| enterovirus b | 16 | species | viruses | viruses | 138949 |
| enterovirus a71 | 47 | no rank | viruses | viruses | 39054 |
| enterovirus a | 12 | species | viruses | viruses | 138948 |
| enterocytozoon bieneusi | 54 | species | plants | fungi | 31281 |
| enterococcus faecium | 116 | species | bacteria | bacteria | 1352 |
| enterococcus faecalis | 132 | species | bacteria | bacteria | 1351 |
| enterococcus casseliflavus ec30 | -1 | no rank | bacteria | bacteria | 565652 |
| enterobacter cloacae | 90 | species | bacteria | bacteria | 550 |
| entamoeba histolytica | 98 | species | invertebrates | protozoa | 5759 |
| encephalitozoon intestinalis | 43 | species | plants | fungi | 58839 |
| encephalitozoon hellem | 43 | species | plants | fungi | 27973 |
| encephalitozoon cuniculi | 58 | species | plants | fungi | 6035 |
| elizabethkingia meningoseptica | 44 | species | bacteria | bacteria | 238 |
| elephantpox virus | -1 | no rank | viruses | viruses | 160797 |
| eikenella corrodens | 47 | species | bacteria | bacteria | 539 |
| ehrlichia ruminantium | 43 | species | bacteria | bacteria | 779 |
| ehrlichia ewingii | 22 | species | bacteria | bacteria | 947 |
| ehrlichia chaffeensis | 56 | species | bacteria | bacteria | 945 |
| ehrlichia canis | 50 | species | bacteria | bacteria | 944 |
| edwardsiella tarda | 37 | species | bacteria | bacteria | 636 |
| ectromelia virus | 47 | species | viruses | viruses | 12643 |
| echinococcus granulosus | 61 | species | invertebrates | helminths | 6210 |
| eastern equine encephalitis virus | 29 | species | viruses | viruses | 11021 |
| dolphin poxvirus 1 | -1 | no rank | viruses | viruses | 256962 |
| dobrava-belgrade virus | 23 | species | viruses | viruses | 12506 |
| dengue virus 4 | 27 | no rank | viruses | viruses | 11070 |
| dengue virus 3 | 26 | no rank | viruses | viruses | 11069 |
| dengue virus 2 | 61 | no rank | viruses | viruses | 11060 |
| dengue virus 1 | 29 | no rank | viruses | viruses | 11053 |
| cystoisospora belli | 32 | species | invertebrates | protozoa | 482538 |
| cyclospora cayetanensis | 30 | species | invertebrates | protozoa | 88456 |
| cryptosporidium parvum | 92 | species | invertebrates | protozoa | 5807 |
| cryptosporidium hominis | 27 | species | invertebrates | protozoa | 237895 |
| coxsackievirus a9 | 36 | no rank | viruses | viruses | 12067 |
| coxsackievirus a7 | 4 | no rank | viruses | viruses | 42787 |
| coxsackievirus a24 | 14 | no rank | viruses | viruses | 12089 |
| coxiella burnetii | 67 | species | bacteria | bacteria | 777 |
| cowpox virus | 71 | species | viruses | viruses | 10243 |
| corynebacterium xerosis | 21 | species | bacteria | bacteria | 1725 |
| corynebacterium jeikeium | 22 | species | bacteria | bacteria | 38289 |
| corynebacterium diphtheriae | 64 | species | bacteria | bacteria | 1717 |
| corynebacterium amycolatum | 18 | species | bacteria | bacteria | 43765 |
| colorado tick fever virus | 17 | species | viruses | viruses | 46839 |
| coccidioides posadasii | 14 | species | plants | fungi | 199306 |
| coccidioides immitis | 54 | species | plants | fungi | 5501 |
| clostridium tetani | 26 | species | bacteria | bacteria | 1513 |
| clostridium septicum | 31 | species | bacteria | bacteria | 1504 |
| clostridium perfringens | 101 | species | bacteria | bacteria | 1502 |
