohydrate may be a monosaccharide, a disaccharide, trisaccharide, oligosaccharide, or polysaccharide. The most basic carbohydrate is a monosaccharide, such as glucose, sucrose, galactose, mannose, ribose, arabinose, xylose, and fructose. Disaccharides are two joined monosaccharides. Exemplary disaccharides include sucrose, maltose, cellobiose, and lactose. Typically, an oligosaccharide includes between three and six monosaccharide units (e.g., raffinose, stachyose), and polysaccharides include six or more monosaccharide units. Exemplary polysaccharides include starch, glycogen, and cellulose. Carbohydrates may contain modified saccharide units such as 2′-deoxyribose wherein a hydroxyl group is removed, 2′-fluororibose wherein a hydroxyl group is replace with a fluorine, or N-acetylglucosamine, a nitrogen-containing form of glucose (e.g., 2′-fluororibose, deoxyribose, and hexose). Carbohydrates may exist in many different forms, for example, conformers, cyclic forms, acyclic forms, stereoisomers, tautomers, anomers, and isomers.

[0104] In some embodiments the composition comprises at least one lipid. As used herein a “lipid” includes fats, oils, triglycerides, cholesterol, phospholipids, fatty acids in any form including free fatty acids. Fats, oils and fatty acids can be saturated, unsaturated (cis or trans) or partially unsaturated (cis or trans). In some embodiments the lipid comprises at least one fatty acid selected from lauric acid (12:0), myristic acid (14:0), palmitic acid (16:0), palmitoleic acid (16:1), margaric acid (17:0), heptadecenoic acid (17:1), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), linolenic acid (18:3), octadecatetraenoic acid (18:4), arachidic acid (20:0), eicosenoic acid (20:1), eicosadienoic acid (20:2), eicosatetraenoic acid (20:4), eicosapentaenoic acid (20:5) (EPA), docosanoic acid (22:0), docosenoic acid (22:1), docosapentaenoic acid (22:5), docosahexaenoic acid (22:6) (DHA), and tetracosanoic acid (24:0). In some embodiments the composition comprises at least one modified lipid, for example a lipid that has been modified by cooking.

[0105] In some embodiments the composition comprises at least one supplemental mineral or mineral source. Examples of minerals include, without limitation: chloride, sodium, calcium, iron, chromium, copper, iodine, zinc, magnesium, manganese, molybdenum, phosphorus, potassium, and selenium. Suitable forms of any of the foregoing minerals include soluble mineral salts, slightly soluble mineral salts, insoluble mineral salts, chelated minerals, mineral complexes, non-reactive minerals such as carbonyl minerals, and reduced minerals, and combinations thereof.

[0106] In some embodiments the composition comprises at least one supplemental vitamin. The at least one vitamin can be fat-soluble or water soluble vitamins. Suitable vitamins include but are not limited to vitamin C, vitamin A, vitamin E, vitamin B12, vitamin K, riboflavin, niacin, vitamin D, vitamin B6, folic acid, pyridoxine, thiamine, pantothenic acid, and biotin. Suitable forms of any of the foregoing are salts of the vitamin, derivatives of the vitamin, compounds having the same or similar activity of the vitamin, and metabolites of the vitamin.

[0107] In some embodiments the composition comprises an excipient. Non-limiting examples of suitable excipients include a buffering agent, a preservative, a stabilizer, a binder, a compaction agent, a lubricant, a dispersion enhancer, a disintegration agent, a flavoring agent, a sweetener, and a coloring agent.

[0108] In some embodiments the excipient is a buffering agent. Non-limiting examples of suitable buffering agents include sodium citrate, magnesium carbonate, magnesium bicarbonate, calcium carbonate, and calcium bicarbonate.

[0109] In some embodiments the excipient comprises a preservative. Non-limiting examples of suitable preservatives include antioxidants, such as alpha-tocopherol and ascorbate, and antimicrobials, such as parabens, chlorobutanol, and phenol.

[0110] In some embodiments the composition comprises a binder as an excipient. Non-limiting examples of suitable binders include starches, pregelatinized starches, gelatin, polyvinylpyrolidone, cellulose, methylcellulose, sodium carboxymethylcellulose, ethylcellulose, polyacrylamides, polyvinyloxoazolidone, polyvinylalcohols, C₁₂-C₁₈ fatty acid alcohol, polyethylene glycol, polyols, saccharides, oligosaccharides, and combinations thereof.

[0111] In some embodiments the composition comprises a lubricant as an excipient. Non-limiting examples of suitable lubricants include magnesium stearate, calcium stearate, zinc stearate, hydrogenated vegetable oils, sterotex, polyoxyethylene monostearate, talc, polyethyleneglycol, sodium benzoate, sodium lauryl sulfate, magnesium lauryl sulfate, and light mineral oil.

[0112] In some embodiments the composition comprises a dispersion enhancer as an excipient. Non-limiting examples of suitable dispersants include starch, alginic acid, polyvinylpyrrolidones, guar gum, kaolin, bentonite, purified wood cellulose, sodium starch glycolate, isoamorphous silicate, and microcrystalline cellulose as high HLB emulsifier surfactants.

[0113] In some embodiments the composition comprises a disintegrant as an excipient. In some embodiments the disintegrant is a non-effervescent disintegrant. Non-limiting examples of suitable non-effervescent disintegrants include starches such as corn starch, potato starch, pregelatinized and modified starches thereof, sweeteners, clays, such as bentonite, micro-crystalline cellulose, alginates, sodium starch glycolate, gums such as agar, guar, locust bean, karaya, pecitin, and tragacanth. In some embodiments the disintegrant is an effervescent disintegrant. Non-limiting examples of suitable effervescent disintegrants include sodium bicarbonate in combination with citric acid, and sodium bicarbonate in combination with tartaric acid.

[0114] In some embodiments the excipient comprises a flavoring agent. Flavoring agents can be chosen from synthetic flavor oils and flavoring aromatics; natural oils; extracts from plants, leaves, flowers, and fruits; and combinations thereof. In some embodiments the flavoring agent is selected from cinnamon oils; oil of wintergreen; peppermint oils; clover oil; hay oil; anise oil; eucalyptus; vanilla; citrus oil such as lemon oil, orange oil, grape and grapefruit oil; and fruit essences including apple, peach, pear, strawberry, raspberry, cherry, plum, pineapple, and apricot.

[0115] In some embodiments the excipient comprises a sweetener. Non-limiting examples of suitable sweeteners include glucose (corn syrup), dextrose, invert sugar, fructose, and mixtures thereof (when not used as a carrier); saccharin and its various salts such as the sodium salt; dipeptide sweeteners such as aspartame; dihydrochalcone compounds, glycyrrhizin; Stevia Rebaudiana (Stevioside); chloro derivatives of sucrose such as sucralose; and sugar alcohols such as sorbitol, mannitol, sylitol, and the like. Also contemplated are hydrogenated starch hydrolysates and the synthetic sweetener 3,6-dihydro-6-methyl-1,2,3-oxathiazin-4-one-2,2-dioxide, particularly the potassium salt (acesulfame-K), and sodium and calcium salts thereof.

[0116] In some embodiments the composition comprises a coloring agent. Non-limiting examples of suitable color agents include food, drug and cosmetic colors (FD&C), drug and cosmetic colors (D&C), and external drug and cosmetic colors (Ext. D&C). The coloring agents can be used as dyes or their corresponding lakes.

[0117] The weight fraction of the excipient or combination of excipients in the formulation is usually about 99% or less, such as about 95% or less, about 90% or less, about 85% or less, about 80% or less, about 75% or less, about 70% or less, about 65% or less, about 60% or less, about 55% or less, 50% or less, about 45% or less, about 40% or less, about 35% or less, about 30% or less, about 25% or less, about 20% or less, about 15% or less, about 10% or less, about 5% or less, about 2% or less, or about 1% or less of the total weight of the composition.

[0118] The bacterial compositions disclosed herein can be formulated into a variety of forms and administered by a number of different means. The compositions can be administered orally, rectally, or parenterally, in formulations containing conventionally acceptable carriers, adjuvants, and vehicles as desired. The term “parenteral” as used herein includes subcutaneous, intravenous, intramuscular, or intrasternal injection and infusion techniques. In an exemplary embodiment, the bacterial composition is administered orally.

[0119] Solid dosage forms for oral administration include capsules, tablets, caplets, pills, troches, lozenges, powders, and granules. A capsule typically comprises a core material comprising a bacterial composition and a shell wall that encapsulates the core material. In some embodiments the core material comprises at least one of a solid, a liquid, and an emulsion. In some embodiments the shell wall material comprises at least one of a soft gelatin, a hard gelatin, and a polymer. Suitable polymers include, but are not limited to: cellulosic polymers such as hydroxypropyl cellulose, hydroxyethyl cellulose, hydroxypropyl methyl cellulose (HPMC), methyl cellulose, ethyl cellulose, cellulose acetate, cellulose acetate phthalate, cellulose acetate trimellitate, hydroxypropylmethyl cellulose phthalate, hydroxypropylmethyl cellulose succinate and carboxymethylcellulose sodium; acrylic acid polymers and copolymers, such as those formed from acrylic acid, methacrylic acid, methyl acrylate, ammonio methylacrylate, ethyl acrylate, methyl methacrylate and/or ethyl methacrylate (e.g., those copolymers sold under the trade name “Eudragit”); vinyl polymers and copolymers such as polyvinyl pyrrolidone, polyvinyl acetate, polyvinylacetate phthalate, vinylacetate crotonic acid copolymer, and ethylene-vinyl acetate copolymers; and shellac (purified lac). In some embodiments at least one polymer functions as taste-masking agents.

[0120] Tablets, pills, and the like can be compressed, multiply compressed, multiply layered, and/or coated. The coating can be single or multiple. In one embodiment, the coating material comprises at least one of a saccharide, a polysaccharide, and glycoproteins extracted from at least one of a plant, a fungus, and a microbe. Non-limiting examples include corn starch, wheat starch, potato starch, tapioca starch, cellulose, hemicellulose, dextrans, maltodextrin, cyclodextrins, inulins, pectin, mannans, gum arabic, locust bean gum, mesquite gum, guar gum, gum karaya, gum ghatti, tragacanth gum, funori, carrageenans, agar, alginates, chitosans, or gellan gum. In some embodiments the coating material comprises a protein. In some embodiments the coating material comprises at least one of a fat and an oil. In some embodiments the at least one of a fat and an oil is high temperature melting. In some embodiments the at least one of a fat and an oil is hydrogenated or partially hydrogenated. In some embodiments the at least one of a fat and an oil is derived from a plant. In some embodiments the at least one of a fat and an oil comprises at least one of glycerides, free fatty acids, and fatty acid esters. In some embodiments the coating material comprises at least one edible wax. The edible wax can be derived from animals, insects, or plants. Non-limiting examples include beeswax, lanolin, bayberry wax, carnauba wax, and rice bran wax. Tablets and pills can additionally be prepared with enteric coatings.

[0121] Alternatively, powders or granules embodying the bacterial compositions disclosed herein can be incorporated into a food product. In some embodiments the food product is a drink for oral administration. Non-limiting examples of a suitable drink include fruit juice, a fruit drink, an artificially flavored drink, an artificially sweetened drink, a carbonated beverage, a sports drink, a liquid diary product, a shake, an alcoholic beverage, a caffeinated beverage, infant formula and so forth. Other suitable means for oral administration include aqueous and nonaqueous solutions, emulsions, suspensions and solutions and/or suspensions reconstituted from non-effervescent granules, containing at least one of suitable solvents, preservatives, emulsifying agents, suspending agents, diluents, sweeteners, coloring agents, and flavoring agents.

[0122] In some embodiments the food product is a solid foodstuff. Suitable examples of a solid foodstuff include without limitation a food bar, a snack bar, a cookie, a brownie, a muffin, a cracker, an ice cream bar, a frozen yogurt bar, and the like.

[0123] In some embodiments, the compositions disclosed herein are incorporated into a therapeutic food. In some embodiments, the therapeutic food is a ready-to-use food that optionally contains some or all essential macronutrients and micronutrients. In some embodiments, the compositions disclosed herein are incorporated into a supplementary food that is designed to be blended into an existing meal. In some embodiments, the supplemental food contains some or all essential macronutrients and micronutrients. In some embodiments, the bacterial compositions disclosed herein are blended with or added to an existing food to fortify the food's protein nutrition. Examples include food staples (grain, salt, sugar, cooking oil, margarine), beverages (coffee, tea, soda, beer, liquor, sports drinks), snacks, sweets and other foods.

[0124] In one embodiment, the formulations are filled into gelatin capsules for oral administration. An example of an appropriate capsule is a 250 mg gelatin capsule containing from 10 (up to 100 mg) of lyophilized powder (10⁸ to 10¹¹ bacteria), 160 mg microcrystalline cellulose, 77.5 mg gelatin, and 2.5 mg magnesium stearate. In an alternative embodiment, from 10⁵ to 10¹² bacteria may be used, 10⁵ to 10⁷, 10⁶ to 10⁷, or 10⁸ to 10¹⁰, with attendant adjustments of the excipients if necessary. In an alternative embodiment an enteric-coated capsule or tablet or with a buffering or protective composition may be used.

[0125] In one embodiment, the number of bacteria of each type may be present in the same amount or in different amounts. For example, in a bacterial composition with two types of bacteria, the bacteria may be present in from a 1:10,000 ratio to a 1:1 ratio, from a 1:10,000 ratio to a 1:1,000 ratio, from a 1:1,000 ratio to a 1:100 ratio, from a 1:100 ratio to a 1:50 ratio, from a 1:50 ratio to a 1:20 ratio, from a 1:20 ratio to a 1:10 ratio, from a 1:10 ratio to a 1:1 ratio. For bacterial compositions comprising at least three types of bacteria, the ratio of type of bacteria may be chosen pairwise from ratios for bacterial compositions with two types of bacteria. For example, in a bacterial composition comprising bacteria A, B, and C, at least one of the ratio between bacteria A and B, the ratio between bacteria B and C, and the ratio between bacteria A and C may be chosen, independently, from the pairwise combinations above.

[0126] Methods of Treating a Subject.

[0127] In some embodiments the proteins and compositions disclosed herein are administered to a patient or a user (sometimes collectively referred to as a “subject”). As used herein “administer” and “administration” encompasses embodiments in which one person directs another to consume a bacterial composition in a certain manner and/or for a certain purpose, and also situations in which a user uses a bacteria composition in a certain manner and/or for a certain purpose independently of or in variance to any instructions received from a second person. Non-limiting examples of embodiments in which one person directs another to consume a bacterial composition in a certain manner and/or for a certain purpose include when a physician prescribes a course of conduct and/or treatment to a patient, when a parent commands a minor user (such as a child) to consume a bacterial composition, when a trainer advises a user (such as an athlete) to follow a particular course of conduct and/or treatment, and when a manufacturer, distributer, or marketer recommends conditions of use to an end user, for example through advertisements or labeling on packaging or on other materials provided in association with the sale or marketing of a product.

[0128] The bacterial compositions offer a protective and/or therapeutic effect against infection by one or more GI pathogens of interest and thus may be administered after an acute case of infection has been resolved in order to prevent relapse, during an acute case of infection as a complement to antibiotic therapy if the bacterial composition is not sensitive to the same antibiotics as the GI pathogen, or to prevent infection or reduce transmission from disease carriers. These pathogens include, but are not limited to, Aeromonas hydrophila, Campylobacter fetus, Plesiomonas shigelloides, Bacillus cereus, Campylobacter jejuni, Clostridium botulinum, Clostridium difficile, Clostridium perfringens, enteroaggregative Escherichia coli, entero hemorrhagic Escherichia coli, enteroinvasive Escherichia coli, enterotoxigenic Escherichia coli (LT and/or ST), Escherichia coli 0157:H7, Helicobacter pylori, Klebsiella pneumonia, Lysteria monocytogenes, Plesiomonas shigelloides, Salmonella spp., Salmonella typhi, Shigella spp., Staphylococcus, Staphylococcus aureus, vancomycin-resistant Enterococcus spp., Vibrio spp., Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, and Yersinia enterocolitica.

[0129] In one embodiment, the pathogen may be Clostridium difficile, Salmonella spp., pathogenic Escherichia coli, Carbapenem-resistent Enterobacteriaceae (CRE), extended spectrum beta-lactam resistant Enterococci (ESBL) and vancomycin-resistant Enterococci (VRE). In yet another embodiment, the pathogen may be Clostridium difficile.

[0130] The present bacterial compositions may be useful in a variety of clinical situations. For example, the bacterial compositions may be administered as a complementary treatment to antibiotics when a patient is suffering from an acute infection, to reduce the risk of recurrence after an acute infection has subsided, or when a patient will be in close proximity to others with or at risk of serious gastrointestinal infections (physicians, nurses, hospital workers, family members of those who are ill or hospitalized).

[0131] The present bacterial compositions may be administered to animals, including humans, laboratory animals (e.g., primates, rats, mice), livestock (e.g., cows, sheep, goats, pigs, turkeys, chickens), and household pets (e.g., dogs, cats, rodents).

