| brevibacillus brevis | 57 | species | bacteria | bacteria | 1393 |
| brevundimonas diminuta | 54 | species | bacteria | bacteria | 293 |
| brevundimonas vesicularis | 15 | species | bacteria | bacteria | 41276 |
| brucella melitensis | 52 | species | bacteria | bacteria | 29459 |
| brugia beaveri | 2 | species | | helminths | |
| brugia guyanensis | 2 | species | | helminths | |
| brugia malayi | 68 | species | invertebrates | helminths | 6279 |
| brugia pahangi | 53 | species | invertebrates | helminths | 6280 |
| brugia timori | 10 | species | invertebrates | helminths | 42155 |
| buffalopox virus | 7 | no rank | viruses | viruses | 32605 |
| bunostomum phlebotomum | 10 | species | invertebrates | helminths | 577651 |
| bunyamwera virus | 31 | species | viruses | viruses | 35304 |
| burkholderia cepacia | 107 | species | bacteria | bacteria | 292 |
| burkholderia mallei | 27 | species | bacteria | bacteria | 13373 |
| burkholderia pseudomallei | 61 | species | bacteria | bacteria | 28450 |
| bussuquara virus | 2 | no rank | viruses | viruses | 64304 |
| bwamba virus | 3 | species | viruses | viruses | 35310 |
| california encephalitis virus | 28 | no rank | viruses | viruses | 35305 |
| calodium hepaticum | 4 | species | | helminths | |
| campylobacter coli | 65 | species | bacteria | bacteria | 195 |
| campylobacter concisus | 20 | species | bacteria | bacteria | 199 |
| campylobacter curvus | 11 | species | bacteria | bacteria | 200 |
| campylobacter fetus | 57 | species | bacteria | bacteria | 196 |
| campylobacter gracilis | 28 | species | bacteria | bacteria | 824 |
| campylobacter hyointestinalis | 23 | species | bacteria | bacteria | 198 |
| campylobacter jejuni | 130 | species | bacteria | bacteria | 197 |
| campylobacter lari | 35 | species | bacteria | bacteria | 201 |
| campylobacter rectus | 41 | species | bacteria | bacteria | 203 |
| campylobacter sputorum | 22 | species | bacteria | bacteria | 206 |
| campylobacter upsaliensis | 26 | species | bacteria | bacteria | 28080 |
| campylobacter ureolyticus | 26 | species | bacteria | bacteria | 827 |
| candida albicans | 181 | species | plants | fungi | 5476 |
| candida catenulata | 13 | species | plants | fungi | 45537 |
| candida magnoliae | 18 | species | plants | fungi | 5490 |
| candida parapsilosis | 68 | species | plants | fungi | 5480 |
| candida rugosa | 67 | species | plants | fungi | 5481 |
| candida tropicalis | 76 | species | plants | fungi | 5482 |
| candida viswanathii | 7 | species | plants | fungi | 5486 |
| candiru virus complex | -3 | no rank | | viruses | |
| capillaria plica | 8 | species | | helminths | 1239593 |
| capnocytophaga canimorsus | 18 | species | bacteria | bacteria | 28188 |
| capnocytophaga cynodegmi | 4 | species | bacteria | bacteria | 28189 |
| capnocytophaga gingivalis | 16 | species | bacteria | bacteria | 1017 |
| capnocytophaga ochracea | 25 | species | bacteria | bacteria | 1018 |
| capnocytophaga sputigena | 17 | species | bacteria | bacteria | 1019 |
| caraparu virus | 3 | species | viruses | viruses | 192196 |
| cardiobacterium hominis | 16 | species | bacteria | bacteria | 2718 |
| carneocephallus brevicaea | -1 | species | | helminths | |
| cathaemasia cabrerai | -3 | species | | helminths | |
| catu virus | 1 | species | | viruses | 1678225 |
