| bartonella elizabethae | 15 | species | bacteria | bacteria | 807 |
| bartonella bacilliformis | 36 | species | bacteria | bacteria | 774 |
| barmah forest virus | 22 | species | viruses | viruses | 11020 |
| banzi virus | 9 | species | viruses | viruses | 38837 |
| banna virus | 8 | species | viruses | viruses | 77763 |
| bangui virus | 1 | species | | viruses | |
| balamuthia mandrillaris | 27 | species | invertebrates | protozoa | 66527 |
| bagaza virus | 2 | species | viruses | viruses | 64290 |
| bacteroides zoogleoformans | 5 | species | bacteria | bacteria | 28119 |
| bacteroides vulgatus | 38 | species | bacteria | bacteria | 821 |
| bacteroides uniformis | 21 | species | bacteria | bacteria | 820 |
| bacteroides thetaiotaomicron | 47 | species | bacteria | bacteria | 818 |
| bacteroides stercoris | 7 | species | bacteria | bacteria | 46506 |
| bacteroides ovatus | 24 | species | bacteria | bacteria | 28116 |
| bacteroides heparinolyticus | 14 | species | bacteria | bacteria | 28113 |
| bacteroides galacturonicus | 1 | species | bacteria | bacteria | 384639 |
| bacteroides fragilis | 97 | species | bacteria | bacteria | 817 |
| bacteroides eggerthii | 4 | species | bacteria | bacteria | 28111 |
| bacteroides caccae | 9 | species | bacteria | bacteria | 47678 |
| bacillus thuringiensis | 129 | species | bacteria | bacteria | 1428 |
| bacillus subtilis | 219 | species | bacteria | bacteria | 1423 |
| bacillus pumilus | 53 | species | bacteria | bacteria | 1408 |
| bacillus mycoides | 28 | species | bacteria | bacteria | 1405 |
| bacillus licheniformis | 78 | species | bacteria | bacteria | 1402 |
| bacillus coagulans | 40 | species | bacteria | bacteria | 1398 |
| bacillus circulans | 69 | species | bacteria | bacteria | 1397 |
| bacillus cereus | 111 | species | bacteria | bacteria | 1396 |
| bacillus anthracis | 122 | species | bacteria | bacteria | 1392 |
| babesia microti | 53 | species | invertebrates | protozoa | 5868 |
| babesia gibsoni | 29 | species | invertebrates | protozoa | 33632 |
| babesia divergens | 31 | species | invertebrates | protozoa | 32595 |
| babesia bovis | 46 | species | invertebrates | protozoa | 5865 |
| auxenochlorella protothecoides | 34 | species | plants | | 3075 |
| austrobilharzia terrigalensis | 11 | species | invertebrates | helminths | 216969 |
| australian bat lyssavirus | 15 | species | viruses | viruses | 90961 |
| aureobasidium pullulans | 46 | species | plants | fungi | 5580 |
| aspergillus wentii | 21 | species | plants | fungi | 5066 |
| aspergillus versicolor | 33 | species | plants | fungi | 46472 |
| aspergillus terreus group | -3 | species | | fungi | |
| aspergillus oryzae | 67 | species | plants | fungi | 5062 |
| aspergillus niger | 110 | species | plants | fungi | 5061 |
| aspergillus nidulans group | 10 | species | | fungi | |
| aspergillus fumigatus group | 4 | species | | fungi | |
| aspergillus flavus group | 19 | species | | fungi | |
| aspergillus flavipes | 13 | species | plants | fungi | 41900 |
| aspergillus fisherianus | -3 | species | | fungi | |
| aspergillus clavatus | 21 | species | plants | fungi | 5057 |
| aspergillus candidus | 20 | species | plants | fungi | 41067 |
| ascocotyle | 13 | genus | invertebrates | helminths | |
| ascaris suum | 65 | species | invertebrates | helminths | 6253 |
| ascaris lumbricoides | 69 | species | invertebrates | helminths | 6252 |