[0132] In the present method, the bacterial composition is administered enterically, in other words by a route of access to the gastrointestinal tract. This includes oral administration, rectal administration (including enema, suppository, or colonoscopy), by an oral or nasal tube (nasogastric, nasojejunal, oral gastric, or oral jejunal), as detailed more fully herein.

[0133] Pretreatment Protocols

[0134] Prior to administration of the bacterial composition, the patient may optionally have a pretreatment protocol to prepare the gastrointestinal tract to receive the bacterial composition. In certain embodiments, the pretreatment protocol is advisable, such as when a patient has an acute infection with a highly resilient pathogen. In other embodiments, the pretreatment protocol is entirely optional, such as when the pathogen causing the infection is not resilient, or the patient has had an acute infection that has been successfully treated but where the physician is concerned that the infection may recur. In these instances, the pretreatment protocol may enhance the ability of the bacterial composition to affect the patient's microbiome.

[0135] As one way of preparing the patient for administration of the microbial ecosystem, at least one antibiotic may be administered to alter the bacteria in the patient. As another way of preparing the patient for administration of the microbial ecosystem, a standard colon-cleansing preparation may be administered to the patient to substantially empty the contents of the colon, such as used to prepare a patient for a colonscopy. By “substantially emptying the contents of the colon,” this application means removing at least 75%, at least 80%, at least 90%, at least 95%, or about 100% of the contents of the ordinary volume of colon contents. Antibiotic treatment may precede the colon-cleansing protocol.

[0136] If a patient has received an antibiotic for treatment of an infection, or if a patient has received an antibiotic as part of a specific pretreatment protocol, in one embodiment the antibiotic should be stopped in sufficient time to allow the antibiotic to be substantially reduced in concentration in the gut before the bacterial composition is administered. In one embodiment, the antibiotic may be discontinued 1, 2, or 3 days before the administration of the bacterial composition. In one embodiment, the antibiotic may be discontinued 3, 4, 5, 6, or 7 antibiotic half-lives before administration of the bacterial composition. In another embodiment, the antibiotic may be chosen so the constituents in the bacterial composition have an MIC50 that is higher than the concentration of the antibiotic in the gut.

[0137] MIC50 of a bacterial composition or the elements in the composition may be determined by methods well known in the art. Reller et al., Antimicrobial Susceptibility Testing: A Review of General Principles and Contemporary Practices, Clinical Infectious Diseases 49(11):1749-1755 (2009). In such an embodiment, the additional time between antibiotic administration and administration of the bacterial composition is not necessary. If the pretreatment protocol is part of treatment of an acute infection, the antibiotic may be chosen so that the infection is sensitive to the antibiotic, but the constituents in the bacterial composition are not sensitive to the antibiotic.

[0138] Routes of Administration

[0139] The bacterial compositions of the invention are suitable for administration to mammals and non-mammalian animals in need thereof. In certain embodiments, the mammalian subject is a human subject who has one or more symptoms of a dysbiosis.

[0140] When the mammalian subject is suffering from a disease, disorder or condition characterized by an aberrant microbiota, the bacterial compositions described herein are suitable for treatment thereof. In some embodiments, the mammalian subject has not received antibiotics in advance of treatment with the bacterial compositions. For example, the mammalian subject has not been administered at least two doses of vancomycin, metronidazole and/or or similar antibiotic compound within one week prior to administration of the therapeutic composition. In other embodiments, the mammalian subject has not previously received an antibiotic compound in the one month prior to administration of the therapeutic composition. In other embodiments, the mammalian subject has received one or more treatments with one or more different antibiotic compounds and such treatment(s) resulted in no improvement or a worsening of symptoms.

[0141] In some embodiments, the gastrointestinal disease, disorder or condition is diarrhea caused by C. difficile including recurrent C. difficile infection, ulcerative colitis, colitis, Crohn's disease, or irritable bowel disease. Beneficially, the therapeutic composition is administered only once prior to improvement of the disease, disorder or condition. In some embodiments the therapeutic composition is administered at intervals greater than two days, such as once every three, four, five or six days, or every week or less frequently than every week. Or the preparation may be administered intermittently according to a set schedule, e.g., once a day, once weekly, or once monthly, or when the subject relapses from the primary illness. In another embodiment, the preparation may be administered on a long-term basis to subjects who are at risk for infection with or who may be carriers of these pathogens, including subjects who will have an invasive medical procedure (such as surgery), who will be hospitalized, who live in a long-term care or rehabilitation facility, who are exposed to pathogens by virtue of their profession (livestock and animal processing workers), or who could be carriers of pathogens (including hospital workers such as physicians, nurses, and other health care professionals).

[0142] In embodiments, the bacterial composition is administered enterically. This preferentially includes oral administration, or by an oral or nasal tube (including nasogastric, nasojejunal, oral gastric, or oral jejunal). In other embodiments, administration includes rectal administration (including enema, suppository, or colonoscopy). The bacterial composition may be administered to at least one region of the gastrointestinal tract, including the mouth, esophagus, stomach, small intestine, large intestine, and rectum. In some embodiments it is administered to all regions of the gastrointestinal tract. The bacterial compositions may be administered orally in the form of medicaments such as powders, capsules, tablets, gels or liquids. The bacterial compositions may also be administered in gel or liquid form by the oral route or through a nasogastric tube, or by the rectal route in a gel or liquid form, by enema or instillation through a colonoscope or by a suppository.

[0143] If the composition is administered colonoscopically and, optionally, if the bacterial composition is administered by other rectal routes (such as an enema or suppository) or even if the subject has an oral administration, the subject may have a colon cleansing preparation. The colon-cleansing preparation can facilitate proper use of the colonoscope or other administration devices, but even when it does not serve a mechanical purpose it can also maximize the proportion of the bacterial composition relative to the other organisms previously residing in the gastrointestinal tract of the subject. Any ordinarily acceptable colon-cleansing preparation may be used such as those typically provided when a subject undergoes a colonoscopy.

[0144] Dosages and Schedule for Administration

[0145] In some embodiments the bacteria and bacterial compositions are provided in a dosage form. In some embodiments the dosage form is designed for administration of at least one OTU or combination thereof disclosed herein, wherein the total amount of bacterial composition administered is selected from 0.1 ng to 10 g, 10 ng to 1 g, 100 ng to 0.1 g, 0.1 mg to 500 mg, 1 mg to 100 mg, or from 10-15 mg. In some embodiments the bacterial composition is consumed at a rate of from 0.1 ng to 10 g a day, 10 ng to 1 g a day, 100 ng to 0.1 g a day, 0.1 mg to 500 mg a day, 1 mg to 100 mg a day, or from 10-15 mg a day, or more.

[0146] In some embodiments the treatment period is at least 1 day, at least 2 days, at least 3 days, at least 4 days, at least 5 days, at least 6 days, at least 1 week, at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 1 month, at least 2 months, at least 3 months, at least 4 months, at least 5 months, at least 6 months, or at least 1 year. In some embodiments the treatment period is from 1 day to 1 week, from 1 week to 4 weeks, from 1 month, to 3 months, from 3 months to 6 months, from 6 months to 1 year, or for over a year.

[0147] In one embodiment, from 10⁵ and 10¹² microorganisms total may be administered to the patient in a given dosage form. In one mode, an effective amount may be provided in from 1 to 500 ml or from 1 to 500 grams of the bacterial composition having from 10⁷ to 10¹¹ bacteria per ml or per gram, or a capsule, tablet or suppository having from 1 mg to 1000 mg lyophilized powder having from 10⁷ to 10¹¹ bacteria. Those receiving acute treatment may receive higher doses than those who are receiving chronic administration (such as hospital workers or those admitted into long-term care facilities).

[0148] Any of the preparations described herein may be administered once on a single occasion or on multiple occasions, such as once a day for several days or more than once a day on the day of administration (including twice daily, three times daily, or up to five times daily). Or the preparation may be administered intermittently according to a set schedule, e.g., once weekly, once monthly, or when the patient relapses from the primary illness. In another embodiment, the preparation may be administered on a long-term basis to individuals who are at risk for infection with or who may be carriers of these pathogens, including individuals who will have an invasive medical procedure (such as surgery), who will be hospitalized, who live in a long-term care or rehabilitation facility, who are exposed to pathogens by virtue of their profession (livestock and animal processing workers), or who could be carriers of pathogens (including hospital workers such as physicians, nurses, and other health care professionals).

[0149] Patient Selection

[0150] Particular bacterial compositions may be selected for individual patients or for patients with particular profiles. For example, 16S sequencing may be performed for a given patient to identify the bacteria present in his or her microbiota. The sequencing may either profile the patient's entire microbiome using 16S sequencing (to the family, genera, or species level), a portion of the patient's microbiome using 16S sequencing, or it may be used to detect the presence or absence of specific candidate bacteria that are biomarkers for health or a particular disease state, such as markers of multi-drug resistant organisms or specific genera of concern such as Escherichia. Based on the biomarker data, a particular composition may be selected for administration to a patient to supplement or complement a patient's microbiota in order to restore health or treat or prevent disease. In another embodiment, patients may be screened to determine the composition of their microbiota to determine the likelihood of successful treatment.

[0151] Combination Therapy

[0152] The bacterial compositions may be administered with other agents in a combination therapy mode, including anti-microbial agents and prebiotics. Administration may be sequential, over a period of hours or days, or simultaneous.

[0153] In one embodiment, the bacterial compositions are included in combination therapy with one or more anti-microbial agents, which include anti-bacterial agents, anti-fungal agents, anti-viral agents and anti-parasitic agents.

[0154] Anti-bacterial agents include cephalosporin antibiotics (cephalexin, cefuroxime, cefadroxil, cefazolin, cephalothin, cefaclor, cefamandole, cefoxitin, cefprozil, and ceftobiprole); fluoroquinolone antibiotics (cipro, Levaquin, floxin, tequin, avelox, and norflox); tetracycline antibiotics (tetracycline, minocycline, oxytetracycline, and doxycycline); penicillin antibiotics (amoxicillin, ampicillin, penicillin V, dicloxacillin, carbenicillin, vancomycin, and methicillin); and carbapenem antibiotics (ertapenem, doripenem, imipenem/cilastatin, and meropenem).

[0155] Anti-viral agents include Abacavir, Acyclovir, Adefovir, Amprenavir, Atazanavir, Cidofovir, Darunavir, Delavirdine, Didanosine, Docosanol, Efavirenz, Elvitegravir, Emtricitabine, Enfuvirtide, Etravirine, Famciclovir, Foscarnet, Fomivirsen, Ganciclovir, Indinavir, Idoxuridine, Lamivudine, Lopinavir Maraviroc, MK-2048, Nelfinavir, Nevirapine, Penciclovir, Raltegravir, Rilpivirine, Ritonavir, Saquinavir, Stavudine, Tenofovir Trifluridine, Valaciclovir, Valganciclovir, Vidarabine, Ibacitabine, Amantadine, Oseltamivir, Rimantidine, Tipranavir, Zalcitabine, Zanamivir and Zidovudine.

[0156] Examples of antifungal compounds include, but are not limited to polyene antifungals such as natamycin, rimocidin, filipin, nystatin, amphotericin B, candicin, and hamycin; imidazole antifungals such as miconazole, ketoconazole, clotrimazole, econazole, omoconazole, bifonazole, butoconazole, fenticonazole, isoconazole, oxiconazole, sertaconazole, sulconazole, and tioconazole; triazole antifungals such as fluconazole, itraconazole, isavuconazole, ravuconazole, posaconazole, voriconazole, terconazole, and albaconazole; thiazole antifungals such as abafungin; allylamine antifungals such as terbinafine, naftifine, and butenafine; and echinocandin antifungals such as anidulafungin, caspofungin, and micafungin. Other compounds that have antifungal properties include, but are not limited to polygodial, benzoic acid, ciclopirox, tolnaftate, undecylenic acid, flucytosine or 5-fluorocytosine, griseofulvin, and haloprogin.

[0157] In one embodiment, the bacterial compositions are included in combination therapy with one or more corticosteroids, mesalazine, mesalamine, sulfasalazine, sulfasalazine derivatives, immunosuppressive drugs, cyclosporin A, mercaptopurine, azathiopurine, prednisone, methotrexate, antihistamines, glucocorticoids, epinephrine, theophylline, cromolyn sodium, anti-leukotrienes, anti-cholinergic drugs for rhinitis, anti-cholinergic decongestants, mast-cell stabilizers, monoclonal anti-IgE antibodies, vaccines, and combinations thereof.

[0158] A prebiotic is a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon host well-being and health. Prebiotics may include complex carbohydrates, amino acids, peptides, or other essential nutritional components for the survival of the bacterial composition. Prebiotics include, but are not limited to, amino acids, biotin, fructooligosaccharide, galactooligosaccharides, inulin, lactulose, mannan oligosaccharides, oligofructose-enriched inulin, oligofructose, oligodextrose, tagatose, trans-galactooligosaccharide, and xylooligosaccharides.

[0159] Methods for Characterization of Bacterial Compositions

[0160] In certain embodiments, provided are methods for testing certain characteristics of bacterial compositions. For example, the sensitivity of bacterial compositions to certain environmental variables is determined, e.g., in order to select for particular desirable characteristics in a given composition, formulation and/or use. For example, the constituents in the bacterial composition may be tested for pH resistance, bile acid resistance, and/or antibiotic sensitivity, either individually on a constituent-by-constituent basis or collectively as a bacterial composition comprised of multiple bacterial constituents (collectively referred to in this section as bacterial composition).

[0161] pH Sensitivity Testing. If a bacterial composition will be administered other than to the colon or rectum (i.e., through, for example, but not limited to, an oral route), optionally testing for pH resistance enhances the selection of bacterial compositions that will survive at the highest yield possible through the varying pH environments of the distinct regions of the GI tract. Understanding how the bacterial compositions react to the pH of the GI tract also assists in formulation, so that the number of bacteria in a dosage form can be increased if beneficial and/or so that the composition may be administered in an enteric-coated capsule or tablet or with a buffering or protective composition. As the pH of the stomach can drop to a pH of 1 to 2 after a high-protein meal for a short time before physiological mechanisms adjust it to a pH of 3 to 4 and often resides at a resting pH of 4 to 5, and as the pH of the small intestine can range from a pH of 6 to 7.4, bacterial compositions can be prepared that survive these varying pH ranges (specifically wherein at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or as much as 100% of the bacteria can survive gut transit times through various pH ranges). This may be tested by exposing the bacterial composition to varying pH ranges for the expected gut transit times through those pH ranges. Therefore, as a nonlimiting example only, 18-hour cultures of bacterial compositions may be grown in standard media, such as gut microbiota medium (“GMM”, see Goodman et al., Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice, PNAS 108(15):6252-6257 (2011)) or another animal-products-free medium, with the addition of pH adjusting agents for a pH of 1 to 2 for 30 minutes, a pH of 3 to 4 for 1 hour, a pH of 4 to 5 for 1 to 2 hours, and a pH of 6 to 7.4 for 2.5 to 3 hours. An alternative method for testing stability to acid is described in U.S. Pat. No. 4,839,281. Survival of bacteria may be determined by culturing the bacteria and counting colonies on appropriate selective or non-selective media.

[0162] Bile Acid Sensitivity Testing. Additionally, in some embodiments, testing for bile-acid resistance enhances the selection of bacterial compositions that will survive exposures to bile acid during transit through the GI tract. Bile acids are secreted into the small intestine and can, like pH, affect the survival of bacterial compositions. This may be tested by exposing the bacterial compositions to bile acids for the expected gut exposure time to bile acids. For example, bile acid solutions may be prepared at desired concentrations using 0.05 mM Tris at pH 9 as the solvent. After the bile acid is dissolved, the pH of the solution may be adjusted to 7.2 with 10% HCl. Bacterial compositions may be cultured in 2.2 ml of a bile acid composition mimicking the concentration and type of bile acids in the patient, 1.0 ml of 10% sterile-filtered feces media and 0.1 ml of an 18-hour culture of the given strain of bacteria. Incubations may be conducted for from 2.5 to 3 hours or longer. An alternative method for testing stability to bile acid is described in U.S. Pat. No. 4,839,281. Survival of bacteria may be determined by culturing the bacteria and counting colonies on appropriate selective or non-selective media.

[0163] Antibiotic Sensitivity Testing. As a further optional sensitivity test, bacterial compositions may be tested for sensitivity to antibiotics. In one embodiment, bacterial compositions may be chosen so that the bacterial constituents are sensitive to antibiotics such that if necessary they can be eliminated or substantially reduced from the patient's gastrointestinal tract by at least one antibiotic targeting the bacterial composition.

[0164] Adherence to Gastrointestinal Cells. The bacterial compositions may optionally be tested for the ability to adhere to gastrointestinal cells. A method for testing adherence to gastrointestinal cells is described in U.S. Pat. No. 4,839,281.

[0165] The specification is most thoroughly understood in light of the teachings of the references cited within the specification. The embodiments within the specification provide an illustration of embodiments and should not be construed to limit the scope. The skilled artisan readily recognizes that many other embodiments are encompassed. All publications and patents cited in this disclosure are incorporated by reference in their entirety. To the extent the material incorporated by reference contradicts or is inconsistent with this specification, the specification will supersede any such material. The citation of any references herein is not an admission that such references are prior art.

