| [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 |
| [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 |
| [pasteurella] aerogenes | 8 | species | bacteria | bacteria | 749 |
| [pasteurella] pneumotropica | 19 | species | bacteria | bacteria | 758 |
| abiotrophia defectiva | 17 | species | bacteria | bacteria | 46125 |
| 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 rauschi | -3 | species | | helminths | |
| achillurbainia nouveli | -3 | species | | helminths | |
| achillurbainia recondita | -3 | species | | helminths | |
| achromobacter piechaudii | 11 | species | bacteria | bacteria | 72556 |
| achromobacter xylosoxidans | 45 | species | bacteria | bacteria | 85698 |
| acidaminococcus fermentans | 30 | species | bacteria | bacteria | 905 |
| acinetobacter baumannii | 88 | species | bacteria | bacteria | 470 |
| 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 |
| 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 suis | 19 | species | bacteria | bacteria | 716 |
| actinobacillus ureae | 12 | species | bacteria | bacteria | 723 |
| actinomadura madurae | 15 | species | bacteria | bacteria | 1993 |
| actinomadura pelletieri | 8 | species | bacteria | bacteria | 111805 |
| 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 |
| adenocephalus pacificus | 5 | species | invertebrates | helminths | 372152 |
| aerococcus viridans | 28 | species | bacteria | bacteria | 1377 |
| aeromonas caviae | 42 | species | bacteria | bacteria | 648 |
| aeromonas hydrophila | 89 | species | bacteria | bacteria | 644 |
| aeromonas sobria | 34 | species | bacteria | bacteria | 646 |
| aeromonas veronii | 25 | species | bacteria | bacteria | 654 |
| aggregatibacter actinomycetemcomitans | 101 | species | bacteria | bacteria | 714 |
| aggregatibacter aphrophilus | 19 | species | bacteria | bacteria | 732 |
| aggregatibacter segnis | 9 | species | bacteria | bacteria | 739 |
| alaria americana | 2 | species | | helminths | |
| alaria marcianae | 9 | species | | helminths | 1684801 |
| alcaligenes faecalis subsp. faecalis | 8 | subspecies | bacteria | bacteria | 32001 |
| alloprevotella tannerae | 7 | species | bacteria | bacteria | 76122 |
| alternaria alternata | 56 | species | plants | fungi | 5599 |
| alternaria caespitosa | 1 | species | plants | fungi | 1342384 |
| alternaria chartarum | 5 | species | plants | fungi | 119957 |
| alternaria chlamydospora | 5 | species | | fungi | 1187911 |
| alternaria dianthicola | 1 | species | plants | fungi | 160388 |
| alternaria infectoria | 12 | species | plants | fungi | 45303 |
| alternaria longipes | 10 | species | plants | fungi | 160389 |
| alternaria stemphyloides | -3 | species | | fungi | |
| alternaria tenuissima | 12 | species | plants | fungi | 119927 |
| amphimerus pseudofelineus | 3 | species | | helminths | |
| amycolatopsis orientalis | 31 | species | bacteria | bacteria | 31958 |
| anaerococcus lactolyticus | 5 | species | bacteria | bacteria | 33032 |
| anaerococcus prevotii | 17 | species | bacteria | bacteria | 33034 |
| anaerococcus vaginalis | 4 | species | bacteria | bacteria | 33037 |
| anaplasma phagocytophilum | 62 | species | bacteria | bacteria | 948 |
| anatrichosoma cutaneum | 1 | species | | helminths | |
| ancylostoma braziliense | 12 | species | invertebrates | helminths | 369059 |
| ancylostoma caninum | 48 | species | invertebrates | helminths | 29170 |
| ancylostoma ceylanicum | 20 | species | invertebrates | helminths | 53326 |
| ancylostoma duodenale | 25 | species | invertebrates | helminths | 51022 |
| ancylostoma malayanum | 1 | species | | helminths | |
| angiostrongylus cantonensis | 35 | species | invertebrates | helminths | 6313 |
| angiostrongylus costaricensis | 14 | species | invertebrates | helminths | 334426 |
| anisakis physeteris | 9 | species | invertebrates | helminths | 290545 |
| anisakis simplex | 37 | species | invertebrates | helminths | 6269 |
| aphanoascus fulvescens | 8 | species | plants | fungi | 73174 |
| apoi virus | 2 | species | viruses | viruses | 64280 |