| lactobacillus gasseri | 37 | species | bacteria | bacteria | 1596 |
| lactobacillus paracasei | 44 | species | bacteria | bacteria | 1597 |
| lactobacillus fermentum | 47 | species | bacteria | bacteria | 1613 |
| lactobacillus salivarius | 36 | species | bacteria | bacteria | 1624 |
| lactobacillus oris | 7 | species | bacteria | bacteria | 1632 |
| listeria innocua | 58 | species | bacteria | bacteria | 1642 |
| bifidobacterium bifidum | 53 | species | bacteria | bacteria | 1681 |
| bifidobacterium breve | 39 | species | bacteria | bacteria | 1685 |
| bifidobacterium catenulatum | 14 | species | bacteria | bacteria | 1686 |
| mycobacterium cookii | 4 | species | bacteria | bacteria | 1775 |
| mycobacterium flavescens | 12 | species | bacteria | bacteria | 1776 |
| mycobacterium terrae | 20 | species | bacteria | bacteria | 1788 |
| nocardiopsis dassonvillei | 11 | species | bacteria | bacteria | 2014 |
| rothia dentocariosa | 19 | species | bacteria | bacteria | 2047 |
| acholeplasma laidlawii | 67 | species | bacteria | bacteria | 2148 |
| bifidobacterium animalis | 32 | species | bacteria | bacteria | 28025 |
| staphylococcus capitis | 20 | species | bacteria | bacteria | 29388 |
| bifidobacterium thermophilum | 12 | species | bacteria | bacteria | 33905 |
| leuconostoc citreum | 21 | species | bacteria | bacteria | 33964 |
| paracoccus aminovorans | 1 | species | bacteria | bacteria | 34004 |
| cellvibrio mixtus | 13 | species | bacteria | bacteria | 39650 |
| mycobacterium austroafricanum | 16 | species | bacteria | bacteria | 39687 |
| borreliella andersonii | 8 | species | bacteria | bacteria | 42109 |
| rothia mucilaginosa | 19 | species | bacteria | bacteria | 43675 |
| corynebacterium amycolatum | 18 | species | bacteria | bacteria | 43765 |
| mycobacterium tilburgii | 1 | species | bacteria | bacteria | 44467 |
| lactobacillus rhamnosus | 71 | species | bacteria | bacteria | 47715 |
| lactobacillus crispatus | 27 | species | bacteria | bacteria | 47770 |
| pseudomonas synxantha | 8 | species | bacteria | bacteria | 47883 |
| mycoplasma haemomuris | 10 | species | bacteria | bacteria | 55966 |
| actinotignum schaalii | 8 | species | bacteria | bacteria | 59505 |
| mycoplasma wenyonii | 8 | species | bacteria | bacteria | 65123 |
| pseudomonas monteilii | 7 | species | bacteria | bacteria | 76759 |
| mycobacterium elephantis | 2 | species | bacteria | bacteria | 81858 |
| brachyspira murdochii | 8 | species | bacteria | bacteria | 84378 |
| mycobacterium monacense | 3 | species | bacteria | bacteria | 85693 |
| bacillus flexus | 5 | species | bacteria | bacteria | 86664 |
| burkholderia multivorans | 21 | species | bacteria | bacteria | 87883 |
| burkholderia stabilis | 13 | species | bacteria | bacteria | 95485 |
| burkholderia cenocepacia | 30 | species | bacteria | bacteria | 95486 |
| lactobacillus mucosae | 9 | species | bacteria | bacteria | 97478 |
| anaerostipes caccae | 5 | species | bacteria | bacteria | 105841 |
| lactobacillus jensenii | 14 | species | bacteria | bacteria | 109790 |
| aeromonas veronii bv. sobria | 14 | no rank | bacteria | bacteria | 114517 |
| paraburkholderia fungorum | 11 | species | bacteria | bacteria | 134537 |
| nocardia cyriacigeorgica | 9 | species | bacteria | bacteria | 135487 |
| bacillus endophyticus | 2 | species | bacteria | bacteria | 135735 |
| weissella cibaria | 12 | species | bacteria | bacteria | 137591 |
| anaplasma ovis | 14 | species | bacteria | bacteria | 142058 |
| paracoccus yeei | 4 | species | bacteria | bacteria | 147645 |
| lactobacillus iners | 10 | species | bacteria | bacteria | 147802 |