| artyfechinostomum mehrai | 2 | species | | helminths | |
| arthroderma uncinatum | 9 | species | plants | fungi | 74035 |
| arthroderma simii | 5 | species | plants | fungi | 63406 |
| arthroderma racemosum | 3 | species | plants | fungi | 231010 |
| arthroderma otae | 39 | species | plants | fungi | 63405 |
| arthroderma obtusum | 8 | species | plants | fungi | 119676 |
| arthroderma fulvum | 4 | species | plants | fungi | 63401 |
| arthroderma cajetani | 8 | species | plants | fungi | 81846 |
| arthrinium phaeospermum | 5 | species | plants | fungi | 112178 |
| arcobacter cryaerophilus | 26 | species | bacteria | bacteria | 28198 |
| arcobacter butzleri | 37 | species | bacteria | bacteria | 28197 |
| arcanobacterium haemolyticum | 22 | species | bacteria | bacteria | 28264 |
| arachnomyces nodosetosus | 12 | species | plants | fungi | 130043 |
| apophysomyces elegans | 24 | species | plants | fungi | 90269 |
| apoi virus | 2 | species | viruses | viruses | 64280 |
| aphanoascus fulvescens | 8 | species | plants | fungi | 73174 |
| anisakis simplex | 37 | species | invertebrates | helminths | 6269 |
| anisakis physeteris | 9 | species | invertebrates | helminths | 290545 |
| angiostrongylus costaricensis | 14 | species | invertebrates | helminths | 334426 |
| angiostrongylus cantonensis | 35 | species | invertebrates | helminths | 6313 |
| ancylostoma malayanum | 1 | species | | helminths | |
| ancylostoma duodenale | 25 | species | invertebrates | helminths | 51022 |
| ancylostoma ceylanicum | 20 | species | invertebrates | helminths | 53326 |
| ancylostoma caninum | 48 | species | invertebrates | helminths | 29170 |
| ancylostoma braziliense | 12 | species | invertebrates | helminths | 369059 |
| anatrichosoma cutaneum | 1 | species | | helminths | |
| anaplasma phagocytophilum | 62 | species | bacteria | bacteria | 948 |
| anaerococcus vaginalis | 4 | species | bacteria | bacteria | 33037 |
| anaerococcus prevotii | 17 | species | bacteria | bacteria | 33034 |
| anaerococcus lactolyticus | 5 | species | bacteria | bacteria | 33032 |
| amycolatopsis orientalis | 31 | species | bacteria | bacteria | 31958 |
| amphimerus pseudofelineus | 3 | species | | helminths | |
| alternaria tenuissima | 12 | species | plants | fungi | 119927 |
| alternaria stemphyloides | -3 | species | | fungi | |
| alternaria longipes | 10 | species | plants | fungi | 160389 |
| alternaria infectoria | 12 | species | plants | fungi | 45303 |
| alternaria dianthicola | 1 | species | plants | fungi | 160388 |
| alternaria chlamydospora | 5 | species | | fungi | 1187911 |
| alternaria chartarum | 5 | species | plants | fungi | 119957 |
| alternaria caespitosa | 1 | species | plants | fungi | 1342384 |
| alternaria alternata | 56 | species | plants | fungi | 5599 |
| alloprevotella tannerae | 7 | species | bacteria | bacteria | 76122 |
| alcaligenes faecalis subsp. faecalis | 8 | subspecies | bacteria | bacteria | 32001 |
| alaria marcianae | 9 | species | | helminths | 1684801 |
| alaria americana | 2 | species | | helminths | |
| aggregatibacter segnis | 9 | species | bacteria | bacteria | 739 |
| aggregatibacter aphrophilus | 19 | species | bacteria | bacteria | 732 |
| aggregatibacter actinomycetemcomitans | 101 | species | bacteria | bacteria | 714 |
| aeromonas veronii | 25 | species | bacteria | bacteria | 654 |