[0166] Unless otherwise indicated, all numbers expressing quantities of ingredients, reaction conditions, and so forth used in the specification, including claims, are to be understood as being modified in all instances by the term “about.” Accordingly, unless otherwise indicated to the contrary, the numerical parameters are approximations and may vary depending upon the desired properties sought to be obtained. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should be construed in light of the number of significant digits and ordinary rounding approaches.

[0167] Unless otherwise indicated, the term “at least” preceding a series of elements is to be understood to refer to every element in the series.

[0168] Below are examples of specific embodiments for carrying out the present invention. The examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperatures, etc.), but some experimental error and deviation should, of course, be allowed for. Examples of the techniques and protocols described herein with regard to therapeutic compositions can be found in, e.g., Remington's Pharmaceutical Sciences, 16th edition, Osol, A. (ed), 1980.

[0169] Construction of binary pairs in a high-throughput 96-well format. To allow high-throughput screening of binary pairs, vials of −80° C. glycerol stock banks were thawed and diluted to 1e8 CFU/mL. Each strain was then diluted 10× (to a final concentration of 1e7 CFU/mL of each strain) into 200 uL of PBS+15% glycerol in the wells of a 96-well plate. Plates were then frozen at −80° C. When needed, plates were removed from −80° C. and thawed at room temperature under anaerobic conditions when testing in a CivSim with Clostridium difficile.

[0170] Construction of ternary combinations in a high-throughput 96-well format. To allow high-throughput screening of ternary combinations, vials of −80° C. glycerol stock banks were thawed and diluted to 1e8 CFU/mL. Each strain was then diluted 10× (to a final concentration of 1e7 CFU/mL of each strain) into 200 uL of PBS+15% glycerol in the wells of a 96-well plate. Plates were then frozen at −80° C. When needed for the assay, plates were removed from −80° C. and thawed at room temperature under anaerobic conditions when testing in a CivSim with Clostridium difficile.

[0171] Construction of a CivSim Assay to Screen for Ecobiotic™ compositions Inhibitory to the Growth of Clostridium difficile. An overnight culture of Clostridium difficile was grown under anaerobic conditions in SweetB-Fosln or other suitable media for the growth of C. difficile. SweetB-Fosln is a complex media composed of brain heart infusion, yeast extract, cysteine, cellobiose, maltose, soluble starch, and fructooligosaccharides/inulin, and hemin, and is buffered with MOPs. After 24 hr of growth the culture was diluted 100,000 fold into a complex media such as SweetB-Fosln which is suitable for the growth of a wide variety of anaerobic bacterial species. The diluted C. difficile mixture was then aliquoted to wells of a 96-well plate (180 uL to each well). 20 uL of a unique binary pair of potential inhibitory species was then added to each well at a final concentration of 1e6 CFU/mL of each species. Alternatively the assay can be tested with binary pairs at different initial concentrations (1e9 CFU/mL, 1e8 CFU/mL, 1e7 CFU/mL, 1e5 CFU/mL, 1e4 CFU/mL, 1e3 CFU/mL, 1e2 CFU/mL). Control wells only inoculated with C. difficile were included for a comparison to the growth of C. difficile without inhibition. Additional wells were used for controls that either inhibit or do not inhibit the growth of C. difficile. One example of a positive control that inhibits growth was a combination of Blautia producta, Clostridium bifermentans and Escherichia coli. One example of a control that shows reduced inhibition of C. difficile growth as a combination of Bacteroides thetaiotaomicron, Bacteroides ovatus and Bacteroides vulgatus. Plates were wrapped with parafilm and incubated for 24 hr at 37° C. under anaerobic conditions. After 24 hr the wells containing C. difficile alone were serially diluted and plated to determine titer. The 96-well plate was then frozen at −80 C before quantifying C. difficile by qPCR assay.

[0172] Construction of a CivSim Assay to Screen for bacterial compositions that produce diffusible products inhibitory to the growth of Clostridium difficile using a filter insert. The CivSim assay described above was modified by using a 0.22 uM filter insert (Millipore™ MultiScreen™ 96-Well Assay Plates—Item MAGVS2210) in 96-well format to physically separate C. difficile from the bacterial compositions. The C. difficile was aliquoted into the 96-well plate while the bacterial compositions were aliquoted into media on the filter overlay. The nutrient media as in contact on both sides of the 0.22 uM filter, allowing exchange of nutrients, small molecules and many macromolecules (e.g., bacteriocins, cell-surface proteins, or polysaccharides) by diffusion. In this embodiment, after 24 hr incubation, the filter insert containing the bacterial compositions was removed. The plate containing C. difficile was then transferred to a 96-well plate reader suitable for measuring optical density (OD) at 600 nm. The growth of C. difficile in the presence of different bacterial compositions was compared based on the OD measurement.

[0173] Construction of a CivSim Assay to Screen for bacterial compositions inhibitory to the growth of Clostridium difficile using Clostridium difficile selective media for quantification. The CivSim assay described above can be modified to determine final C. difficile titer by serially diluting and plating to C. difficile selective media (Bloedt et al 2009) such as CCFA (cycloserine cefoxitin fructose agar, Anaerobe Systems), CDSA (Clostridium difficile selective agar, which is cycloserine cefoxitin mannitol agar, Becton Dickinson).

[0174] A. Standard Curve Preparation

[0175] The standard curve was generated from a well on each assay plate containing only pathogenic C. difficile grown in SweetB+Fosln media as provided herein and quantified by selective spot plating. Serial dilutions of the culture were performed in sterile phosphate-buffered saline. Genomic DNA was extracted from the standard curve samples along with the other wells.

[0176] B. Genomic DNA Extraction

[0177] Genomic DNA was extracted from 5 μl of each sample using a dilution, freeze/thaw, and heat lysis protocol. 5 μL of thawed samples were added to 45 μL of UltraPure water (Life Technologies, Carlsbad, Calif.) and mixed by pipetting. The plates with diluted samples were frozen at −20° C. until use for qPCR which includes a heated lysis step prior to amplification. Alternatively the genomic DNA could be isolated using the Mo Bio Powersoil®-htp 96 Well Soil DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), Mo Bio Powersoil® DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.), or the QIAamp DNA Stool Mini Kit (QIAGEN, Valencia, Calif.) according to the manufacturer's instructions.

[0178] C. qPCR Composition and Conditions

[0179] The qPCR reaction mixture contained 1× SsoAdvanced Universal Probes Supermix, 900 nM of Wr-tcdB-F primer (AGCAGTTGAATATAGTGGTTTAGTTAGAGTTG, IDT, Coralville, Iowa), 900 nM of Wr-tcdB-R primer (CATGCTTTTTTAGTTTCTGGATTGAA, IDT, Coralville, Iowa), 250 nM of Wr-tcdB-P probe (6FAM-CATCCAGTCTCAATTGTATATGTTTCTCCA-MGB, Life Technologies, Grand Island, N.Y.), and Molecular Biology Grade Water (Mo Bio Laboratories, Carlsbad, Calif.) to 18 μl (Primers adapted from: Wroblewski, D. et al., Rapid Molecular Characterization of Clostridium difficile and Assessment of Populations of C. difficile in Stool Specimens, Journal of Clinical Microbiology 47:2142-2148 (2009)). This reaction mixture was aliquoted to wells of a Hard-shell Low-Profile Thin Wall 96-well Skirted PCR Plate (BioRad, Hercules, Calif.). To this reaction mixture, 2 μl of diluted, frozen, and thawed samples were added and the plate sealed with a Microseal ‘B’ Adhesive Seal (BioRad, Hercules, Calif.). The qPCR was performed on a BioRad C1000™ Thermal Cycler equipped with a CFX96™ Real-Time System (BioRad, Hercules, Calif.). The thermocycling conditions were 95° C. for 15 minutes followed by 45 cycles of 95° C. for 5 seconds, 60° C. for 30 seconds, and fluorescent readings of the FAM channel. Alternatively, the qPCR could be performed with other standard methods known to those skilled in the art.

[0180] D. Data Analysis

[0181] The Cq value for each well on the FAM channel was determined by the CFX Manager™ 3.0 software. The log₁₀ (cfu/mL) of C. difficile each experimental sample was calculated by inputting a given sample's Cq value into a linear regression model generated from the standard curve comparing the Cq values of the standard curve wells to the known log₁₀ (cfu/mL) of those samples. The log inhibition was calculated for each sample by subtracting the log₁₀ (cfu/mL) of C. difficile in the sample from the log₁₀ (cfu/mL) of C. difficile in the sample on each assay plate used for the generation of the standard curve that has no additional bacteria added. The mean log inhibition was calculated for all replicates for each composition.

[0182] A histogram of the range and standard deviation of each composition was plotted. Ranges or standard deviations of the log inhibitions that were distinct from the overall distribution were examined as possible outliers. If the removal of a single log inhibition datum from one of the binary pairs that were identified in the histograms would bring the range or standard deviation in line with those from the majority of the samples, that datum was removed as an outlier, and the mean log inhibition was recalculated.

[0183] The pooled variance of all samples evaluated in the assay was estimated as the average of the sample variances weighted by the sample's degrees of freedom. The pooled standard error was then calculated as the square root of the pooled variance divided by the square root of the number of samples. Confidence intervals for the null hypothesis were determined by multiplying the pooled standard error to the z score corresponding to a given percentage threshold. Mean log inhibitions outside the confidence interval were considered to be inhibitory if positive or stimulatory if negative with the percent confidence corresponding to the interval used. Samples with mean log inhibition greater than the 99% confidence interval (C.I) of the null hypothesis are reported as ++++, those with a 95%<C.I.<99% as +++, those with a 90%<C.I.<95% as ++, those with a 80%<C.I.<90% as + while samples with mean log inhibition less than than the 99% confidence interval (C.I) of the null hypothesis are reported as −−−−, those with a 95%<C.I.<99% as −−−, those with a 90%<C.I.<95% as −−, those with a 80%<C.I.<90% as −.

[0184] Many binary pairs inhibit C. difficile Table 5. 622 of 989 combinations show inhibition with a confidence interval>80%; 545 of 989 with a C.I.>90%; 507 of 989 with a C.I.>95%; 430 of 989 with a C.I. of >99%. Non-limiting but exemplary binary pairs include those with mean log reduction greater than 0.366, e.g. Allistipes shahii paired with Blautia producta, Clostridium hathaweyi, or Colinsella aerofaciens, or Clostidium mayombei paired with C. innocuum, C. tertium, Colinsella aerofaciens, or any of the other 424 combinations shown in Table 5. Equally important, the CivSim assay describes binary pairs that do not effectively inhibit C. difficile. 188 of 989 combinations promote growth with >80% confidence; 52 of 989 show a lack of inhibition with >90% confidence; 22 of 989 show a lack of inhibition with >95% confidence; 3 of 989, including B. producta combined with Coprococcus catus, Alistipes shahii combined with Dorea formicigenerans, and Eubacterium rectale combined with Roseburia intestinalis, show a lack of inhibition with >99% confidence. 249 of 989 combinations are neutral in the assay, meaning they neither promote nor inhibit C. difficile growth to the limit of measurement.

[0185] Ternary combinations with mean log inhibition greater than 0.312 are reported as ++++(≧99% confidence interval (C.I.) of the null hypothesis), those with mean log inhibition between 0.221 and 0.312 as +++(95%<C.I.<99%), those with mean log inhibition between 0.171 and 0.221 as ++(90%<C.I.<95%), those with mean log inhibition between 0.113 and 0.171 as +(80%<C.I.<90%), those with mean log inhibition between −0.113 and −0.171 as −(80%<C.I.<90%), those with mean log inhibition between −0.171 and −0.221 as −−(90%<C.I.<95%), those with mean log inhibition between −0.221 and −0.312 as −−−(95%<C.I.<99%), and those with mean log inhibition less than −0.312 as −−−−(99%<C.I.).

[0186] The CivSim shows that many ternary combinations inhibit C. difficile. 39 of 56 combinations show inhibition with a confidence interval>80%; 36 of 56 with a C.I.>90%; 36 of 56 with a C.I.>95%; 29 of 56 with a C.I. of >99%. Non-limiting but exemplary ternary combinations include those with mean log reduction greater than 0.171, e.g. any combination shown in Table 6 with a score of ++++, such as Colinsella aerofaciens, Coprococcus comes, and Blautia producta. Equally important, the CivSim assay describes ternary combinations that do not effectively inhibit C. difficile. 5 of 56 combinations promote growth with >80% confidence; 2 of 56 promote growth with >90% confidence; 1 of 56, Coprococcus comes, Clostridium symbiosum and Eubacterium rectale, promote growth with >95% confidence. 12 of 56 combinations are neutral in the assay, meaning they neither promote nor inhibit C. difficile growth to the limit of measurement.

[0187] A. Genomic DNA Extraction

[0188] Genomic DNA is extracted from pure microbial cultures using a hot alkaline lysis method. 2 μl of microbial culture is added to 18 μl of Lysis Buffer (25 mM NaOH, 0.2 mM EDTA) and the mixture is incubated at 95° C. for 30 minutes. Subsequently, the samples are cooled to 4° C. and neutralized by the addition of 20 μl of Neutralization Buffer (40 mM Tris-HCl) and then diluted 10-fold in Elution Buffer (10 mM Tris-HCl). Alternatively, genomic DNA is extracted from pure microbial cultures using commercially available kits such as the Mo Bio Ultraclean® Microbial DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.) or by standard methods known to those skilled in the art.

[0189] B. PCR

[0190] To amplify bacterial 16S rDNA, 2 μl of extracted gDNA is added to a 20 μl final volume PCR reaction. The PCR reaction also contains 1× HotMasterMix (5PRIME, Gaithersburg, Md.), 250 nM of 27f primer (AGRGTTTGATCMTGGCTCAG, IDT, Coralville, Iowa), and 250 nM of 1492r primer (TACGGYTACCTTGTTAYGACTT, IDT, Coralville, Iowa), with Molecular Biology Grade Water (Mo Bio Laboratories, Carlsbad, Calif.) for the balance of the volume. Alternatively, other universal bacterial primers or thermostable polymerases known to those skilled in the art are used.

[0191] The PCR performed on commercially available thermocyclers such as a BioRad MyCycler™ Thermal Cycler (BioRad, Hercules, Calif.). The reactions are run at 94° C. for 2 minutes followed by 30 cycles of 94° C. for 30 seconds, 51° C. for 30 seconds, and 68° C. for 1 minute 30 seconds, followed by a 7 minute extension at 72° C. and an indefinite hold at 4° C. Following PCR, gel electrophoresis of a portion of the reaction products is used to confirm successful amplification of a −1.5 kb product.

[0192] C. PCR Cleanup

[0193] To remove nucleotides and oligonucleotides from the PCR products, 1 μl of HT ExoSap-IT (Affymetrix, Santa Clara, Calif.) is added to 2.5 μl of PCR product followed by a 15 minute incubation at 37° C. and then a 15 minute inactivation at 80° C.

[0194] D. Sanger Sequencing

[0195] For each sample, two sequencing reactions are performed, one using each primer: 27f and 1492r. 40 ng of ExoSap-IT-cleaned PCR products are mixed with 25 pmol of sequencing primer and Molecular Biology Grade Water (Mo Bio Laboratories, Carlsbad, Calif.) to 15 μl total volume. This reaction is submitted to a commercial sequencing organization such as Genewiz (South Plainfield, N.J.) for Sanger sequencing.

[0196] E. Genomic DNA Extraction

[0197] Genomic DNA is extracted from pure microbial cultures using a hot alkaline lysis method. 2 μl of microbial culture is added to 18 μl of Lysis Buffer (25 mM NaOH, 0.2 mM EDTA) and the mixture is incubated at 95° C. for 30 minutes. Subsequently, the samples are cooled to 4° C. and neutralized by the addition of 18 μl of Neutralization Buffer (40 mM Tris-HCl) and then diluted 10-fold in Elution Buffer (10 mM Tris-HCl). Alternatively, genomic DNA is extracted from pure microbial cultures using commercially available kits such as the Mo Bio Ultraclean® Microbial DNA Isolation Kit (Mo Bio Laboratories, Carlsbad, Calif.) or by standard methods known to those in skilled in the art.

[0198] F. PCR

[0199] To amplify the V4 region of bacterial 16S rDNA, 2 μl of extracted gDNA is added to a 20 μl final volume PCR reaction. The PCR reaction also contains 1× HotMasterMix (5PRIME, Gaithersburg, Md.), 200 nM of V4_—515 f_adapt (AATGATACGGCGACCACCGAGATCTACACTATGGTAATTGTGTGCCAGCMGCCGCG GTAA, IDT, Coralville, Iowa), and 200 nM of barcoded 806rbc (CAAGCAGAAGACGGCATACGAGAT_—12bpGolayBarcode_AGTCAGTCAGCCGGACTAC HVGGGTWTCTAAT, IDT, Coralville, Iowa), with Molecular Biology Grade Water (Mo Bio Laboratories, Carlsbad, Calif.) for the balance of the volume. These primers incorporate adapters for Illumina sequencing by synthesis. Optionally, identical replicate, triplicate, or quadruplicate reactions may be performed. Alternatively other universal bacterial primers or thermostable polymerases known to those skilled in the art are used.

