| clostridium botulinum | 106 | species | bacteria | bacteria | 1491 |
| clostridium perfringens | 101 | species | bacteria | bacteria | 1502 |
| clostridium septicum | 31 | species | bacteria | bacteria | 1504 |
| clostridium tetani | 26 | species | bacteria | bacteria | 1513 |
| coccidioides immitis | 54 | species | plants | fungi | 5501 |
| coccidioides posadasii | 14 | species | plants | fungi | 199306 |
| colorado tick fever virus | 17 | species | viruses | viruses | 46839 |
| corynebacterium amycolatum | 18 | species | bacteria | bacteria | 43765 |
| corynebacterium diphtheriae | 64 | species | bacteria | bacteria | 1717 |
| corynebacterium jeikeium | 22 | species | bacteria | bacteria | 38289 |
| corynebacterium xerosis | 21 | species | bacteria | bacteria | 1725 |
| cowpox virus | 71 | species | viruses | viruses | 10243 |
| coxiella burnetii | 67 | species | bacteria | bacteria | 777 |
| coxsackievirus a24 | 14 | no rank | viruses | viruses | 12089 |
| coxsackievirus a7 | 4 | no rank | viruses | viruses | 42787 |
| coxsackievirus a9 | 36 | no rank | viruses | viruses | 12067 |
| cryptosporidium hominis | 27 | species | invertebrates | protozoa | 237895 |
| cryptosporidium parvum | 92 | species | invertebrates | protozoa | 5807 |
| cyclospora cayetanensis | 30 | species | invertebrates | protozoa | 88456 |
| cystoisospora belli | 32 | species | invertebrates | protozoa | 482538 |
| dengue virus 1 | 29 | no rank | viruses | viruses | 11053 |
| dengue virus 2 | 61 | no rank | viruses | viruses | 11060 |
| dengue virus 3 | 26 | no rank | viruses | viruses | 11069 |
| dengue virus 4 | 27 | no rank | viruses | viruses | 11070 |
| dobrava-belgrade virus | 23 | species | viruses | viruses | 12506 |
| dolphin poxvirus 1 | -1 | no rank | viruses | viruses | 256962 |
| eastern equine encephalitis virus | 29 | species | viruses | viruses | 11021 |
| echinococcus granulosus | 61 | species | invertebrates | helminths | 6210 |
| ectromelia virus | 47 | species | viruses | viruses | 12643 |
| edwardsiella tarda | 37 | species | bacteria | bacteria | 636 |
| ehrlichia canis | 50 | species | bacteria | bacteria | 944 |
| ehrlichia chaffeensis | 56 | species | bacteria | bacteria | 945 |
| ehrlichia ewingii | 22 | species | bacteria | bacteria | 947 |
| ehrlichia ruminantium | 43 | species | bacteria | bacteria | 779 |
| eikenella corrodens | 47 | species | bacteria | bacteria | 539 |
| elephantpox virus | -1 | no rank | viruses | viruses | 160797 |
| elizabethkingia meningoseptica | 44 | species | bacteria | bacteria | 238 |
| encephalitozoon cuniculi | 58 | species | plants | fungi | 6035 |
| encephalitozoon hellem | 43 | species | plants | fungi | 27973 |
| encephalitozoon intestinalis | 43 | species | plants | fungi | 58839 |
| entamoeba histolytica | 98 | species | invertebrates | protozoa | 5759 |
| enterobacter cloacae | 90 | species | bacteria | bacteria | 550 |
| enterococcus casseliflavus ec30 | -1 | no rank | bacteria | bacteria | 565652 |
| enterococcus faecalis | 132 | species | bacteria | bacteria | 1351 |
| enterococcus faecium | 116 | species | bacteria | bacteria | 1352 |
| enterocytozoon bieneusi | 54 | species | plants | fungi | 31281 |
| enterovirus a | 12 | species | viruses | viruses | 138948 |
| enterovirus a71 | 47 | no rank | viruses | viruses | 39054 |
| enterovirus b | 16 | species | viruses | viruses | 138949 |
| enterovirus c | 118 | species | viruses | viruses | 138950 |
