| [actinobacillus] rossii | 5 | species | bacteria | bacteria | 123820 |
| [bacteroides] pectinophilus | 1 | species | bacteria | bacteria | 384638 |
| [candida] glabrata | 87 | species | plants | fungi | 5478 |
| [candida] haemulonis | 9 | species | plants | fungi | 45357 |
| [candida] intermedia | 14 | species | plants | fungi | 45354 |
| [candida] zeylanoides | 17 | species | plants | fungi | 5493 |
| [clostridium] colinum | 4 | species | bacteria | bacteria | 36835 |
| [clostridium] piliforme | 15 | species | bacteria | bacteria | 1524 |
| [enterobacter] aerogenes | 75 | species | bacteria | bacteria | 548 |
| [eubacterium] brachy | 9 | species | bacteria | bacteria | 35517 |
| [eubacterium] combesii | 2 | species | bacteria | bacteria | 39481 |
| [eubacterium] contortum | 2 | species | bacteria | bacteria | 39482 |
| [eubacterium] nodatum | 17 | species | bacteria | bacteria | 35518 |
| [eubacterium] rectale | 27 | species | bacteria | bacteria | 39491 |
| [eubacterium] saphenum | 8 | species | bacteria | bacteria | 51123 |
| [eubacterium] sulci | 5 | species | bacteria | bacteria | 143393 |
| [eubacterium] tenue | 5 | species | bacteria | bacteria | 1737 |
| [haemophilus] ducreyi | 57 | species | bacteria | bacteria | 730 |
| [haemophilus] parasuis | 29 | species | bacteria | bacteria | 738 |
| [pasteurella] aerogenes | 8 | species | bacteria | bacteria | 749 |
| [pasteurella] mairii | 2 | species | bacteria | bacteria | 757 |
| [pasteurella] pneumotropica | 19 | species | bacteria | bacteria | 758 |
| abiotrophia | 21 | genus | bacteria | | 46123 |
| abiotrophia defectiva | 17 | species | bacteria | bacteria | 46125 |
| abiotrophia para-adiacens | 2 | species | bacteria | bacteria | 191553 |
| acanthamoeba astronyxis | 6 | species | invertebrates | protozoa | 65658 |
| acanthamoeba castellanii | 78 | species | invertebrates | protozoa | 5755 |
| acanthamoeba culbertsoni | 15 | species | invertebrates | protozoa | 43142 |
| acanthamoeba hatchetti | 5 | species | invertebrates | protozoa | 65660 |
| acanthamoeba palestinensis | 9 | species | invertebrates | protozoa | 28015 |
| acanthamoeba polyphaga | 40 | species | invertebrates | protozoa | 5757 |
| acanthamoeba rhysodes | 5 | species | invertebrates | protozoa | 32599 |
| acanthocephalus | 27 | genus | invertebrates | | 185725 |
| acanthocephalus jacksoni | 5 | species | | helminths | |
| acanthocephalus rauschi | -3 | species | | helminths | |
| acanthopleuribacter | 1 | genus | bacteria | | 442869 |
| acarapis woodi | 25 | species | invertebrates | | 478375 |
| acaricomes | 3 | genus | bacteria | | 291967 |
| acetivibrio | 19 | genus | bacteria | | 35829 |
| acetonema | 4 | genus | bacteria | | 2373 |
| achillurbainia nouveli | -3 | species | | helminths | |
| achillurbainia recondita | -3 | species | | helminths | |
| acholeplasma | 62 | genus | bacteria | | 2147 |
| achromobacter | 65 | genus | bacteria | | 222 |
| achromobacter piechaudii | 11 | species | bacteria | bacteria | 72556 |
| achromobacter xylosoxidans | 45 | species | bacteria | bacteria | 85698 |
| acidaminococcus | 30 | genus | bacteria | | 904 |
| acidaminococcus fermentans | 30 | species | bacteria | bacteria | 905 |
| acidobacterium | 42 | genus | bacteria | | 33973 |
| acidovorax | 31 | genus | bacteria | | 12916 |