[0200] The PCR performed on commercially available thermocyclers such as a BioRad MyCycler™ Thermal Cycler (BioRad, Hercules, Calif.). The reactions are run at 94° C. for 3 minutes followed by 25 cycles of 94° C. for 45 seconds, 50° C. for 1 minute, and 72° C. for 1 minute 30 seconds, followed by a 10 minute extension at 72° C. and a indefinite hold at 4° C. Following PCR, gel electrophoresis of a portion of the reaction products is used to confirm successful amplification of a −0.4 kb product.

[0201] G. PCR Cleanup

[0202] To remove nucleotides and oligonucleotides from the PCR products, the entire remaining volume of the PCR, or of the multiple PCRs, is cleaned up using the Mo Bio Ultraclean®-htp 96 Well PCR Clean-up Kit (Mo Bio Laboratories, Carlsbad, Calif.) according to the manufacturer's instructions or other commercially available kits such as the QIAquick 96 PCR Purification Kit (QIAGEN, Valencia, Calif.).

[0203] H. DNA Quantification & Pooling

[0204] The cleaned PCR products are quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies, Grand Island, N.Y.) according to the manufacturer's instructions. Following quantification, the barcoded cleaned PCR products are combined such that each distinct PCR product is at an equimolar ratio to create a prepared Illumina library.

[0205] I. Illumina Sequencing

[0206] The prepared library is sequenced on Illumina HiSeq or MiSeq sequencers (Illumina, San Diego, Calif.) with cluster generation, template hybridization, iso-thermal amplification, linearization, blocking and denaturization and hybridization of the sequencing primers performed according to the manufacturer's instructions. 16SV4SeqFw (TATGGTAATTGTGTGCCAGCMGCCGCGGTAA), 16SV4SeqRev (AGTCAGTCAGCCGGACTACHVGGGTWTCTAAT), and 16SV4Index (ATTAGAWACCCBDGTAGTCCGGCTGACTGACT) (IDT, Coralville, Iowa) are used for sequencing. This sequencing can optionally be performed by a contract research organization such as Metanome (Houston, Tex.), Ambry Genetics (Aliso Viejo, Calif.), Edge Bio (Gaithersburg, Md.), or Covance (Princeton, N.J.).

[0207] J. Taxonomic Assignment to Sequence Read Data

[0208] Nucleic acid sequences are analyzed and taxonomic and phylogenetic assignments of specific OTUs are made using sequence similarity and phylogenetic methods that are well known to those skilled in the art, including but not limited to maximum likelihood phylogenetic reconstruction (see e.g. Liu K, Linder CR, and Warnow T. 2011. RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation. PLoS ONE 6: e27731. McGuire G, Denham MC, and Balding DJ. 2001. Models of sequence evolution for DNA sequences containing gaps. Mol. Biol. Evol 18: 481-490. Wróbel B. 2008. Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods. J. Appl. Genet. 49: 49-67.) From these taxonomic assignments OTUs in the dataset are defined. The certainty of the OTU call is defined based on the OTU's sequence similarity to a reference nucleic acid sequence and the proximity of the OTU sequence relative to one or more reference sequences in the phylogeny. The specificity of an OTU's taxonomic and phlylogenetic assignment determines whether the match is assigned at the level of Family, Genus, Species, or Strain, and the confidence of this assignment is determined based on the position of bootstrap supported branches in the reference phylogenetic tree relative to the placement of the OTU sequence being interrogated.

[0209] The in vitro assay is used to screen for combinations of bacteria inhibitory to the growth of E. coli by modifying the media used for growth of the pathogen inoculum. One of several choices of media is used for growth of the pathogen such as Reinforced Clostridial Media (RCM), Brain Heart Infusion Broth (BHI) or Luria Bertani Broth (LB) (also known as Lysogeny Broth). E. coli is quantified by using alternative selective media specific for E. coli or using qPCR probes specific for the pathogen. For example, aerobic growth on MacConkey lactose medium selects for enteric Gram negatives, including E. coli. qPCR is conducted using probes specific for the shiga toxin of pathogenic E. coli.

[0210] The in vitro assay is used to screen for combinations of bacteria inhibitory to the growth of Vancomycin-Resistant Enterococcus spp. (VRE) by modifying the media used for growth of the pathogen inoculum. Several choices of media are used for growth of the pathogen such as Reinforced Clostridial Media (RCM), Brain Heart Infusion Broth (BHI) or Luria Bertani Broth (LB). VRE is quantified by using alternative selective media specific for VRE or using qPCR probes specific for the pathogen. For example, m-Enterococcus agar containing sodium azide is selective for Enterococcus spp. and a small number of other species. Probes specific to the van genes conferring vancomycin resistance are used in the qPCR.

[0211] The in vitro assay is used to screen for combinations of bacteria inhibitory to the growth of Salmonella spp. by modifying the media used for growth of the pathogen inoculum. Several choices of media are used for growth of the pathogen such as Reinforced Clostridial Media (RCM), Brain Heart Infusion Broth (BHI) or Luria Bertani Broth (LB). Salmonella spp. are quantified by using alternative selective media specific for Salmonella spp. or using qPCR probes specific for the pathogen. For example, MacConkey agar is used to select for Salmonella spp. and the invA gene is targeted with qPCR probes; this gene encodes an invasion protein carried by many pathogenic Salmonella spp. and is used in invading eukaryotic cells.

[0212] Method of Preparing the Bacterial Composition for Administration to a Subject

[0213] Two strains for the bacterial composition are independently cultured and mixed together before administration. Both strains are independently be grown at 37° C., pH 7, in a GMM or other animal-products-free medium, pre-reduced with 1 g/L cysteine.HCl. After each strain reaches a sufficient biomass, it is preserved for banking by adding 15% glycerol and then frozen at −80° C. in 1 ml cryotubes.

[0214] Each strain is then be cultivated to a concentration of 10¹⁰ CFU/mL, then concentrated 20-fold by tangential flow microfiltration; the spent medium is exchanged by diafiltering with a preservative medium consisting of 2% gelatin, 100 mM trehalose, and 10 mM sodium phosphate buffer, or other suitable preservative medium. The suspension is freeze-dried to a powder and titrated.

[0215] After drying, the powder is blended with microcrystalline cellulose and magnesium stearate and formulated into a 250 mg gelatin capsule containing 10 mg of lyophilized powder (10⁸ to 10¹¹ bacteria), 160 mg microcrystalline cellulose, 77.5 mg gelatin, and 2.5 mg magnesium stearate.

[0216] A patient has suffered from recurrent bouts of C. difficile. In the most recent acute phase of illness, the patient is treated with an antibiotic sufficient to ameliorate the symptoms of the illness. In order to prevent another relapse of C. difficile, the patient is administered one of the present bacterial compositions. Specifically, the patient is administered Bacillus circulans and Roseburia inulinivorans at a dose of 10⁸ bacteria total in a lyophilized form, specifically in a 250 mg gelatin capsule containing 10 mg of lyophilized bacteria, 160 mg microcrystalline cellulose, 77.5 mg gelatin, and 2.5 mg magnesium stearate. The patient takes the capsule by mouth and resumes a normal diet after 4, 8, 12, or 24 hours. In another embodiment, the patient may take the capsule by mouth before, during, or immediately after a meal.

[0217] Feces is collected before and at 1 day, 3 days, 1 week, and 1 month after administration. The presence of C. difficile is found in the feces before administration of the bacterial composition, but feces collections after administration show reducing (such as at least 50% less, 60%, 70%, 80%, 90%, or 95%) to no detectable levels of C. difficile, as measured by qPCR, as described above. ELISA for toxin protein or traditional microbiological identification techniques may also be used.

[0218] As another measure of patient success, a positive response may be defined as absence of diarrhea, which itself is defined as 3 or more loose or watery stools per day for at least 2 consecutive days or 8 or more loose or watery stools in 48 hours, or persisting diarrhea (due to other causes) with repeating (three times) negative stool tests for toxins of C. difficile.

[0219] Treatment failure is defined as persisting diarrhea with a positive C. difficile toxin stool test or no reduction in levels of C. difficile, as measured by qPCR sequencing. ELISA or traditional microbiological identification techniques may also be used.

[0220] A patient has suffered from recurrent bouts of C. difficile. In the most recent acute phase of illness, the patient is treated with an antibiotic sufficient to ameliorate the symptoms of the illness. In order to prevent another relapse of C. difficile, the patient is administered one of the present bacterial compositions. Specifically, the patient is administered a bacterial composition containing two bacterial types from Table 1 or Table 3, or a combination from Table 2, at a dose of 10⁸ bacteria total in a lyophilized form formulated in an enteric coated capsule. Example of the patient or samples derived from the patient is expected to demonstrate at least one measure of success as described herein (reducing levels of C. difficile as measured by qPCR, ELISA, or traditional microbiological identification; absence of diarrhea; persisting diarrhea with repeating (three times) negative stool tests for toxins of C. difficile.

[0221] Other embodiments will be apparent to those skilled in the art from consideration of the specification and practice of the embodiments. Consider the specification and examples as exemplary only, with a true scope and spirit being indicated by the following claims.

