| enterococcus hirae | 63 | species | bacteria | bacteria | 1354 |
| enterococcus faecium | 116 | species | bacteria | bacteria | 1352 |
| enterococcus faecalis | 132 | species | bacteria | bacteria | 1351 |
| enterobacter cloacae | 90 | species | bacteria | bacteria | 550 |
| entamoeba histolytica | 98 | species | invertebrates | protozoa | 5759 |
| encephalomyocarditis virus | 105 | no rank | viruses | viruses | 12104 |
| encephalitozoon cuniculi | 58 | species | plants | fungi | 6035 |
| echinococcus granulosus | 61 | species | invertebrates | helminths | 6210 |
| cryptosporidium parvum | 92 | species | invertebrates | protozoa | 5807 |
| cryptococcus neoformans | 126 | species | plants | fungi | 5207 |
| coxiella burnetii | 67 | species | bacteria | bacteria | 777 |
| cowpox virus | 71 | species | viruses | viruses | 10243 |
| clostridium perfringens | 101 | species | bacteria | bacteria | 1502 |
| clostridium botulinum | 106 | species | bacteria | bacteria | 1491 |
| clostridioides difficile | 127 | species | bacteria | bacteria | 1496 |
| classical swine fever virus | 84 | species | viruses | viruses | 11096 |
| citrobacter freundii | 70 | species | bacteria | bacteria | 546 |
| chlamydia trachomatis | 129 | species | bacteria | bacteria | 813 |
| chlamydia psittaci | 63 | species | bacteria | bacteria | 83554 |
| chlamydia pneumoniae | 143 | species | bacteria | bacteria | 83558 |
| chlamydia abortus | 63 | species | bacteria | bacteria | 83555 |
| chicken anemia virus | 60 | species | viruses | viruses | 12618 |
| canine parvovirus | 65 | no rank | viruses | viruses | 10788 |
| canine distemper virus | 60 | species | viruses | viruses | 11232 |
| candida tropicalis | 76 | species | plants | fungi | 5482 |
| candida albicans | 181 | species | plants | fungi | 5476 |
| campylobacter jejuni | 130 | species | bacteria | bacteria | 197 |
| campylobacter coli | 65 | species | bacteria | bacteria | 195 |
| burkholderia cepacia | 107 | species | bacteria | bacteria | 292 |
| brucella abortus | 76 | species | bacteria | bacteria | 235 |
| bovine viral diarrhea virus 1 | 80 | species | viruses | viruses | 11099 |
| bovine spongiform encephalopathy agent | 101 | species | | | |
| bovine papillomavirus | 95 | species | viruses | viruses | 10571 |
| bovine leukemia virus | 65 | species | viruses | viruses | 11901 |
| bovine herpesvirus 1 | 70 | species | viruses | viruses | 10320 |
| borreliella burgdorferi | 144 | species | bacteria | bacteria | 139 |
| borna disease virus | 65 | species | viruses | viruses | 12455 |
| bordetella pertussis | 122 | species | bacteria | bacteria | 520 |
| bluetongue virus | 64 | species | viruses | viruses | 40051 |
| bartonella henselae | 77 | species | bacteria | bacteria | 38323 |
| bacteroides fragilis | 97 | species | bacteria | bacteria | 817 |
| bacillus subtilis | 219 | species | bacteria | bacteria | 1423 |
| bacillus licheniformis | 78 | species | bacteria | bacteria | 1402 |
| bacillus cereus | 111 | species | bacteria | bacteria | 1396 |
| bacillus anthracis | 122 | species | bacteria | bacteria | 1392 |
| aspergillus niger | 110 | species | plants | fungi | 5061 |
| ascaris suum | 65 | species | invertebrates | helminths | 6253 |
| anaplasma phagocytophilum | 62 | species | bacteria | bacteria | 948 |
| aggregatibacter actinomycetemcomitans | 101 | species | bacteria | bacteria | 714 |
| aeromonas hydrophila | 89 | species | bacteria | bacteria | 644 |
| actinobacillus pleuropneumoniae | 59 | species | bacteria | bacteria | 715 |
| acinetobacter baumannii | 88 | species | bacteria | bacteria | 470 |
| [enterobacter] aerogenes | 75 | species | bacteria | bacteria | 548 |
| [candida] glabrata | 87 | species | plants | fungi | 5478 |