| [clostridium] clostridioforme | 18 | species | bacteria | bacteria | 1531 |
| [clostridium] innocuum | 13 | species | bacteria | bacteria | 1522 |
| aegyptianella moshkovskii | -3 | species | | bacteria | |
| aelurostrongylus falciformis | 1 | species | | helminths | |
| aelurostrongylus pridhami | 2 | species | | helminths | |
| agriostomum cursoni | -3 | species | | helminths | |
| agriostomum equidentatum | -3 | species | | helminths | |
| agriostomum gungunis | -3 | species | | helminths | |
| aichivirus a | 19 | species | viruses | viruses | 72149 |
| alloiococcus otitis | 15 | species | bacteria | bacteria | 1652 |
| amidostomum | 6 | genus | invertebrates | | 108464 |
| amidostomum acutum | 3 | species | | helminths | |
| amidostomum cygni | 1 | species | invertebrates | helminths | 108465 |
| amidostomum simile | -3 | species | | helminths | |
| amidostomum skrjabini | 1 | species | | helminths | |
| anaerobiospirillum succiniproducens | -3 | species | | bacteria | |
| anaticola crassicornis | 1 | species | invertebrates | | 160206 |
| angiostrongylus dujardini | 2 | species | invertebrates | helminths | 274538 |
| angiostrongylus gubernaculatus | 2 | species | | helminths | |
| angiostrongylus michiganensis | 2 | species | | helminths | |
| angiostrongylus ondatrae | -3 | species | | helminths | |
| angiostrongylus schmidti | 2 | species | | helminths | |
| aphanoascus terreus | 3 | species | plants | fungi | 121129 |
| arcanobacterium pluranimalium | 2 | species | bacteria | bacteria | 108028 |
| arcobacter trophiarum | 1 | species | bacteria | bacteria | 708186 |
| argas reflexus | 11 | species | invertebrates | tick | 34604 |
| ascaris | 90 | genus | invertebrates | | 6251 |
| ascarops strongylina | 7 | species | | helminths | |
| aureimonas altamirensis | 4 | species | bacteria | bacteria | 370622 |
| babesia argentina | 21 | species | | protozoa | |
| babesia berbera | 1 | species | | protozoa | |
| babesia muratovi | 1 | species | invertebrates | protozoa | 196496 |
| babesia pitheci | -3 | species | | protozoa | |
| babesia rodhaini | 16 | species | invertebrates | protozoa | 5870 |
| bacillus mojavensis | 13 | species | bacteria | bacteria | 72360 |
| bartonella capreoli | 2 | species | bacteria | bacteria | 155192 |
| besnoitia darlingi | 7 | species | invertebrates | protozoa | 190281 |
| besnoitia tarandi | 3 | species | invertebrates | protozoa | 279368 |
| besnoitia wallacei | 3 | species | | protozoa | |
| bhalfilaria ladamii | -3 | species | | helminths | |
| bicaulus | -3 | genus | | | |
| bicaulus sagittatus | -3 | species | | helminths | |
| bordetella holmesii | 14 | species | bacteria | bacteria | 35814 |
| bordetella trematum | 3 | species | bacteria | bacteria | 123899 |
| borrelia anserina | 10 | species | bacteria | bacteria | 143 |
| borrelia theileri | 5 | species | bacteria | bacteria | 43082 |
| botrytis | 90 | genus | plants | | 33196 |
| bourgelatia diducta | 1 | species | | helminths | |
| bovicola painei | -3 | species | | | |
| brachyspira aalborgi | 19 | species | bacteria | bacteria | 29522 |
| brachyspira canis | 3 | species | bacteria | bacteria | 235984 |
| brachyspira muridarum | -3 | species | bacteria | bacteria | 797079 |
| brachyspira muris | -3 | species | bacteria | bacteria | 797080 |
| brachyspira rattus | -3 | species | bacteria | bacteria | 797076 |
| brucella canis | 26 | species | bacteria | bacteria | 36855 |
| brucella neotomae | 7 | species | bacteria | bacteria | 29460 |
| brugia ceylonensis | 2 | species | | helminths | |
| brugia patei | 5 | species | invertebrates | helminths | 42154 |
| brugia tupaiae | 2 | species | | helminths | |
| calyptrozyma arxii | 1 | species | plants | fungi | 89418 |
| campylobacter insulaenigrae | 3 | species | bacteria | bacteria | 260714 |
| campylobacter lanienae | 6 | species | bacteria | bacteria | 75658 |
| candidatus neoehrlichia mikurensis | 6 | species | bacteria | bacteria | 89586 |
| canine minute virus | 13 | species | viruses | viruses | 329639 |
| capillaria annulosa | -3 | species | | helminths | |
| capillaria bacielata | -3 | species | | helminths | |
| capillaria cantenata | -3 | species | | helminths | |
| capillaria catostomi | 2 | species | | helminths | |
| capillaria didelphis | 2 | species | | helminths | |
| capillaria eupomotis | -3 | species | | helminths | |
| capillaria gastrica | 1 | species | invertebrates | helminths | 119096 |
| capillaria intestinalis | -3 | species | | helminths | |
| capillaria lewaschoffi | -3 | species | | helminths | |
| capillaria papillosa | -3 | species | | helminths | |
| capillaria petrushewskii | -3 | species | | helminths | |
| capillaria prashadi | -3 | species | | helminths | |
| capillaria tavernae | -3 | species | | helminths | |
| capillaria tomentosa | 1 | species | | helminths | |
| capillaria tuberculata | -3 | species | | helminths | |
| centrocestus kurkawai | -3 | species | | helminths | |
| centrocestus longus | -3 | species | | helminths | |
| cephalopsis titillator | -3 | species | | fly | |
| cephenemyia apicata | 2 | species | | fly | |
| cephenemyia auribarbis | 2 | species | | fly | 1888233 |
| cephenemyia pratti | -3 | species | | fly | |
| cephenemyia stimulator | 2 | species | invertebrates | fly | 170895 |
| cephenemyia trompe | 10 | species | invertebrates | fly | 204915 |
| cephenemyia ulrichii | 1 | species | invertebrates | fly | 204916 |
| chelopistes meleagridis | 2 | species | | | |
| chicken astrovirus 1 | -3 | no rank | viruses | viruses | 544802 |
| chicken astrovirus 2 | -3 | species | viruses | viruses | 544801 |
| chicken enteric coronavirus | -3 | species | viruses | viruses | 229103 |
| chilodonella hexasticha | 6 | species | | protozoa | 1938391 |
| chlamydia suis | 13 | species | bacteria | bacteria | 83559 |
| choniangium epistomum | -3 | species | | helminths | |
| choniangium magnostomum | -3 | species | | helminths | |
| chrysops discalis | 1 | species | | fly | |
| cobboldia elephantis | 1 | species | | fly | |
| cobboldia loxodontis | -3 | species | | fly | |
| cochlosoma anatis | 8 | species | invertebrates | protozoa | 227314 |