TABLE 1
OTU	Domain	Phylum	Class	Order	Family	Genus
Abiotrophia defectiva	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Abiotrophia
Abiotrophia para-adiacens	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Abiotrophia
Abiotrophia sp. oral clone P4PA_155 P1	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Abiotrophia
Acetanaerobacterium elongatum	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Acetanaerobacterium
Acetivibrio cellulolyticus	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Acetivibrio
Acetivibrio ethanolgignens	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Acetivibrio
Acetobacter aceti	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacter fabarum	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacter lovaniensis	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacter malorum	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacter orientalis	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacter pasteurianus	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacter pomorum	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacter syzygii	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacter tropicalis	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Acetobacter
Acetobacteraceae bacterium AT-5844	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	unclassified
Acholeplasma laidlawii	Bacteria	Tenericutes	Mollicutes	Acholeplasmatales	Acholeplasmataceae	Acholeplasma
Achromobacter denitrificans	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Achromobacter
Achromobacter piechaudii	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Achromobacter
Achromobacter xylosoxidans	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Achromobacter
Acidaminococcus fermentans	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Acidaminococcaceae	Acidaminococcus
Acidaminococcus intestini	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Acidaminococcaceae	Acidaminococcus
Acidaminococcus sp. D21	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Acidaminococcaceae	Acidaminococcus
Acidilobus saccharovorans	Archaea	Crenarchaeota	Thermoprotei	Acidilobales	Acidilobaceae	Acidilobus
Acidithiobacillus ferrivorans	Bacteria	Proteobacteria	Gammaproteobacteria	Acidithiobacillales	Acidithiobacillaceae	Acidithiobacillus
Acidovorax sp. 98-63833	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	Acidovorax
Acidovorax sp. c109	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Acinetobacter baumannii	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter calcoaceticus	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter genomosp. C1	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter haemolyticus	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter johnsonii	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter junii	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter lwoffii	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter parvus	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter radioresistens	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter schindleri	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter sp. 56A1	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter sp. CIP 101934	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter sp. CIP 102143	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter sp. CIP 53.82	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter sp. M16-22	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter sp. RUH2624	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Acinetobacter sp. SH024	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Acinetobacter
Actinobacillus minor	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Actinobacillus
Actinobacillus pleuropneumoniae	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Actinobacillus
Actinobacillus succinogenes	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Aggregatibacter
Actinobacillus succinogenes	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Actinobacillus
Actinobacillus ureae	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Actinobacillus
Actinobaculum massiliae	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinobaculum
Actinobaculum schaalii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinobaculum
Actinobaculum sp. BM#101342	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinobaculum
Actinobaculum sp. P2P_19 P1	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinobaculum
Actinomyces cardiffensis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces europaeus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces funkei	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces genomosp. C1	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces genomosp. C2	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces genomosp. P1 oral clone MB6_C03	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces georgiae	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces israelii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces massiliensis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces meyeri	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces naeslundii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces nasicola	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces neuii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces odontolyticus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces oricola	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces orihominis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces oris	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. 7400942	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. c109	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. CCUG 37290	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. ChDC B197	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. GEJ15	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. HKU31	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. ICM34	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. ICM41	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. ICM47	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. ICM54	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. M2231/94/1	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral clone GU009	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral clone GU067	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral clone IO076	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral clone IO077	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral clone IP073	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral clone IP081	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral clone JA063	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral taxon 170	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral taxon 171	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral taxon 178	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral taxon 180	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral taxon 848	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. oral taxon C55	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces sp. TeJ5	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces urogenitalis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Actinomyces viscosus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Actinomyces
Adlercreutzia equolifaciens	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Adlercreutzia
Aerococcus sanguinicola	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Aerococcus
Aerococcus urinae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Aerococcus
Aerococcus urinaeequi	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Aerococcus
Aerococcus viridans	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Aerococcus
Aeromicrobium marinum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardioidaceae	Aeromicrobium
Aeromicrobium sp. JC14	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardioidaceae	Aeromicrobium
Aeromonas allosaccharophila	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	Aeromonas
Aeromonas enteropelogenes	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	Aeromonas
Aeromonas hydrophila	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	Aeromonas
Aeromonas jandaei	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	Aeromonas
Aeromonas salmonicida	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	Aeromonas
Aeromonas trota	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	Aeromonas
Aeromonas veronii	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Aeromonadaceae	Aeromonas
Afipia genomosp. 4	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bradyrhizobiaceae	Afipia
Aggregatibacter actinomycetemcomitans	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Aggregatibacter
Aggregatibacter aphrophilus	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Aggregatibacter
Aggregatibacter segnis	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Aggregatibacter
Agrobacterium radiobacter	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	Agrobacterium
Agrobacterium tumefaciens	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Rhizobiaceae	Agrobacterium
Agrococcus jenensis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Agrococcus
Akkermansia muciniphila	Bacteria	Verrucomicrobia	Verrucomicrobiae	Verrucomicrobiales	Verrucomicrobiaceae	Akkermansia
Alcaligenes faecalis	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Alcaligenes
Alcaligenes sp. CO14	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Alcaligenes
Alcaligenes sp. S3	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Alcaligenes
Alicyclobacillus acidocaldarius	Bacteria	Firmicutes	Bacilli	Bacillales	Alicyclobacillaceae	Alicyclobacillus
Alicyclobacillus acidoterrestris	Bacteria	Firmicutes	Bacilli	Bacillales	Alicyclobacillaceae	Alicyclobacillus
Alicyclobacillus contaminans	Bacteria	Firmicutes	Bacilli	Bacillales	Alicyclobacillaceae	Alicyclobacillus
Alicyclobacillus cycloheptanicus	Bacteria	Firmicutes	Bacilli	Bacillales	Alicyclobacillaceae	Alicyclobacillus
Alicyclobacillus herbarius	Bacteria	Firmicutes	Bacilli	Bacillales	Alicyclobacillaceae	Alicyclobacillus
Alicyclobacillus pomorum	Bacteria	Firmicutes	Bacilli	Bacillales	Alicyclobacillaceae	Alicyclobacillus
Alicyclobacillus sp. CCUG 53762	Bacteria	Firmicutes	Bacilli	Bacillales	Alicyclobacillaceae	Alicyclobacillus
Alistipes finegoldii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes
Alistipes indistinctus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes
Alistipes onderdonkii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes
Alistipes putredinis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes
Alistipes shahii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes
Alistipes sp. HGB5	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes
Alistipes sp. JC50	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes
Alistipes sp. RMA 9912	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Rikenellaceae	Alistipes
Alkaliphilus metalliredigenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Alkaliphilus
Alkaliphilus oremlandii	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Alkaliphilus
Alloscardovia omnicolens	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Alloscardovia
Alloscardovia sp. OB7196	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Alloscardovia
Anaerobaculum hydrogeniformans	Bacteria	Synergistetes	Synergistia	Synergistales	Synergistaceae	Anaerobaculum
Anaerobiospirillum succiniciproducens	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Succinivibrionaceae	Anaerobiospirillum
Anaerobiospirillum thomasii	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Succinivibrionaceae	Anaerobiospirillum
Anaerococcus hydrogenalis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus lactolyticus	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus octavius	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus prevotii	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. 8404299	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. 8405254	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. 9401487	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. 9403502	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. gpac104	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. gpac126	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. gpac155	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. gpac199	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus sp. gpac215	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus tetradius	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerococcus vaginalis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Anaerococcus
Anaerofustis stercorihominis	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Anaerofustis
Anaeroglobus geminatus	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Anaeroglobus
Anaerosporobacter mobilis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Anaerosporobacter
Anaerostipes caccae	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Anaerostipes
Anaerostipes sp. 3_2_56FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Anaerostipes
Anaerotruncus colihominis	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Anaerotruncus
Anaplasma marginale	Bacteria	Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	Anaplasma
Anaplasma phagocytophilum	Bacteria	Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	Anaplasma
Aneurinibacillus aneurinilyticus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Aneurinibacillus
Aneurinibacillus danicus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Aneurinibacillus
Aneurinibacillus migulanus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Aneurinibacillus
Aneurinibacillus terranovensis	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Aneurinibacillus
Aneurinibacillus thermoaerophilus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Aneurinibacillus
Anoxybacillus contaminans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Anoxybacillus
Anoxybacillus flavithermus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Anoxybacillus
Arcanobacterium haemolyticum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Arcanobacterium
Arcanobacterium pyogenes	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Trueperella
Arcobacter butzleri	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	Arcobacter
Arcobacter cryaerophilus	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	Arcobacter
Arthrobacter agilis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Arthrobacter
Arthrobacter arilaitensis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Arthrobacter
Arthrobacter bergerei	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Arthrobacter
Arthrobacter globiformis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Arthrobacter
Arthrobacter nicotianae	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Arthrobacter
Atopobium minutum	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Atopobium
Atopobium parvulum	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Atopobium
Atopobium rimae	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Atopobium
Atopobium sp. BS2	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Atopobium
Atopobium sp. F0209	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Atopobium
Atopobium sp. ICM42b10	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Atopobium
Atopobium sp. ICM57	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Atopobium
Atopobium vaginae	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Atopobium
Aurantimonas coralicida	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Aurantimonadaceae	Aurantimonas
Aureimonas altamirensis	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Aurantimonadaceae	Aurantimonas
Auritibacter ignavus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Auritidibacter
Averyella dalhousiensis	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Averyella
Bacillus aeolius	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus aerophilus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus aestuarii	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus alcalophilus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus amyloliquefaciens	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus atrophaeus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus badius	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus cereus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus circulans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus clausii	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus coagulans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus firmus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus flexus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus fordii	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus gelatini	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus halmapalus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus halodurans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus herbersteinensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus horti	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus idriensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus lentus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus licheniformis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus megaterium	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus nealsonii	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus niabensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus niacini	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus pocheonensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus pumilus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus safensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus simplex	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sonorensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. 10403023 MM10403188	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. 2_A_57_CT2	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. 2008724126	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. 2008724139	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. 7-16AIA	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. 9-3AIA	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. AP8	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. B27(2008)	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. BT1B_CT2	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. GB1.1	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. GB9	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. HU19.1	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. HU29	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. HU33.1	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. JC6	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. oral taxon F26	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. oral taxon F28	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. oral taxon F79	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. SRC_DSF1	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. SRC_DSF10	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. SRC_DSF2	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. SRC_DSF6	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. tc09	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sp. zh168	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus sphaericus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Lysinibacillus
Bacillus sporothermodurans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus subtilis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus thermoamylovorans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus thuringiensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacillus weihenstephanensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Bacteroidales bacterium ph8	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroidales genomosp. P1	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroidales genomosp. P2 oral clone MB1_G13	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroidales genomosp. P3 oral clone MB1_G34	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroidales genomosp. P4 oral clone MB2_G17	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroidales genomosp. P5 oral clone MB2_P04	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroidales genomosp. P6 oral clone MB3_C19	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroidales genomosp. P7 oral clone MB3_P19	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroidales genomosp. P8 oral clone MB4_G15	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	unclassified	unclassified
Bacteroides acidifaciens	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides barnesiae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides caccae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides cellulosilyticus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides clarus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides coagulans	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	unclassified
Bacteroides coprocola	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides coprophilus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides dorei	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides eggerthii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides faecis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides finegoldii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides fluxus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides fragilis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides galacturonicus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides helcogenes	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides heparinolyticus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides intestinalis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides massiliensis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides nordii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides oleiciplenus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides ovatus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides pectinophilus	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Bacteroides plebeius	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides pyogenes	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides salanitronis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides salyersiae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 1_1_14	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 1_1_30	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 1_1_6	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 1_1_6	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 2_1_22	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 2_1_56FAA	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 2_2_4	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 20_3	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 3_1_19	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 3_1_23	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 3_1_33FAA	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 3_1_40A	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 3_2_5	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 315-5	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 31SF15	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 31SF18	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 35AE31	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 35AE37	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 35BE34	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 35BE35	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 4_1_36	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 4_3_47FAA	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. 9_1_42FAA	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. AR20	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. AR29	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. B2	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. D1	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. D2	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. D20	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. D22	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. F-4	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. NB-8	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. WH2	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. XB12B	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides sp. XB44A	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides stercoris	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides thetaiotaomicron	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides uniformis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides ureolyticus	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Campylobacteraceae	Campylobacter
Bacteroides vulgatus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroides xylanisolvens	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Bacteroidetes bacterium oral taxon D27	Bacteria	Bacteroidetes	unclassified	unclassified	unclassified	unclassified
Bacteroidetes bacterium oral taxon F31	Bacteria	Bacteroidetes	unclassified	unclassified	unclassified	unclassified
Bacteroidetes bacterium oral taxon F44	Bacteria	Bacteroidetes	unclassified	unclassified	unclassified	unclassified
Barnesiella intestinihominis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Barnesiella
Barnesiella viscericola	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Barnesiella
Bartonella bacilliformis	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	Bartonella
Bartonella grahamii	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	Bartonella
Bartonella henselae	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	Bartonella
Bartonella quintana	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	Bartonella
Bartonella tamiae	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	Bartonella
Bartonella washoensis	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bartonellaceae	Bartonella
Bdellovibrio sp. MPA	Bacteria	Proteobacteria	Deltaproteobacteria	Bdellovibrionales	Bdellovibrionaceae	Bdellovibrio
Bifidobacteriaceae genomosp. C1	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	unclassified	unclassified
Bifidobacterium adolescentis	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium angulatum	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium animalis	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium bifidum	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium breve	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium catenulatum	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium gallicum	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium infantis	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium kashiwanohense	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium longum	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium pseudocatenulatum	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium pseudolongum	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium scardovii	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium sp. HM2	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium sp. HMLN12	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium sp. M45	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium sp. MSX5B	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium sp. TM-7	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium thermophilum	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Bifidobacterium
Bifidobacterium urinalis	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Alloscardovia
Bilophila wadsworthia	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Bilophila
Bisgaard Taxon	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Pasteurella
Blastomonas natatoria	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Blastomonas
Blautia coccoides	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia glucerasea	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia glucerasei	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia hansenii	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia hydrogenotrophica	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia luti	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia producta	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia schinkii	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia sp. M25	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia stercoris	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Blautia wexlerae	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Brachybacterium alimentarium	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dermabacteraceae	Brachybacterium
Brachybacterium conglomeratum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dermabacteraceae	Brachybacterium
Brachybacterium tyrofermentans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dermabacteraceae	Brachybacterium
Brachyspira aalborgi	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Brachyspiraceae	Brachyspira
Brachyspira pilosicoli	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Brachyspiraceae	Brachyspira
Brachyspira sp. HIS3	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Brachyspiraceae	Brachyspira
Brachyspira sp. HIS4	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Brachyspiraceae	Brachyspira
Brachyspira sp. HIS5	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Brachyspiraceae	Brachyspira
Brevibacillus agri	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus brevis	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus centrosporus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus choshinensis	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus invocatus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus laterosporus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus parabrevis	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus reuszeri	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus sp. phR	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacillus thermoruber	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Brevibacillus
Brevibacterium aurantiacum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevibacterium casei	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevibacterium epidermidis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevibacterium frigoritolerans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Bacillus
Brevibacterium linens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevibacterium mcbrellneri	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevibacterium paucivorans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevibacterium sanguinis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevibacterium sp. H15	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevibacterium sp. JC43	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Brevibacteriaceae	Brevibacterium
Brevundimonas subvibrioides	Bacteria	Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	Brevundimonas
Bryantella formatexigens	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Bryantella
Buchnera aphidicola	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Buchnera
Bulleidia extructa	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Bulleidia
Butyricicoccus pullicaecorum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Butyricicoccus
Butyricimonas virosa	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Butyricimonas
Butyrivibrio crossotus	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Butyrivibrio
Butyrivibrio fibrisolvens	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Butyrivibrio
Caldimonas manganoxidans	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	Caldimonas
Caminicella sporogenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Caminicella
Candidatus Arthromitus sp. SFB-mouse-Yit	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Candidatus Arthromitus
Candidatus Sulcia muelleri	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Candidatus Sulcia
Capnocytophaga canimorsus	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga genomosp. C1	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga gingivalis	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga granulosa	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga ochracea	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sp. GEJ8	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sp. oral clone AH015	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sp. oral clone ASCH05	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sp. oral clone ID062	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sp. oral strain A47ROY	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sp. oral strain S3	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sp. oral taxon 338	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sp. S1b	Bacteria	Bacteroidetes	Flavobacteria	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Capnocytophaga sputigena	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Capnocytophaga
Cardiobacterium hominis	Bacteria	Proteobacteria	Gammaproteobacteria	Cardiobacteriales	Cardiobacteriaceae	Cardiobacterium
Cardiobacterium valvarum	Bacteria	Proteobacteria	Gammaproteobacteria	Cardiobacteriales	Cardiobacteriaceae	Cardiobacterium
Carnobacterium divergens	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Carnobacterium
Carnobacterium maltaromaticum	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Carnobacterium
Catabacter hongkongensis	Bacteria	Firmicutes	Clostridia	Clostridiales	Catabacteriaceae	Catabacter
Catenibacterium mitsuokai	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Catenibacterium
Catonella genomosp. P1 oral clone MB5_P12	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Catonella
Catonella morbi	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Catonella
Catonella sp. oral clone FL037	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Catonella
Cedecea davisae	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Cedecea
Cellulosimicrobium funkei	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Promicromonosporaceae	Cellulosimicrobium
Cetobacterium somerae	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Cetobacterium
Chlamydiales bacterium NS11	Bacteria	Chlamydiae	Chlamydiia	Chlamydiales	unclassified	unclassified
Chlamydiales bacterium NS13	Bacteria	Chlamydiae	Chlamydiia	Chlamydiales	unclassified	unclassified
Chlamydiales bacterium NS16	Bacteria	Chlamydiae	Chlamydiia	Chlamydiales	unclassified	unclassified
Chloroflexi genomosp. P1	Bacteria	Chloroflexi	unclassified	unclassified	unclassified	unclassified
Christensenella minuta	Bacteria	Firmicutes	Clostridia	Clostridiales	Christensenellaceae	Christensenella
Chromobacterium violaceum	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Chromobacterium
Chryseobacterium anthropi	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Chryseobacterium
Chryseobacterium gleum	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Chryseobacterium
Chryseobacterium hominis	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Chryseobacterium
Citrobacter amalonaticus	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter braakii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter farmeri	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter freundii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter gillenii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter koseri	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter murliniae	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter rodentium	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter sedlakii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter sp. 30_2	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter sp. KMSI-3	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter werkmanii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Citrobacter youngae	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Citrobacter