| burkholderia dolosa | 7 | species | bacteria | bacteria | 152500 |
| sphingomonas melonis | 5 | species | bacteria | bacteria | 152682 |
| cupriavidus taiwanensis | 16 | species | bacteria | bacteria | 164546 |
| mycoplasma ovis | 10 | species | bacteria | bacteria | 171632 |
| varibaculum cambriense | 2 | species | bacteria | bacteria | 184870 |
| pseudobutyrivibrio xylanivorans | 4 | species | bacteria | bacteria | 185007 |
| butyrivibrio hungatei | 6 | species | bacteria | bacteria | 185008 |
| bacillus aquimaris | 4 | species | bacteria | bacteria | 189382 |
| microbacterium paraoxydans | 3 | species | bacteria | bacteria | 199592 |
| enterobacter kobei | 4 | species | bacteria | bacteria | 208224 |
| candidatus mycoplasma haemominutum | 19 | species | bacteria | bacteria | 209446 |
| bifidobacterium longum | 58 | species | bacteria | bacteria | 216816 |
| paenibacillus pasadenensis | 1 | species | bacteria | bacteria | 217090 |
| pseudomonas meridiana | 1 | species | bacteria | bacteria | 219573 |
| mycoplasma coccoides | 14 | species | bacteria | bacteria | 220926 |
| psychrobacter pulmonis | 1 | species | bacteria | bacteria | 228654 |
| brevibacterium sanguinis | 1 | species | bacteria | bacteria | 232444 |
| mycobacterium parascrofulaceum | 3 | species | bacteria | bacteria | 240125 |
| actinomadura meyerae | 1 | species | bacteria | bacteria | 240840 |
| mycobacterium sherrisii | 3 | species | bacteria | bacteria | 243061 |
| bacillus fordii | 2 | species | bacteria | bacteria | 254759 |
| yersinia aleksiciae | 1 | species | bacteria | bacteria | 263819 |
| cellulosimicrobium funkei | 3 | species | bacteria | bacteria | 264251 |
| staphylococcus pseudintermedius | 14 | species | bacteria | bacteria | 283734 |
| enterobacter ludwigii | 3 | species | bacteria | bacteria | 299767 |
| janibacter anophelis | 2 | species | bacteria | bacteria | 319054 |
| sphingomonas rhizogenes | -3 | species | bacteria | bacteria | 327691 |
| mycobacterium colombiense | 4 | species | bacteria | bacteria | 339268 |
| mycobacterium arupense | 4 | species | bacteria | bacteria | 342002 |
| candidatus mycoplasma turicensis | 10 | species | bacteria | bacteria | 346879 |
| bacillus thioparans | 1 | species | bacteria | bacteria | 370439 |
| bacteroides xylanisolvens | 2 | species | bacteria | bacteria | 371601 |
| mycobacterium seoulense | 1 | species | bacteria | bacteria | 386911 |
| mycobacterium senuense | 1 | species | bacteria | bacteria | 386913 |
| streptococcus merionis | 1 | species | bacteria | bacteria | 400065 |
| paraburkholderia rhizoxinica | 4 | species | bacteria | bacteria | 412963 |
| asaia lannensis | 2 | species | bacteria | bacteria | 415421 |
| paraburkholderia endofungorum | 1 | species | bacteria | bacteria | 417203 |
| prevotella amnii | 1 | species | bacteria | bacteria | 419005 |
| mycobacterium insubricum | 1 | species | bacteria | bacteria | 444597 |
| mycobacterium conceptionense | 2 | species | bacteria | bacteria | 451644 |
| mycobacterium noviomagense | 1 | species | bacteria | bacteria | 459858 |
| pantoea eucrina | 1 | species | bacteria | bacteria | 472693 |
| pantoea brenneri | 1 | species | bacteria | bacteria | 472694 |
| pantoea septica | 1 | species | bacteria | bacteria | 472695 |
| pantoea conspicua | 1 | species | bacteria | bacteria | 472705 |
| candidatus mycoplasma haemovis | -3 | species | bacteria | bacteria | 488178 |
| staphylococcus rostri | 1 | species | bacteria | bacteria | 522262 |
| enterococcus faecium e1071 | -3 | no rank | bacteria | bacteria | 535205 |