| enterovirus d | 5 | species | viruses | viruses | 138951 |
| enterovirus d70 | 24 | no rank | viruses | viruses | 12090 |
| epizootic haematopoietic necrosis virus | 19 | species | viruses | viruses | 100217 |
| erysipelothrix rhusiopathiae | 28 | species | bacteria | bacteria | 1648 |
| escherichia coli | 524 | species | bacteria | bacteria | 562 |
| euphorbia pseudograntii | 6 | species | plants | | 212327 |
| filobasidiella neoformans | 25 | species | | | |
| flexal mammarenavirus | -1 | species | viruses | viruses | 45220 |
| foot-and-mouth disease virus | 89 | species | viruses | viruses | 12110 |
| francisella tularensis | 74 | species | bacteria | bacteria | 263 |
| fusarium graminearum | 56 | species | plants | fungi | 5518 |
| fusarium oxysporum | 93 | species | plants | fungi | 5507 |
| fusarium solani | 73 | species | plants | fungi | 169388 |
| fusobacterium necrophorum | 40 | species | bacteria | bacteria | 859 |
| gb virus c | 69 | species | viruses | viruses | 54290 |
| giardia intestinalis | 53 | species | invertebrates | protozoa | 5741 |
| goatpox virus | 4 | species | viruses | viruses | 186805 |
| guanarito mammarenavirus | 15 | species | viruses | viruses | 45219 |
| gymnodinium catenatum | 41 | species | plants | protozoa | 39447 |
| haemophilus aegyptius | 17 | species | bacteria | bacteria | 197575 |
| haemophilus influenzae | 148 | species | bacteria | bacteria | 727 |
| haemophilus parahaemolyticus | 24 | species | bacteria | bacteria | 735 |
| haemophilus parainfluenzae | 30 | species | bacteria | bacteria | 729 |
| hantaan virus | 61 | species | viruses | viruses | 11599 |
| hendra virus | 43 | species | viruses | viruses | 63330 |
| hepatitis b virus | 246 | species | viruses | viruses | 10407 |
| hepatitis c virus | 289 | species | viruses | viruses | 11103 |
| histoplasma capsulatum | 72 | species | plants | fungi | 5037 |
| histoplasma capsulatum var. duboisii | 13 | varietas | plants | | 149546 |
| hu39694 virus | -3 | no rank | viruses | viruses | 69244 |
| human coronavirus 229e | 39 | species | viruses | viruses | 11137 |
| human coronavirus oc43 | 29 | no rank | viruses | viruses | 31631 |
| human hepatitis a virus | 64 | no rank | viruses | viruses | 208726 |
| human herpesvirus 1 | 171 | species | viruses | viruses | 10298 |
| human herpesvirus 2 | 96 | species | viruses | viruses | 10310 |
| human herpesvirus 3 | 113 | species | viruses | viruses | 10335 |
| human herpesvirus 4 | 257 | species | viruses | viruses | 10376 |
| human herpesvirus 5 | 159 | species | viruses | viruses | 10359 |
| human herpesvirus 6 | 94 | species | viruses | viruses | 10368 |
| human herpesvirus 7 | 48 | species | viruses | viruses | 10372 |
| human immunodeficiency virus 1 | 410 | species | viruses | viruses | 11676 |
| human immunodeficiency virus 2 | 399 | species | viruses | viruses | 11709 |
| human mastadenovirus a | 1 | species | viruses | viruses | 129875 |
| human mastadenovirus b | 3 | species | viruses | viruses | 108098 |
| human mastadenovirus c | 5 | species | viruses | viruses | 129951 |
| human mastadenovirus d | 5 | species | viruses | viruses | 130310 |
| human mastadenovirus e | 2 | species | viruses | viruses | 130308 |
| human mastadenovirus f | 1 | species | viruses | viruses | 130309 |
| human metapneumovirus | 63 | species | viruses | viruses | 162145 |
| human papillomavirus | 235 | species | viruses | viruses | 10566 |