Cloacibacillus evryensis	Bacteria	Synergistetes	Synergistia	Synergistales	Synergistaceae	Cloacibacillus
Clostridiaceae bacterium END-2	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	unclassified
Clostridiaceae bacterium JC13	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	unclassified
Clostridiales bacterium 1_7_47FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales bacterium 9400853	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales bacterium 9403326	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales bacterium oral clone P4PA_66 P1	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales bacterium oral taxon 093	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales bacterium oral taxon F32	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales bacterium ph2	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales bacterium SY8519	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales genomosp. BVAB3	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales sp. SM4/1	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridiales sp. SS3/4	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	Clostridiales
Clostridiales sp. SSC/2	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Clostridium acetobutylicum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium aerotolerans	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium aldenense	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium aldrichii	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium algidicarnis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium algidixylanolyticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium aminovalericum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium amygdalinum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium argentinense	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium asparagiforme	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium baratii	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium bartlettii	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Clostridium beijerinckii	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium bifermentans	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Clostridium bolteae	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium butyricum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium cadaveris	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium carboxidivorans	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium carnis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium celatum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium celerecrescens	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium cellulosi	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium chauvoei	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium citroniae	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium clariflavum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium clostridioforme	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium coccoides	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Clostridium cochlearium	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium cocleatum	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Clostridium colicanis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium colinum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium disporicum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium estertheticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium fallax	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium favososporum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium felsineum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium frigidicarnis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium gasigenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium ghonii	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Clostridium glycolicum	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Clostridium glycyrrhizinilyticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium haemolyticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium hathewayi	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium hiranonis	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Clostridium histolyticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium hylemonae	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium indolis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium innocuum	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Clostridium irregulare	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Clostridium isatidis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium kluyveri	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium lactatifermentans	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium lavalense	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium leptum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium limosum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium magnum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium malenominatum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium mayombei	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium methylpentosum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium nexile	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium novyi	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium orbiscindens	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	Flavonifractor
Clostridium oroticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium paraputrificum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium phytofermentans	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium piliforme	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium putrefaciens	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium quinii	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium ramosum	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Clostridium rectum	Bacteria	Fusobacteria	unclassified	unclassified	unclassified	unclassified
Clostridium saccharogumia	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium saccharolyticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium saccharolyticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sardiniense	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sartagoforme	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium scindens	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium septicum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sordellii	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Clostridium sp. 7_2_43FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. D5	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. HGF2	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. HPB-46	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. JC122	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. L2-50	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. LMG 16094	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. M62/1	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. MLG055	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. MT4 E	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. NMBHI-1	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. NML 04A032	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. SS2/1	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. SY8519	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. TM-40	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. YIT 12069	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sp. YIT 12070	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sphenoides	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium spiroforme	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Clostridium sporogenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sporosphaeroides	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium stercorarium	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sticklandii	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Clostridium straminisolvens	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium subterminale	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium sulfidigenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium symbiosum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium tertium	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium tetani	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium thermocellum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium tyrobutyricum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium viride	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Clostridium xylanolyticum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Clostridium
Collinsella aerofaciens	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Collinsella
Collinsella intestinalis	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Collinsella
Collinsella stercoris	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Collinsella
Collinsella tanakaei	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Collinsella
Comamonadaceae bacterium NML000135	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	unclassified
Comamonadaceae bacterium NML790751	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	unclassified
Comamonadaceae bacterium NML910035	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	unclassified
Comamonadaceae bacterium NML910036	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	unclassified
Comamonadaceae bacterium oral taxon F47	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	unclassified
Comamonas sp. NSP5	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	Comamonas
Conchiformibius kuhniae	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Conchiformibius
Coprobacillus cateniformis	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Coprobacillus
Coprobacillus sp. 29_1	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Coprobacillus
Coprobacillus sp. D7	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Coprobacillus
Coprococcus catus	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Coprococcus
Coprococcus comes	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Coprococcus
Coprococcus eutactus	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Coprococcus
Coprococcus sp. ART55/1	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Coprococcus
Coriobacteriaceae bacterium BV3Ac1	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	unclassified
Coriobacteriaceae bacterium JC110	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	unclassified
Coriobacteriaceae bacterium phI	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	unclassified
Corynebacterium accolens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium ammoniagenes	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium appendicis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium argentoratense	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium atypicum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium aurimucosum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium bovis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium canis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium casei	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium confusum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium coyleae	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium durum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium efficiens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium falsenii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium flavescens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium genitalium	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium glaucum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium glucuronolyticum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium glutamicum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium hansenii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium imitans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium kroppenstedtii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium lipophiloflavum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium macginleyi	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium mastitidis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium matruchotii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium minutissimum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium mucifaciens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium propinquum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium pseudodiphtheriticum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium pseudogenitalium	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium pseudotuberculosis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium pyruviciproducens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium renale	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium resistens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium riegelii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium simulans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium singulare	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium sp. 1 ex sheep	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium sp. L-2012475	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium sp. NML 93-0481	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium sp. NML 97-0186	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium sp. NML 99-0018	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium sundsvallense	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium tuberculostearicum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium tuscaniae	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium ulcerans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium ureicelerivorans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Corynebacterium variabile	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Corynebacteriaceae	Corynebacterium
Cronobacter malonaticus	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Cronobacter
Cronobacter sakazakii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Cronobacter
Cronobacter turicensis	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Cronobacter
Cryptobacterium curtum	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Cryptobacterium
Cupriavidus metallidurans	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Cupriavidus
Cytophaga xylanolytica	Bacteria	Bacteroidetes	Cytophagia	Cytophagales	Cytophagaceae	Cytophaga
Deferribacteres sp. oral clone JV001	Bacteria	Deferribacteres	Deferribacteres	unclassified	unclassified	unclassified
Deferribacteres sp. oral clone JV006	Bacteria	Deferribacteres	Deferribacteres	unclassified	unclassified	unclassified
Deferribacteres sp. oral clone JV023	Bacteria	Deferribacteres	Deferribacteres	unclassified	unclassified	unclassified
Deinococcus radiodurans	Bacteria	Deinococcus-Thermus	Deinococci	Deinococcales	Deinococcaceae	Deinococcus
Deinococcus sp. R-43890	Bacteria	Deinococcus-Thermus	Deinococci	Deinococcales	Deinococcaceae	Deinococcus
Delftia acidovorans	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	Delftia
Dermabacter hominis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dermabacteraceae	Dermabacter
Dermacoccus sp. Ellin185	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dermacoccaceae	Dermacoccus
Desmospora activa	Bacteria	Firmicutes	Bacilli	Bacillales	Thermoactinomycetaceae	Desmospora
Desmospora sp. 8437	Bacteria	Firmicutes	Bacilli	Bacillales	Thermoactinomycetaceae	Desmospora
Desulfitobacterium frappieri	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptococcaceae	Desulfitobacterium
Desulfitobacterium hafniense	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptococcaceae	Desulfitobacterium
Desulfobulbus sp. oral clone CH031	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfobacterales	Desulfobulbaceae	Desulfobulbus
Desulfotomaculum nigrificans	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptococcaceae	Desulfotomaculum
Desulfovibrio desulfuricans	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Desulfovibrio
Desulfovibrio fairfieldensis	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Desulfovibrio
Desulfovibrio piger	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Desulfovibrio
Desulfovibrio sp. 3_1_syn3	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Desulfovibrio
Desulfovibrio vulgaris	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfovibrionales	Desulfovibrionaceae	Desulfovibrio
Dialister invisus	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Dialister
Dialister micraerophilus	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Dialister
Dialister microaerophilus	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Dialister
Dialister pneumosintes	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Dialister
Dialister propionicifaciens	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Dialister
Dialister sp. oral taxon 502	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Dialister
Dialister succinatiphilus	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Dialister
Dietzia natronolimnaea	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dietziaceae	Dietzia
Dietzia sp. BBDP51	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dietziaceae	Dietzia
Dietzia sp. CA149	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dietziaceae	Dietzia
Dietzia timorensis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Dietziaceae	Dietzia
Dorea formicigenerans	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Dorea
Dorea longicatena	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Dorea
Dysgonomonas gadei	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Dysgonomonas
Dysgonomonas mossii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Dysgonomonas
Edwardsiella tarda	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Edwardsiella
Eggerthella lenta	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Eggerthella
Eggerthella sinensis	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Eggerthella
Eggerthella sp. 1_3_56FAA	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Eggerthella
Eggerthella sp. HGA1	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Eggerthella
Eggerthella sp. YY7918	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Eggerthella
Eikenella corrodens	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Eikenella
Enhydrobacter aerosaccus	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Enhydrobacter
Enterobacter aerogenes	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter asburiae	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter cancerogenus	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter cloacae	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter cowanii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter hormaechei	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter sp. 247BMC	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter sp. 638	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter sp. JC163	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter sp. SCSS	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacter sp. TSE38	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Enterobacter
Enterobacteriaceae bacterium 9_2_54FAA	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	unclassified
Enterobacteriaceae bacterium CF01Ent-1	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	unclassified
Enterobacteriaceae bacterium Smarlab 3302238	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	unclassified
Enterococcus avium	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus caccae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus casseliflavus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus durans	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus faecalis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus faecium	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus gallinarum	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus gilvus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus hawaiiensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus hirae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus italicus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus mundtii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus raffinosus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus sp. BV2CASA2	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus sp. CCRI-16620	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus sp. F95	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus sp. RfL6	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Enterococcus thailandicus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Enterococcus
Eremococcus coleocola	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Eremococcus
Erysipelothrix inopinata	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Erysipelothrix
Erysipelothrix rhusiopathiae	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Erysipelothrix
Erysipelothrix tonsillarum	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Erysipelothrix
Erysipelotrichaceae bacterium 3_1_53	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Erysipelotrichaceae bacterium 5_2_54FAA	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Escherichia albertii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia
Escherichia coli	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia
Escherichia fergusonii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia
Escherichia hermannii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia
Escherichia sp. 1_1_43	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia
Escherichia sp. 4_1_40B	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia
Escherichia sp. B4	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia
Escherichia vulneris	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Escherichia
Ethanoligenens harbinense	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ethanoligenens
Eubacteriaceae bacterium P4P_50 P4	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	unclassified
Eubacterium barkeri	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium biforme	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Eubacterium brachy	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium budayi	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium callanderi	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium cellulosolvens	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium contortum	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium coprostanoligenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium cylindroides	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Eubacterium desmolans	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium dolichum	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Eubacterium eligens	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium fissicatena	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium hadrum	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Anaerostipes
Eubacterium hallii	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium infirmum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XIII. Incertae Sedis	unclassified
Eubacterium limosum	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium moniliforme	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium multiforme	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium nitritogenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium nodatum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XIII. Incertae Sedis	unclassified
Eubacterium ramulus	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium rectale	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium ruminantium	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium saburreum	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Lachnoanaerobaculum
Eubacterium saphenum	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium siraeum	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. 3_1_31	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. AS15b	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. OBRC9	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. oral clone GI038	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. oral clone IR009	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. oral clone JH012	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. oral clone JI012	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. oral clone JN088	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. oral clone JS001	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. oral clone OH3A	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium sp. WAL 14571	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium tenue	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Eubacterium tortuosum	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	unclassified
Eubacterium ventriosum	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium xylanophilum	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Eubacterium
Eubacterium yurii	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Ewingella americana	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Ewingella
Exiguobacterium acetylicum	Bacteria	Firmicutes	Bacilli	Bacillales	unclassified	Exiguobacterium
Facklamia hominis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Aerococcaceae	Facklamia
Faecalibacterium prausnitzii	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Faecalibacterium
Filifactor alocis	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	Filifactor
Filifactor villosus	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	Filifactor
Finegoldia magna	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Finegoldia
Flavobacteriaceae genomosp. C1	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	unclassified
Flavobacterium sp. NF2-1	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Flavobacterium
Flavonifractor plautii	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	unclassified
Flexispira rappini	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Flexispira
Flexistipes sinusarabici	Bacteria	Deferribacteres	Deferribacteres	Deferribacterales	Deferribacteraceae	Flexistipes
Francisella novicida	Bacteria	Proteobacteria	Gammaproteobacteria	Thiotrichales	Francisellaceae	Francisella
Francisella philomiragia	Bacteria	Proteobacteria	Gammaproteobacteria	Thiotrichales	Francisellaceae	Francisella
Fulvimonas sp. NML 060897	Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Fulvimonas
Fusobacterium canifelinum	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium genomosp. C1	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium genomosp. C2	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium gonidiaformans	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium mortiferum	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium naviforme	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium necrogenes	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium necrophorum	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium nucleatum	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium periodonticum	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium russii	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. 1_1_41FAA	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. 11_3_2	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. 12_1B	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. 2_1_31	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. 3_1_27	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. 3_1_33	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. 3_1_36A2	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. 3_1_5R	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. AC18	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. ACB2	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. AS2	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. CM1	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. CM21	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. CM22	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. D12	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. oral clone ASCF06	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium sp. oral clone ASCF11	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium ulcerans	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Fusobacterium varium	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Fusobacteriaceae	Fusobacterium
Gardnerella vaginalis	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Gardnerella
Gemella haemolysans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillales Family XI. Incertae Sedis	Gemella
Gemella morbillorum	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillales Family XI. Incertae Sedis	Gemella
Gemella sanguinis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillales Family XI. Incertae Sedis	Gemella
Gemella sp. oral clone ASCE02	Bacteria	Firmicutes	Bacilli	Bacillales	unclassified	Gemella
Gemella sp. oral clone ASCF04	Bacteria	Firmicutes	Bacilli	Bacillales	unclassified	Gemella
Gemella sp. oral clone ASCF12	Bacteria	Firmicutes	Bacilli	Bacillales	unclassified	Gemella
Gemella sp. WAL 1945J	Bacteria	Firmicutes	Bacilli	Bacillales	unclassified	Gemella
Gemmiger formicilis	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Hyphomicrobiaceae	Gemmiger
Geobacillus kaustophilus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Geobacillus
Geobacillus sp. E263	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Geobacillus
Geobacillus sp. WCH70	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Geobacillus
Geobacillus stearothermophilus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Geobacillus
Geobacillus thermocatenulatus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Geobacillus
Geobacillus thermodenitrificans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Geobacillus
Geobacillus thermoglucosidasius	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Geobacillus
Geobacillus thermoleovorans	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Geobacillus
Geobacter bemidjiensis	Bacteria	Proteobacteria	Deltaproteobacteria	Desulfuromonadales	Geobacteraceae	Geobacter
Gloeobacter violaceus	Bacteria	Cyanobacteria	Gloeobacteria	Gloeobacterales	unclassified	Gloeobacter
Gluconacetobacter azotocaptans	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Gluconacetobacter
Gluconacetobacter diazotrophicus	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Gluconacetobacter
Gluconacetobacter entanii	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Gluconacetobacter
Gluconacetobacter europaeus	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Gluconacetobacter
Gluconacetobacter hansenii	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Gluconacetobacter
Gluconacetobacter johannae	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Gluconacetobacter
Gluconacetobacter oboediens	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Gluconacetobacter
Gluconacetobacter xylinus	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Gluconacetobacter
Gordonia bronchialis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Gordoniaceae	Gordonia
Gordonia polyisoprenivorans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Gordoniaceae	Gordonia
Gordonia sp. KTR9	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Gordoniaceae	Gordonia
Gordonia sputi	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Gordoniaceae	Gordonia
Gordonia terrae	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Gordoniaceae	Gordonia
Gordonibacter pamelaeae	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Gordonibacter
Gracilibacter thermotolerans	Bacteria	Firmicutes	Clostridia	Clostridiales	Gracilibacteraceae	Gracilibacter
Gramella forsetii	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Gramella
Granulicatella adiacens	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella
Granulicatella elegans	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella
Granulicatella paradiacens	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella
Granulicatella sp. M658/99/3	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella
Granulicatella sp. oral clone ASC02	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella
Granulicatella sp. oral clone ASCA05	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella
Granulicatella sp. oral clone ASCB09	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella
Granulicatella sp. oral clone ASCG05	Bacteria	Firmicutes	Bacilli	Lactobacillales	Carnobacteriaceae	Granulicatella
Grimontia hollisae	Bacteria	Proteobacteria	Gammaproteobacteria	Vibrionales	Vibrionaceae	unclassified
Haematobacter sp. BC14248	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	Haematobacter
Haemophilus aegyptius	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus genomosp. P2 oral clone MB3_C24	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus genomosp. P3 oral clone MB3_C38	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus haemolyticus	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus parahaemolyticus	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus parainfluenzae	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus paraphrophaemolyticus	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus parasuis	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus somnus	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Histophilus
Haemophilus sp. 70334	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus sp. HK445	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus sp. oral clone ASCA07	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus sp. oral clone ASCG06	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus sp. oral clone BJ021	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus sp. oral clone BJ095	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus sp. oral clone JM053	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus sp. oral taxon 851	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Haemophilus sputorum	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Haemophilus
Hafnia alvei	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Hafnia
Halomonas elongata	Bacteria	Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	Halomonas
Halomonas johnsoniae	Bacteria	Proteobacteria	Gammaproteobacteria	Oceanospirillales	Halomonadaceae	Halomonas
Halorubrum lipolyticum	Archaea	Euryarchaeota	Halobacteria	Halobacteriales	Halobacteriaceae	Halorubrum
Helicobacter bilis	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter
Helicobacter canadensis	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter
Helicobacter cinaedi	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter
Helicobacter pullorum	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter
Helicobacter sp. None	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter
Helicobacter winghamensis	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Helicobacter
Heliobacterium modesticaldum	Bacteria	Firmicutes	Clostridia	Clostridiales	Heliobacteriaceae	Heliobacterium
Herbaspirillum seropedicae	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	Herbaspirillum
Herbaspirillum sp. JC206	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	Herbaspirillum
Histophilus somni	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Histophilus
Holdemania filiformis	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Holdemania
Hydrogenoanaerobacterium saccharovorans	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Hydrogenoanaerobacterium
Hyperthermus butylicus	Archaea	Crenarchaeota	Thermoprotei	Desulfurococcales	Pyrodictiaceae	Hyperthermus