| cedecea davisae | 3 | species | bacteria | bacteria | 158484 |
| cedecea lapagei | 2 | species | bacteria | bacteria | 158823 |
| cedecea neteri | 2 | species | bacteria | bacteria | 158822 |
| cellulosimicrobium cellulans | 19 | species | bacteria | bacteria | 1710 |
| centipeda periodontii | 7 | species | bacteria | bacteria | 82203 |
| centrocestus armatus | 3 | species | | helminths | |
| centrocestus formosanus | 13 | species | invertebrates | helminths | 234883 |
| cephaliophora irregularis | 2 | species | plants | fungi | 77528 |
| chaetomium atrobrunneum | 5 | species | plants | fungi | 460864 |
| chaetomium funicola | 5 | species | plants | fungi | 79816 |
| chaetomium globosum | 30 | species | plants | fungi | 38033 |
| chaetomium perpulchrum | 1 | species | | fungi | |
| chaetomium strumarium | 1 | species | | fungi | 1170767 |
| chaetophoma dermo-unguis | -3 | species | | fungi | |
| chandipura virus | 10 | species | viruses | viruses | 11272 |
| changuinola virus | -3 | species | | viruses | 40052 |
| cheilospirura | 5 | genus | | | |
| chikungunya virus | 39 | species | viruses | viruses | 37124 |
| chlamydia pneumoniae | 143 | species | bacteria | bacteria | 83558 |
| chlamydia psittaci | 63 | species | bacteria | bacteria | 83554 |
| chlamydia trachomatis | 129 | species | bacteria | bacteria | 813 |
| chlamydoabsidia padenii | -3 | species | plants | fungi | 90267 |
| chromobacterium violaceum | 53 | species | bacteria | bacteria | 536 |
| chryseobacterium balustinum | 10 | species | bacteria | bacteria | 246 |
| citrobacter amalonaticus | 12 | species | bacteria | bacteria | 35703 |
| citrobacter braakii | 10 | species | bacteria | bacteria | 57706 |
| citrobacter farmeri | 4 | species | bacteria | bacteria | 67824 |
| citrobacter freundii | 70 | species | bacteria | bacteria | 546 |
| citrobacter koseri | 31 | species | bacteria | bacteria | 545 |
| citrobacter rodentium | 45 | species | bacteria | bacteria | 67825 |
| citrobacter sedlakii | 6 | species | bacteria | bacteria | 67826 |
| citrobacter werkmanii | 4 | species | bacteria | bacteria | 67827 |
| citrobacter youngae | 5 | species | bacteria | bacteria | 133448 |
| cladophialophora arxii | 2 | species | plants | fungi | 82108 |
| cladophialophora bantiana | 21 | species | plants | fungi | 89940 |
| cladophialophora boppii | 2 | species | plants | fungi | 82106 |
| cladophialophora carrionii | 15 | species | plants | fungi | 86049 |
| cladophialophora devriesii | 1 | species | plants | fungi | 82107 |
| cladorrhinum bulbillosum | 1 | species | plants | fungi | 585595 |
| cladosporium cladosporioides | 29 | species | plants | fungi | 29917 |
| cladosporium oxysporum | 8 | species | plants | fungi | 29919 |
| cladosporium sphaerospermum | 18 | species | plants | fungi | 92950 |
| clavispora lusitaniae | 40 | species | plants | fungi | 36911 |
| clinostomum complanatum | 6 | species | invertebrates | helminths | 235145 |
| clostridioides difficile | 127 | species | bacteria | bacteria | 1496 |
| clostridium baratii | 16 | species | bacteria | bacteria | 1561 |
| clostridium botulinum | 106 | species | bacteria | bacteria | 1491 |
| clostridium butyricum | 53 | species | bacteria | bacteria | 1492 |
| clostridium chauvoei | 15 | species | bacteria | bacteria | 46867 |
| clostridium fallax | 5 | species | bacteria | bacteria | 1533 |