| acinetobacter | 122 | genus | bacteria | | 469 |
| acinetobacter baumannii | 88 | species | bacteria | bacteria | 470 |
| acinetobacter baumannii a118 | 1 | no rank | bacteria | bacteria | 927193 |
| acinetobacter calcoaceticus | 77 | species | bacteria | bacteria | 471 |
| acinetobacter haemolyticus | 15 | species | bacteria | bacteria | 29430 |
| acinetobacter johnsonii | 26 | species | bacteria | bacteria | 40214 |
| acinetobacter junii | 20 | species | bacteria | bacteria | 40215 |
| acinetobacter lwoffii | 27 | species | bacteria | bacteria | 28090 |
| acinetobacter radioresistens | 23 | species | bacteria | bacteria | 40216 |
| acremonium curvulum | 2 | species | plants | fungi | 687987 |
| acremonium potronii | 1 | species | plants | fungi | 281365 |
| acremonium recifei | 4 | species | | fungi | |
| acremonium roseogriseum | -3 | species | | fungi | |
| acrophialophora fusispora | 7 | species | plants | fungi | 391091 |
| actinoalloteichus | 5 | genus | bacteria | | 65496 |
| actinobacillus | 107 | genus | bacteria | | 713 |
| actinobacillus arthritidis | 4 | species | bacteria | bacteria | 157339 |
| actinobacillus capsulatus | 3 | species | bacteria | bacteria | 717 |
| actinobacillus equuli | 15 | species | bacteria | bacteria | 718 |
| actinobacillus hominis | 4 | species | bacteria | bacteria | 719 |
| actinobacillus lignieresii | 15 | species | bacteria | bacteria | 720 |
| actinobacillus pleuropneumoniae | 59 | species | bacteria | bacteria | 715 |
| actinobacillus porcitonsillarum | 4 | species | bacteria | bacteria | 189834 |
| actinobacillus seminis | 16 | species | bacteria | bacteria | 722 |
| actinobacillus suis | 19 | species | bacteria | bacteria | 716 |
| actinobacillus ureae | 12 | species | bacteria | bacteria | 723 |
| actinobaculum | 9 | genus | bacteria | | 76833 |
| actinobaculum suis | 11 | species | bacteria | bacteria | 1657 |
| actinomadura | 34 | genus | bacteria | | 1988 |
| actinomadura madurae | 15 | species | bacteria | bacteria | 1993 |
| actinomadura pelletieri | 8 | species | bacteria | bacteria | 111805 |
| actinomyces | 78 | genus | bacteria | | 1654 |
| actinomyces actinoides | -3 | species | | bacteria | |
| actinomyces bovis | 13 | species | bacteria | bacteria | 1658 |
| actinomyces georgiae | 5 | species | bacteria | bacteria | 52768 |
| actinomyces gerencseriae | 12 | species | bacteria | bacteria | 52769 |
| actinomyces israelii | 25 | species | bacteria | bacteria | 1659 |
| actinomyces meyeri | 12 | species | bacteria | bacteria | 52773 |
| actinomyces naeslundii | 49 | species | bacteria | bacteria | 1655 |
| actinomyces neuii | 8 | species | bacteria | bacteria | 33007 |
| actinomyces odontolyticus | 23 | species | bacteria | bacteria | 1660 |
| actinomyces radingae | 5 | species | bacteria | bacteria | 131110 |
| actinomyces turicensis | 8 | species | bacteria | bacteria | 131111 |
| actinoplanes | 40 | genus | bacteria | | 1865 |
| actiomadura | -3 | genus | | | |
| adenocephalus pacificus | 5 | species | invertebrates | helminths | 372152 |
| adenoviridae | 18 | family | viruses | | 10508 |
| aegyptianella | 8 | genus | bacteria | | 203861 |
| aegyptianella pullorum | 6 | species | bacteria | bacteria | 203862 |
| aerococcus | 31 | genus | bacteria | | 1375 |