Hyphomicrobium sulfonivorans	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Hyphomicrobiaceae	Hyphomicrobium
Hyphomonas neptunium	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodobacterales	Hyphomonadaceae	Hyphomonas
Ignatzschineria indica	Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Ignatzschineria
Ignatzschineria sp. NML 95-0260	Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Ignatzschineria
Ignicoccus islandicus	Archaea	Crenarchaeota	Thermoprotei	Desulfurococcales	Desulfurococcaceae	Ignicoccus
Inquilinus limosus	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Rhodospirillaceae	Inquilinus
Janibacter limosus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Intrasporangiaceae	Janibacter
Janibacter melonis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Intrasporangiaceae	Janibacter
Janthinobacterium sp. SY12	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	Janthinobacterium
Johnsonella ignava	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Johnsonella
Jonquetella anthropi	Bacteria	Synergistetes	Synergistia	Synergistales	Synergistaceae	Jonquetella
Kerstersia gyiorum	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	unclassified
Kingella denitrificans	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Kingella
Kingella genomosp. P1 oral cone MB2_C20	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Kingella
Kingella kingae	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Kingella
Kingella oralis	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Kingella
Kingella sp. oral clone ID059	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Kingella
Klebsiella sp. AS10	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. Co9935	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. enrichment culture clone SRC_DSD25	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. OBRC7	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. SP-BA	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. SRC_DSD1	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. SRC_DSD11	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. SRC_DSD12	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. SRC_DSD15	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. SRC_DSD2	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella sp. SRC_DSD6	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Klebsiella variicola	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Klebsiella
Kluyvera ascorbata	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Kluyvera
Kluyvera cryocrescens	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Kluyvera
Kocuria marina	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Kocuria
Kocuria palustris	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Kocuria
Kocuria rhizophila	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Kocuria
Kocuria rosea	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Kocuria
Kocuria varians	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Kocuria
Lachnobacterium bovis	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Lachnobacterium
Lachnospira multipara	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Lachnospira
Lachnospira pectinoschiza	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Lachnospira
Lachnospiraceae bacterium 1_1_57FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 1_4_56FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 2_1_46FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 2_1_58FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 3_1_57FAA_CT1	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 4_1_37FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 5_1_57FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 5_1_63FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 6_1_63FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 8_1_57FAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium 9_1_43BFAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium A4	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium DJF VP30	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium ICM62	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium MSX33	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium oral taxon 107	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae bacterium oral taxon F15	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lachnospiraceae genomosp. C1	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Lactobacillus acidipiscis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus acidophilus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus alimentarius	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus amylolyticus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus amylovorus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus antri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus brevis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus buchneri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus casei	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus catenaformis	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Eggerthia
Lactobacillus coleohominis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus coryniformis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus crispatus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus curvatus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus delbrueckii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus dextrinicus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus farciminis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus fermentum	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus gasseri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus gastricus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus genomosp. C1	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus genomosp. C2	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus helveticus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus hilgardii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus hominis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus iners	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus jensenii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus johnsonii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus kalixensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus kefiranofaciens	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus kefiri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus kimchii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus leichmannii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus mucosae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus murinus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus nodensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus oeni	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus oris	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus parabrevis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus parabuchneri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus paracasei	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus parakefiri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus pentosus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus perolens	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus plantarum	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus pontis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus reuteri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus rhamnosus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus rogosae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus ruminis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sakei	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus salivarius	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus saniviri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus senioris	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. 66c	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. BT6	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0701	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0702	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0703	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0704	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0705	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0707	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0709	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0711	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0712	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0713	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0716	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0718	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. KLDS 1.0719	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. oral clone HT002	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. oral clone HT070	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus sp. oral taxon 052	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus tucceti	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus ultunensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus vaginalis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus vini	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactobacillus vitulinus	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Kandleria
Lactobacillus zeae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Lactobacillus
Lactococcus garvieae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Lactococcus
Lactococcus lactis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Lactococcus
Lactococcus raffinolactis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Lactococcus
Lactonifactor longoviformis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Lactonifactor
Laribacter hongkongensis	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Laribacter
Lautropia mirabilis	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Lautropia
Lautropia sp. oral clone AP009	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Lautropia
Leminorella grimontii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Leminorella
Leminorella richardii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Leminorella
Leptotrichia buccalis	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia genomosp. C1	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia goodfellowii	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia hofstadii	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia shahii	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia sp. neutropenicPatient	Bacteria	Fusobacteria	Fusobacteria	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia sp. oral clone GT018	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia sp. oral clone GT020	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia sp. oral clone HE012	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia sp. oral clone IK040	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia sp. oral clone P2PB_51 P1	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leptotrichia sp. oral taxon 223	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Leptotrichia
Leuconostoc carnosum	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc
Leuconostoc citreum	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc
Leuconostoc gasicomitatum	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc
Leuconostoc inhae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc
Leuconostoc kimchii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc
Leuconostoc lactis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc
Leuconostoc mesenteroides	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc
Leuconostoc pseudomesenteroides	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Leuconostoc
Listeria innocua	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae	Listeria
Listeria ivanovii	Bacteria	Firmicutes	Bacilli	Bacillales	Listeriaceae	Listeria
Luteococcus sanguinis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Luteococcus
Lutispora thermophila	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Lutispora
Lysinibacillus fusiformis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Lysinibacillus
Lysinibacillus sphaericus	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Lysinibacillus
Macrococcus caseolyticus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Macrococcus
Mannheimia haemolytica	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Mannheimia
Marvinbryantia formatexigens	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	unclassified
Massilia sp. CCUG 43427A	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	Massilia
Megamonas funiformis	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Megamonas
Megamonas hypermegale	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Megamonas
Megasphaera elsdenii	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Megasphaera
Megasphaera genomosp. C1	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Megasphaera
Megasphaera genomosp. type_l	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Megasphaera
Megasphaera micronuciformis	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Megasphaera
Megasphaera sp. BLPYG-07	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Megasphaera
Megasphaera sp. UPII 199-6	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Megasphaera
Metallosphaera sedula	Archaea	Crenarchaeota	Thermoprotei	Sulfolobales	Sulfolobaceae	Metallosphaera
Methanobacterium formicicum	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobacterium
Methanobrevibacter acididurans	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter arboriphilus	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter curvatus	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter cuticularis	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter filiformis	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter gottschalkii	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter millerae	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter olleyae	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter oralis	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter ruminantium	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter smithii	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter thaueri	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter woesei	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanobrevibacter wolinii	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanobrevibacter
Methanosphaera stadtmanae	Archaea	Euryarchaeota	Methanobacteria	Methanobacteriales	Methanobacteriaceae	Methanosphaera
Methylobacterium extorquens	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Methylobacteriaceae	Methylobacterium
Methylobacterium podarium	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Methylobacteriaceae	Methylobacterium
Methylobacterium radiotolerans	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Methylobacteriaceae	Methylobacterium
Methylobacterium sp. 1sub	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Methylobacteriaceae	Methylobacterium
Methylobacterium sp. MM4	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Methylobacteriaceae	Methylobacterium
Methylocella silvestris	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Beijerinckiaceae	Methylocella
Methylophilus sp. ECd5	Bacteria	Proteobacteria	Betaproteobacteria	Methylophilales	Methylophilaceae	Methylophilus
Microbacterium chocolatum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium flavescens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium gubbeenense	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium lacticum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium oleivorans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium oxydans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium paraoxydans	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium phyllosphaerae	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium schleiferi	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium sp. 768	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium sp. oral strain C24KA	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Microbacterium testaceum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Microbacterium
Micrococcus antarcticus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Micrococcus
Micrococcus luteus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Micrococcus
Micrococcus lylae	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Micrococcus
Micrococcus sp. 185	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Micrococcus
Microcystis aeruginosa	Bacteria	Cyanobacteria	unclassified	Chroococcales	unclassified	Microcystis
Mitsuokella jalaludinii	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Mitsuokella
Mitsuokella multacida	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Mitsuokella
Mitsuokella sp. oral taxon 521	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Mitsuokella
Mitsuokella sp. oral taxon G68	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Mitsuokella
Mobiluncus curtisii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Mobiluncus
Mobiluncus mulieris	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Mobiluncus
Moellerella wisconsensis	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Moellerella
Mogibacterium diversum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XIII. Incertae Sedis	Mogibacterium
Mogibacterium neglectum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XIII. Incertae Sedis	Mogibacterium
Mogibacterium pumilum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XIII. Incertae Sedis	Mogibacterium
Mogibacterium timidum	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XIII. Incertae Sedis	Mogibacterium
Mollicutes bacterium pACH93	Bacteria	Tenericutes	Mollicutes	unclassified	unclassified	unclassified
Moorella thermoacetica	Bacteria	Firmicutes	Clostridia	Thermoanaerobacterales	Thermoanaerobacteraceae	Moorella
Moraxella catarrhalis	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Moraxella
Moraxella lincolnii	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Moraxella
Moraxella osloensis	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Moraxella
Moraxella sp. 16285	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Moraxella
Moraxella sp. GM2	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Moraxella
Morganella morganii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Morganella
Morganella sp. JB-T16	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Morganella
Morococcus cerebrosus	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Morococcus
Moryella indoligenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Moryella
Mycobacterium sp. 1761	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. 1776	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. 1781	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. 1791	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. 1797	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. AQ1GA4	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. B10-07.09.0206	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. GN-10546	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. GN-10827	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. GN-11124	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. GN-9188	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. GR-2007-210	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. HE5	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. NLA001000736	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycobacterium sp. W	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Mycobacteriaceae	Mycobacterium
Mycoplasma agalactiae	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma amphoriforme	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma arthritidis	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma bovoculi	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma faucium	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma fermentans	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma flocculare	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma genitalium	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma hominis	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma orale	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma ovipneumoniae	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma penetrans	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma pneumoniae	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma putrefaciens	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasma salivarium	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Mycoplasma
Mycoplasmataceae genomosp. P1 oral clone MB1_G23	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	unclassified
Myroides odoratimimus	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Myroides
Myroides sp. MY15	Bacteria	Bacteroidetes	Flavobacteriia	Flavobacteriales	Flavobacteriaceae	Myroides
Neisseria bacilliformis	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria cinerea	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria elongata	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria flavescens	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria genomosp. P2 oral clone MB5_P15	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria lactamica	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria macacae	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria mucosa	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria pharyngis	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria polysaccharea	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria sicca	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria sp. KEM232	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria sp. oral clone AP132	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria sp. oral clone JC012	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria sp. oral strain B33KA	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria sp. oral taxon 014	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria sp. SMC-A9199	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria sp. TM10_1	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neisseria subflava	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Neisseria
Neorickettsia risticii	Bacteria	Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	Neorickettsia
Neorickettsia sennetsu	Bacteria	Proteobacteria	Alphaproteobacteria	Rickettsiales	Anaplasmataceae	Neorickettsia
Nocardia brasiliensis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Nocardia
Nocardia cyriacigeorgica	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Nocardia
Nocardia farcinica	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Nocardia
Nocardia puris	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Nocardia
Nocardia sp. 01-Je-025	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Nocardia
Nocardiopsis dassonvillei	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiopsaceae	Nocardiopsis
Novosphingobium aromaticivorans	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Novosphingobium
Oceanobacillus caeni	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Oceanobacillus
Oceanobacillus sp. Ndiop	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Oceanobacillus
Ochrobactrum anthropi	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Brucellaceae	Ochrobactrum
Ochrobactrum intermedium	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Brucellaceae	Ochrobactrum
Ochrobactrum pseudintermedium	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Brucellaceae	Ochrobactrum
Odoribacter laneus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Odoribacter
Odoribacter splanchnicus	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Odoribacter
Okadaella gastrococcus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Okadaella
Oligella ureolytica	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Oligella
Oligella urethralis	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Oligella
Olsenella genomosp. C1	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Olsenella
Olsenella profusa	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Olsenella
Olsenella sp. F0004	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Olsenella
Olsenella sp. oral taxon 809	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Olsenella
Olsenella uli	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Olsenella
Opitutus terrae	Bacteria	Verrucomicrobia	Opitutae	Opitutales	Opitutaceae	Opitutus
Oribacterium sinus	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Oribacterium sp. ACB1	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Oribacterium sp. ACB7	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Oribacterium sp. CM12	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Oribacterium sp. ICM51	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Oribacterium sp. OBRC12	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Oribacterium sp. oral taxon 078	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Oribacterium sp. oral taxon 102	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Oribacterium sp. oral taxon 108	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Oribacterium
Ornithinibacillus bavariensis	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Ornithinibacillus
Ornithinibacillus sp. 7-10AIA	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Ornithinibacillus
Oscillibacter sp. G2	Bacteria	Firmicutes	Clostridia	Clostridiales	Oscillospiraceae	Oscillibacter
Oscillibacter valericigenes	Bacteria	Firmicutes	Clostridia	Clostridiales	Oscillospiraceae	Oscillibacter
Oscillospira guilliermondii	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Oscillospira
Oxalobacter formigenes	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Oxalobacteraceae	Oxalobacter
Paenibacillus barcinonensis	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus barengoltzii	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus chibensis	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus cookii	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus durus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus glucanolyticus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus lactis	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus lautus	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus pabuli	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus polymyxa	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus popilliae	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus sp. CIP 101062	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus sp. HGF5	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus sp. HGF7	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus sp. JC66	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus sp. oral taxon F45	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus sp. R-27413	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus sp. R-27422	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Paenibacillus timonensis	Bacteria	Firmicutes	Bacilli	Bacillales	Paenibacillaceae	Paenibacillus
Pantoea agglomerans	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Pantoea
Pantoea ananatis	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Pantoea
Pantoea brenneri	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Pantoea
Pantoea citrea	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Tatumella
Pantoea conspicua	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Pantoea
Pantoea septica	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Pantoea
Papillibacter cinnamivorans	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Papillibacter
Parabacteroides distasonis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides
Parabacteroides goldsteinii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides
Parabacteroides gordonii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides
Parabacteroides johnsonii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides
Parabacteroides merdae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides
Parabacteroides sp. D13	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides
Parabacteroides sp. NS31-3	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Parabacteroides
Parachlamydia sp. UWE25	Bacteria	Chlamydiae	Chlamydiae	Chlamydiales	Parachlamydiaceae	Parachlamydia
Paracoccus denitrificans	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	Paracoccus
Paracoccus marcusii	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	Paracoccus
Paraprevotella clara	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Paraprevotella
Paraprevotella xylaniphila	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Paraprevotella
Parascardovia denticolens	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Parascardovia
Parasutterella excrementihominis	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Parasutterella
Parasutterella secunda	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Parasutterella
Parvimonas micra	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	unclassified
Parvimonas sp. oral taxon 110	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	unclassified
Pasteurella bettyae	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Pasteurella
Pasteurella dagmatis	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Pasteurella
Pasteurella multocida	Bacteria	Proteobacteria	Gammaproteobacteria	Pasteurellales	Pasteurellaceae	Pasteurella
Pediococcus acidilactici	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Pediococcus
Pediococcus pentosaceus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Lactobacillaceae	Pediococcus
Peptococcus niger	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptococcaceae	Peptococcus
Peptococcus sp. oral clone JM048	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptococcaceae	Peptococcus
Peptococcus sp. oral taxon 167	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptococcaceae	Peptococcus
Peptoniphilus asaccharolyticus	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus duerdenii	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus harei	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus indolicus	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus ivorii	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus lacrimalis	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus sp. gpac007	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus sp. gpac018A	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus sp. gpac077	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus sp. gpac148	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus sp. JC140	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus sp. oral taxon 386	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptoniphilus sp. oral taxon 836	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Peptoniphilus
Peptostreptococcaceae bacterium ph1	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	unclassified
Peptostreptococcus anaerobius	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	Peptostreptococcus
Peptostreptococcus micros	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	unclassified
Peptostreptococcus sp. 9succ1	Bacteria	Firmicutes	Clostridia	Clostridiales	Incertae Sedis XI	Peptoniphilus
Peptostreptococcus sp. oral clone AP24	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	Peptostreptococcus
Peptostreptococcus sp. oral clone FJ023	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	Peptostreptococcus
Peptostreptococcus sp. P4P_31 P3	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	Peptostreptococcus
Peptostreptococcus stomatis	Bacteria	Firmicutes	Clostridia	Clostridiales	Peptostreptococcaceae	Peptostreptococcus
Phascolarctobacterium faecium	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Acidaminococcaceae	Phascolarctobacterium
Phascolarctobacterium sp. YIT 12068	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Acidaminococcaceae	Phascolarctobacterium
Phascolarctobacterium succinatutens	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Acidaminococcaceae	Phascolarctobacterium
Phenylobacterium zucineum	Bacteria	Proteobacteria	Alphaproteobacteria	Caulobacterales	Caulobacteraceae	Phenylobacterium
Photorhabdus asymbiotica	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Photorhabdus
Pigmentiphaga daeguensis	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Alcaligenaceae	Pigmentiphaga
Planomicrobium koreense	Bacteria	Firmicutes	Bacilli	Bacillales	Planococcaceae	Planomicrobium
Plesiomonas shigelloides	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Plesiomonas
Porphyromonadaceae bacterium NML 060648	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	unclassified
Porphyromonas asaccharolytica	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas endodontalis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas gingivalis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas levii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas macacae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas somerae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas sp. oral clone BB134	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas sp. oral clone F016	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas sp. oral clone P2PB_52 P1	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas sp. oral clone P4GB_100 P2	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas sp. UQD 301	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Porphyromonas uenonis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Porphyromonas
Prevotella albensis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella amnii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella bergensis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella bivia	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella brevis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella buccae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella buccalis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella copri	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella corporis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella dentalis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella denticola	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella disiens	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella genomosp. C1	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella genomosp. C2	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella genomosp. P7 oral clone MB2_P31	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella genomosp. P8 oral clone MB3_P13	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella genomosp. P9 oral clone MB7_G16	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella heparinolytica	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Bacteroidaceae	Bacteroides