| clostridium botulinum | 106 | species | bacteria | bacteria | 1491 |
| clostridioides difficile | 127 | species | bacteria | bacteria | 1496 |
| claviceps sorghi | 5 | species | plants | fungi | 96774 |
| clavibacter michiganensis subsp. sepedonicus | 25 | subspecies | bacteria | bacteria | 31964 |
| 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 |
| chinese wheat mosaic virus | 4 | species | viruses | viruses | 83544 |
| chikungunya virus | 39 | species | viruses | viruses | 37124 |
| castelo dos sonhos virus | 1 | no rank | viruses | viruses | 139033 |
| capnocytophaga canimorsus | 18 | species | bacteria | bacteria | 28188 |
| cantagalo virus | 5 | no rank | viruses | viruses | 124313 |
| candidatus liberibacter asiaticus | 17 | species | bacteria | bacteria | 34021 |
| candidatus liberibacter africanus | 9 | species | bacteria | bacteria | 34020 |
| candida albicans | 181 | species | plants | fungi | 5476 |
| camelpox virus | 21 | species | viruses | viruses | 28873 |
| california encephalitis virus | 28 | no rank | viruses | viruses | 35305 |
| cacao swollen shoot virus | 10 | species | viruses | viruses | 31559 |
| burkholderia pseudomallei | 61 | species | bacteria | bacteria | 28450 |
| burkholderia mallei | 27 | species | bacteria | bacteria | 13373 |
| burkholderia cepacia | 107 | species | bacteria | bacteria | 292 |
| buffalopox virus | 7 | no rank | viruses | viruses | 32605 |
| brucella suis | 38 | species | bacteria | bacteria | 29461 |
| brucella melitensis | 52 | species | bacteria | bacteria | 29459 |
| brucella canis | 26 | species | bacteria | bacteria | 36855 |
| brucella abortus | 76 | species | bacteria | bacteria | 235 |
| borreliella burgdorferi | 144 | species | bacteria | bacteria | 139 |
| borrelia turicatae | 21 | species | bacteria | bacteria | 142 |
| borrelia recurrentis | 21 | species | bacteria | bacteria | 44449 |
| borrelia hermsii | 44 | species | bacteria | bacteria | 140 |
| borna disease virus | 65 | species | viruses | viruses | 12455 |
| bordetella pertussis | 122 | species | bacteria | bacteria | 520 |
| bluetongue virus | 64 | species | viruses | viruses | 40051 |
| blastomyces dermatitidis | 50 | species | plants | fungi | 5039 |
| blastocystis hominis | 41 | species | plants | | 12968 |
| bermejo virus | 1 | no rank | viruses | viruses | 69243 |
| bean 58058 virus | 2 | no rank | viruses | viruses | 67082 |
| baylisascaris transfuga | 5 | species | invertebrates | helminths | 6260 |
| baylisascaris procyonis | 22 | species | invertebrates | helminths | 6259 |
| bartonella quintana | 54 | species | bacteria | bacteria | 803 |
| bartonella henselae | 77 | species | bacteria | bacteria | 38323 |
| bartonella bacilliformis | 36 | species | bacteria | bacteria | 774 |
| barley yellow mosaic virus | 25 | species | viruses | viruses | 12465 |
| barley yellow dwarf virus | 47 | species | viruses | viruses | 12037 |
| barley stripe mosaic virus | 32 | species | viruses | viruses | 12327 |
| barley mild mosaic virus | 19 | species | viruses | viruses | 12466 |
| banna virus | 8 | species | viruses | viruses | 77763 |
| balamuthia mandrillaris | 27 | species | invertebrates | protozoa | 66527 |
| bacteroides thetaiotaomicron | 47 | species | bacteria | bacteria | 818 |
| bacteroides fragilis | 97 | species | bacteria | bacteria | 817 |