Prevotella histicola	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella intermedia	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella loescheii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella maculosa	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella marshii	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella melaninogenica	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella micans	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella multiformis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella multisaccharivorax	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella nanceiensis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella nigrescens	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella oralis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella oris	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella oulorum	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella pallens	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella ruminicola	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella salivae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. BI-42	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. CM38	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. ICM1	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. ICM55	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. JCM 6330	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone AA020	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone ASCG10	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone ASCG12	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone AU069	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone CY006	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone DA058	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone FL019	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone FU048	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone FW035	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone GI030	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone GI032	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone GI059	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone GU027	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone HF050	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone ID019	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone IDR-CEC-0024	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone IDR-CEC-0032	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone IDR-CEC-0055	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone IK053	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone IK062	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral clone P4PB_83 P2	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon 292	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon 299	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon 300	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon 302	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Alloprevotella
Prevotella sp. oral taxon 310	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon 317	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon 472	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon 781	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon 782	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon F68	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon G60	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon G70	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. oral taxon G71	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. SEQ053	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. SEQ065	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. SEQ072	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. SEQ116	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. SG12	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. sp24	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella sp. sp34	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella stercorea	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella tannerae	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Alloprevotella
Prevotella timonensis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotella veroralis	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	Prevotella
Prevotellaceae bacterium P4P_62 P1	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Prevotellaceae	unclassified
Prochlorococcus marinus	Bacteria	Cyanobacteria	unclassified	Prochlorales	Prochlorococcaceae	Prochlorococcus
Propionibacteriaceae bacterium NML 02-0265	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	unclassified
Propionibacterium acidipropionici	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium acnes	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium avidum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium freudenreichii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium granulosum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium jensenii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium propionicum	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium sp. 434-HC2	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium sp. H456	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium sp. LG	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium sp. oral taxon 192	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium sp. S555a	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Propionibacterium thoenii	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Propionibacterium
Proteus mirabilis	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Proteus
Proteus penneri	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Proteus
Proteus sp. HS7514	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Proteus
Proteus vulgaris	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Proteus
Providencia alcalifaciens	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Providencia
Providencia rettgeri	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Providencia
Providencia rustigianii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Providencia
Providencia stuartii	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Providencia
Pseudoclavibacter sp. Timone	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Pseudoclavibacter
Pseudoflavonifractor capillosus	Bacteria	Firmicutes	Clostridia	Clostridiales	unclassified	Pseudoflavonifractor
Pseudomonas aeruginosa	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas fluorescens	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas gessardii	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas mendocina	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas monteilii	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas poae	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas pseudoalcaligenes	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas putida	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas sp. 2_1_26	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas sp. G1229	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas sp. NP522b	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas stutzeri	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas tolaasii	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudomonas viridiflava	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Pseudomonadaceae	Pseudomonas
Pseudoramibacter alactolyticus	Bacteria	Firmicutes	Clostridia	Clostridiales	Eubacteriaceae	Pseudoramibacter
Psychrobacter arcticus	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Psychrobacter
Psychrobacter cibarius	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Psychrobacter
Psychrobacter cryohalolentis	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Psychrobacter
Psychrobacter faecalis	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Psychrobacter
Psychrobacter nivimaris	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Psychrobacter
Psychrobacter pulmonis	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Psychrobacter
Psychrobacter sp. 13983	Bacteria	Proteobacteria	Gammaproteobacteria	Pseudomonadales	Moraxellaceae	Psychrobacter
Pyramidobacter piscolens	Bacteria	Synergistetes	Synergistia	Synergistales	Synergistaceae	Pyramidobacter
Ralstonia pickettii	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Ralstonia
Ralstonia sp. 5_7_47FAA	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Burkholderiaceae	Ralstonia
Raoultella ornithinolytica	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Raoultella
Raoultella planticola	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Raoultella
Raoultella terrigena	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Raoultella
Rhodobacter sp. oral taxon C30	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	Rhodobacter
Rhodobacter sphaeroides	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodobacterales	Rhodobacteraceae	Rhodobacter
Rhodococcus corynebacterioides	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Rhodococcus
Rhodococcus equi	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Rhodococcus
Rhodococcus erythropolis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Rhodococcus
Rhodococcus fascians	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiaceae	Rhodococcus
Rhodopseudomonas palustris	Bacteria	Proteobacteria	Alphaproteobacteria	Rhizobiales	Bradyrhizobiaceae	Rhodopseudomonas
Robinsoniella peoriensis	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Robinsoniella
Roseburia cecicola	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia
Roseburia faecalis	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia
Roseburia faecis	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia
Roseburia hominis	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia
Roseburia intestinalis	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia
Roseburia inulinivorans	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia
Roseburia sp. 11SE37	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia
Roseburia sp. 11SE38	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Roseburia
Roseiflexus castenholzii	Bacteria	Chloroflexi	Chloroflexi	Chloroflexales	Chloroflexaceae	Roseiflexus
Roseomonas cervicalis	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Roseomonas
Roseomonas mucosa	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Roseomonas
Roseomonas sp. NML94-0193	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Roseomonas
Roseomonas sp. NML97-0121	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Roseomonas
Roseomonas sp. NML98-0009	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Roseomonas
Roseomonas sp. NML98-0157	Bacteria	Proteobacteria	Alphaproteobacteria	Rhodospirillales	Acetobacteraceae	Roseomonas
Rothia aeria	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Rothia
Rothia dentocariosa	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Rothia
Rothia mucilaginosa	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Rothia
Rothia nasimurium	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Rothia
Rothia sp. oral taxon 188	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Micrococcaceae	Rothia
Ruminobacter amylophilus	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Succinivibrionaceae	Ruminobacter
Ruminococcaceae bacterium D16	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	unclassified
Ruminococcus albus	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus bromii	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus callidus	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus champanellensis	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus flavefaciens	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus gnavus	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Ruminococcus hansenii	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Ruminococcus lactaris	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus obeum	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Ruminococcus sp. 18P13	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus sp. 5_1_39BFAA	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus sp. 9SE51	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus sp. ID8	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus sp. K-1	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Ruminococcus
Ruminococcus torques	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Blautia
Saccharomonospora viridis	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Pseudonocardiaceae	Saccharomonospora
Sarcina ventriculi	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiaceae	Sarcina
Scardovia inopinata	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Scardovia
Scardovia wiggsiae	Bacteria	Actinobacteria	Actinobacteria	Bifidobacteriales	Bifidobacteriaceae	Scardovia
Segniliparus rotundus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Segniliparaceae	Segniliparus
Segniliparus rugosus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Segniliparaceae	Segniliparus
Selenomonas artemidis	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas dianae	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas flueggei	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas genomosp. C1	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas genomosp. C2	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas genomosp. P5	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas genomosp. P6 oral clone MB3_C41	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas genomosp. P7 oral clone MB5_C08	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas genomosp. P8 oral clone MB5_P06	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas infelix	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas noxia	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas ruminantium	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. FOBRC9	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone FT050	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone GI064	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone GT010	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone HU051	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone IK004	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone IQ048	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone JI021	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone JS031	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone OH4A	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral clone P2PA_80 P4	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral taxon 137	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sp. oral taxon 149	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Selenomonas sputigena	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Selenomonas
Serratia fonticola	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Serratia
Serratia liquefaciens	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Serratia
Serratia marcescens	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Serratia
Serratia odorifera	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Serratia
Serratia proteamaculans	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Serratia
Shewanella putrefaciens	Bacteria	Proteobacteria	Gammaproteobacteria	Alteromonadales	Shewanellaceae	Shewanella
Shuttleworthia satelles	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Shuttleworthia
Shuttleworthia sp. MSX8B	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Shuttleworthia
Shuttleworthia sp. oral taxon G69	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Shuttleworthia
Simonsiella muelleri	Bacteria	Proteobacteria	Betaproteobacteria	Neisseriales	Neisseriaceae	Simonsiella
Slackia equolifaciens	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Slackia
Slackia exigua	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Slackia
Slackia faecicanis	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Slackia
Slackia heliotrinireducens	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Slackia
Slackia isoflavoniconvertens	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Slackia
Slackia piriformis	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Slackia
Slackia sp. NATTS	Bacteria	Actinobacteria	Actinobacteria	Coriobacteriales	Coriobacteriaceae	Slackia
Solobacterium moorei	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Solobacterium
Sphingobacterium faecium	Bacteria	Bacteroidetes	Sphingobacteriia	Sphingobacteriales	Sphingobacteriaceae	Sphingobacterium
Sphingobacterium mizutaii	Bacteria	Bacteroidetes	Sphingobacteriia	Sphingobacteriales	Sphingobacteriaceae	Sphingobacterium
Sphingobacterium multivorum	Bacteria	Bacteroidetes	Sphingobacteriia	Sphingobacteriales	Sphingobacteriaceae	Sphingobacterium
Sphingobacterium spiritivorum	Bacteria	Bacteroidetes	Sphingobacteriia	Sphingobacteriales	Sphingobacteriaceae	Sphingobacterium
Sphingomonas echinoides	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Sphingomonas
Sphingomonas sp. oral clone FI012	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Sphingomonas
Sphingomonas sp. oral clone FZ016	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Sphingomonas
Sphingomonas sp. oral taxon A09	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Sphingomonas
Sphingomonas sp. oral taxon F71	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Sphingomonas
Sphingopyxis alaskensis	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Sphingopyxis
Spiroplasma insolitum	Bacteria	Tenericutes	Mollicutes	Entomoplasmatales	Spiroplasmataceae	Spiroplasma
Sporobacter termitidis	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Sporobacter
Sporolactobacillus inulinus	Bacteria	Firmicutes	Bacilli	Bacillales	Sporolactobacillaceae	Sporolactobacillus
Sporolactobacillus nakayamae	Bacteria	Firmicutes	Bacilli	Bacillales	Sporolactobacillaceae	Sporolactobacillus
Sporosarcina newyorkensis	Bacteria	Firmicutes	Bacilli	Bacillales	Planococcaceae	Sporosarcina
Sporosarcina sp. 2681	Bacteria	Firmicutes	Bacilli	Bacillales	Planococcaceae	Sporosarcina
Staphylococcaceae bacterium NML 92-0017	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	unclassified
Staphylococcus aureus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus auricularis	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus capitis	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus caprae	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus carnosus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus cohnii	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus condimenti	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus epidermidis	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus equorum	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus fleurettii	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus haemolyticus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus hominis	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus lugdunensis	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus pasteuri	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus pseudintermedius	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus saccharolyticus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus saprophyticus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus sciuri	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus sp. clone bottae7	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus sp. H292	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus sp. H780	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus succinus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus vitulinus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus warneri	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Staphylococcus xylosus	Bacteria	Firmicutes	Bacilli	Bacillales	Staphylococcaceae	Staphylococcus
Stenotrophomonas maltophilia	Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Stenotrophomonas
Stenotrophomonas sp. FG-6	Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Stenotrophomonas
Streptobacillus moniliformis	Bacteria	Fusobacteria	Fusobacteriia	Fusobacteriales	Leptotrichiaceae	Streptobacillus
Streptococcus agalactiae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus alactolyticus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus anginosus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus austrails	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus bovis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus canis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus constellatus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus cristatus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus downei	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus dysgalactiae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus equi	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus equinus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus gallolyticus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus genomosp. C1	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus genomosp. C2	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus genomosp. C3	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus genomosp. C4	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus genomosp. C5	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus genomosp. C6	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus genomosp. C7	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus genomosp. C8	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus gordonii	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus infantarius	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus infantis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus intermedius	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus lutetiensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus massiliensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus milleri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus mitis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus mutans	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus oligofermentans	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus oralis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus parasanguinis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus pasteurianus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus peroris	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus pneumoniae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus porcinus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus pseudopneumoniae	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus pseudoporcinus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus ratti	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus salivarius	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sanguinis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sinensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. 16362	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. 2_1_36FAA	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. 2285-97	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. 69130	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. AC15	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. ACS2	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. AS20	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. BS35a	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. C150	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. CM6	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. CM7	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. ICM10	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. ICM12	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. ICM2	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. ICM4	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. ICM45	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. M143	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. M334	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. OBRC6	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASB02	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCA03	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCA04	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCA09	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCB04	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCB06	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCC04	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCC05	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCC12	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCD01	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCD09	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCD10	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCE03	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCE04	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCE05	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCE06	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCE09	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCE10	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCE12	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCF05	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCF07	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCF09	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone ASCG04	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone BW009	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone CH016	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone GK051	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone GM006	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone P2PA_41 P2	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone P4PA_13 P3	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral clone P4PA_30 P4	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral taxon 071	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral taxon G59	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral taxon G62	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. oral taxon G63	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus sp. SHV515	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus suis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus thermophilus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus uberis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus urinalis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus vestibularis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptococcus viridans	Bacteria	Firmicutes	Bacilli	Lactobacillales	Streptococcaceae	Streptococcus
Streptomyces albus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Streptomycetaceae	Streptomyces
Streptomyces griseus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Streptomycetaceae	Streptomyces
Streptomyces sp. 1 AIP-2009	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Streptomycetaceae	Streptomyces
Streptomyces sp. SD 511	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Streptomycetaceae	Streptomyces
Streptomyces sp. SD 524	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Streptomycetaceae	Streptomyces
Streptomyces sp. SD 528	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Streptomycetaceae	Streptomyces
Streptomyces sp. SD 534	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Streptomycetaceae	Streptomyces
Streptomyces thermoviolaceus	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Streptomycetaceae	Streptomyces
Subdoligranulum variabile	Bacteria	Firmicutes	Clostridia	Clostridiales	Ruminococcaceae	Subdoligranulum
Succinatimonas hippei	Bacteria	Proteobacteria	Gammaproteobacteria	Aeromonadales	Succinivibrionaceae	Succinatimonas
Sutterella morbirenis	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Sutterella
Sutterella parvirubra	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Sutterella
Sutterella sanguinus	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Sutterella
Sutterella sp. YIT 12072	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Sutterella
Sutterella stercoricanis	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Sutterella
Sutterella wadsworthensis	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Sutterellaceae	Sutterella
Synergistes genomosp. C1	Bacteria	Synergistetes	Synergistia	Synergistales	Synergistaceae	Synergistes
Synergistes sp. RMA 14551	Bacteria	Synergistetes	Synergistia	Synergistales	Synergistaceae	Synergistes
Synergistetes bacterium ADV897	Bacteria	Synergistetes	unclassified	unclassified	unclassified	unclassified
Synergistetes bacterium LBVCM1157	Bacteria	Synergistetes	unclassified	unclassified	unclassified	unclassified
Synergistetes bacterium oral clone 03 5 D05	Bacteria	Synergistetes	unclassified	unclassified	unclassified	unclassified
Synergistetes bacterium oral taxon 362	Bacteria	Synergistetes	unclassified	unclassified	unclassified	unclassified
Synergistetes bacterium oral taxon D48	Bacteria	Synergistetes	unclassified	unclassified	unclassified	unclassified
Syntrophococcus sucromutans	Bacteria	Firmicutes	Clostridia	Clostridiales	Lachnospiraceae	Syntrophococcus
Syntrophomonadaceae genomosp. P1	Bacteria	Firmicutes	Clostridia	Clostridiales	Syntrophomonadaceae	unclassified
Tannerella forsythia	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Tannerella
Tannerella sp. 6_1_58FAA_CT1	Bacteria	Bacteroidetes	Bacteroidia	Bacteroidales	Porphyromonadaceae	Tannerella
Tatlockia micdadei	Bacteria	Proteobacteria	Gammaproteobacteria	Legionellales	Legionellaceae	Tatlockia
Tatumella ptyseos	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Tatumella
Tessaracoccus sp. oral taxon F04	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Propionibacteriaceae	Tessaracoccus
Tetragenococcus halophilus	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Tetragenococcus
Tetragenococcus koreensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Tetragenococcus
Thermoanaerobacter pseudethanolicus	Bacteria	Firmicutes	Clostridia	Thermoanaerobacterales	Thermoanaerobacteraceae	Thermoanaerobacter
Thermobifida fusca	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Nocardiopsaceae	Thermobifida
Thermofilum pendens	Archaea	Crenarchaeota	Thermoprotei	Thermoproteales	Thermofilaceae	Thermofilum
Thermus aquaticus	Bacteria	Deinococcus-Thermus	Deinococci	Thermales	Thermaceae	Thermus
Tissierella praeacuta	Bacteria	Firmicutes	Clostridia	Clostridiales	Clostridiales Family XI. Incertae Sedis	Tissierella
Trabulsiella guamensis	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Trabulsiella
Treponema genomosp. P1	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema genomosp. P4 oral clone MB2_G19	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema genomosp. P5 oral clone MB3_P23	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema genomosp. P6 oral clone MB4_G11	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema phagedenis	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. 6:H:D15A-4	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. clone DDKL-4	Bacteria	Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral clone JU025	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral clone JU031	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral clone P2PB_53 P3	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 228	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 230	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 231	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 232	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 235	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 239	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 247	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 250	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 251	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 254	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 265	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 270	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 271	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 508	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon 518	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. oral taxon G85	Bacteria	Spirochaetes	Spirochaetia	Spirochaetales	Spirochaetaceae	Treponema
Treponema sp. ovine footrot	Bacteria	Spirochaetes	Spirochaetes	Spirochaetales	Spirochaetaceae	Treponema
Tropheryma whipplei	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	unclassified	Tropheryma
Trueperella pyogenes	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Actinomycetaceae	Trueperella
Tsukamurella paurometabola	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Tsukamurellaceae	Tsukamurella
Tsukamurella tyrosinosolvens	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Tsukamurellaceae	Tsukamurella
Turicibacter sanguinis	Bacteria	Firmicutes	Erysipelotrichi	Erysipelotrichales	Erysipelotrichaceae	Turicibacter
Ureaplasma parvum	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Ureaplasma
Ureaplasma urealyticum	Bacteria	Tenericutes	Mollicutes	Mycoplasmatales	Mycoplasmataceae	Ureaplasma
Ureibacillus composti	Bacteria	Firmicutes	Bacilli	Bacillales	Planococcaceae	Ureibacillus
Ureibacillus suwonensis	Bacteria	Firmicutes	Bacilli	Bacillales	Planococcaceae	Ureibacillus
Ureibacillus terrenus	Bacteria	Firmicutes	Bacilli	Bacillales	Planococcaceae	Ureibacillus
Ureibacillus thermophilus	Bacteria	Firmicutes	Bacilli	Bacillales	Planococcaceae	Ureibacillus
Ureibacillus thermosphaericus	Bacteria	Firmicutes	Bacilli	Bacillales	Planococcaceae	Ureibacillus
Vagococcus fluvialis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Enterococcaceae	Vagococcus
Veillonella atypica	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella dispar	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella genomosp. P1 oral clone MB5_P17	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella montpellierensis	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella parvula	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. 3_1_44	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. 6_1_27	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. ACP1	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. AS16	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. BS32b	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. ICM51a	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. MSA12	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. NVG 100cf	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. OK11	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. oral clone ASCA08	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. oral clone ASCB03	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. oral clone ASCG01	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. oral clone ASCG02	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. oral clone OH1A	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonella sp. oral taxon 158	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	Veillonella
Veillonellaceae bacterium oral taxon 131	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	unclassified
Veillonellaceae bacterium oral taxon 155	Bacteria	Firmicutes	Negativicutes	Selenomonadales	Veillonellaceae	unclassified
Victivallaceae bacterium NML 080035	Bacteria	Lentisphaerae	unclassified	unclassified	Victivallaceae	unclassified
Victivallis vadensis	Bacteria	Lentisphaerae	unclassified	unclassified	Victivallaceae	Victivallis
Virgibacillus proomii	Bacteria	Firmicutes	Bacilli	Bacillales	Bacillaceae	Virgibacillus
Weissella beninensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Weissella
Weissella cibaria	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Weissella
Weissella confusa	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Weissella
Weissella hellenica	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Weissella
Weissella kandleri	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Weissella
Weissella koreensis	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Weissella
Weissella paramesenteroides	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Weissella
Weissella sp. KLDS 7.0701	Bacteria	Firmicutes	Bacilli	Lactobacillales	Leuconostocaceae	Weissella
Wolinella succinogenes	Bacteria	Proteobacteria	Epsilonproteobacteria	Campylobacterales	Helicobacteraceae	Wolinella
Xanthomonadaceae bacterium NML 03-0222	Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	unclassified
Xanthomonas campestris	Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Xanthomonas
Xanthomonas sp. kmd_489	Bacteria	Proteobacteria	Gammaproteobacteria	Xanthomonadales	Xanthomonadaceae	Xanthomonas
Xenophilus aerolatus	Bacteria	Proteobacteria	Betaproteobacteria	Burkholderiales	Comamonadaceae	Xenophilus
Yokenella regensburgei	Bacteria	Proteobacteria	Gammaproteobacteria	Enterobacteriales	Enterobacteriaceae	Yokenella
Zimmermannella bifida	Bacteria	Actinobacteria	Actinobacteria	Actinomycetales	Microbacteriaceae	Pseudoclavibacter
Zymomonas mobilis	Bacteria	Proteobacteria	Alphaproteobacteria	Sphingomonadales	Sphingomonadaceae	Zymomonas