| chandipura virus | 10 | species | viruses | viruses | 11272 |
| chaetophoma dermo-unguis | -3 | species | | fungi | |
| chaetomium strumarium | 1 | species | | fungi | 1170767 |
| chaetomium perpulchrum | 1 | species | | fungi | |
| chaetomium globosum | 30 | species | plants | fungi | 38033 |
| chaetomium funicola | 5 | species | plants | fungi | 79816 |
| chaetomium atrobrunneum | 5 | species | plants | fungi | 460864 |
| cephaliophora irregularis | 2 | species | plants | fungi | 77528 |
| centrocestus formosanus | 13 | species | invertebrates | helminths | 234883 |
| centrocestus armatus | 3 | species | | helminths | |
| centipeda periodontii | 7 | species | bacteria | bacteria | 82203 |
| cellulosimicrobium cellulans | 19 | species | bacteria | bacteria | 1710 |
| cedecea neteri | 2 | species | bacteria | bacteria | 158822 |
| cedecea lapagei | 2 | species | bacteria | bacteria | 158823 |
| cedecea davisae | 3 | species | bacteria | bacteria | 158484 |
| catu virus | 1 | species | | viruses | 1678225 |
| cathaemasia cabrerai | -3 | species | | helminths | |
| carneocephallus brevicaea | -1 | species | | helminths | |
| cardiobacterium hominis | 16 | species | bacteria | bacteria | 2718 |
| caraparu virus | 3 | species | viruses | viruses | 192196 |
| capnocytophaga sputigena | 17 | species | bacteria | bacteria | 1019 |
| capnocytophaga ochracea | 25 | species | bacteria | bacteria | 1018 |
| capnocytophaga gingivalis | 16 | species | bacteria | bacteria | 1017 |
| capnocytophaga cynodegmi | 4 | species | bacteria | bacteria | 28189 |
| capnocytophaga canimorsus | 18 | species | bacteria | bacteria | 28188 |
| capillaria plica | 8 | species | | helminths | 1239593 |
| candiru virus complex | -3 | no rank | | viruses | |
| candida viswanathii | 7 | species | plants | fungi | 5486 |
| candida tropicalis | 76 | species | plants | fungi | 5482 |
| candida rugosa | 67 | species | plants | fungi | 5481 |
| candida parapsilosis | 68 | species | plants | fungi | 5480 |
| candida magnoliae | 18 | species | plants | fungi | 5490 |
| candida catenulata | 13 | species | plants | fungi | 45537 |
| candida albicans | 181 | species | plants | fungi | 5476 |
| campylobacter ureolyticus | 26 | species | bacteria | bacteria | 827 |
| campylobacter upsaliensis | 26 | species | bacteria | bacteria | 28080 |
| campylobacter sputorum | 22 | species | bacteria | bacteria | 206 |
| campylobacter rectus | 41 | species | bacteria | bacteria | 203 |
| campylobacter lari | 35 | species | bacteria | bacteria | 201 |
| campylobacter jejuni | 130 | species | bacteria | bacteria | 197 |
| campylobacter hyointestinalis | 23 | species | bacteria | bacteria | 198 |
| campylobacter gracilis | 28 | species | bacteria | bacteria | 824 |
| campylobacter fetus | 57 | species | bacteria | bacteria | 196 |
| campylobacter curvus | 11 | species | bacteria | bacteria | 200 |
| campylobacter concisus | 20 | species | bacteria | bacteria | 199 |
| campylobacter coli | 65 | species | bacteria | bacteria | 195 |
| calodium hepaticum | 4 | species | | helminths | |
| california encephalitis virus | 28 | no rank | viruses | viruses | 35305 |
| bwamba virus | 3 | species | viruses | viruses | 35310 |
| bussuquara virus | 2 | no rank | viruses | viruses | 64304 |
| burkholderia pseudomallei | 61 | species | bacteria | bacteria | 28450 |
| burkholderia mallei | 27 | species | bacteria | bacteria | 13373 |
| burkholderia cepacia | 107 | species | bacteria | bacteria | 292 |
| bunyamwera virus | 31 | species | viruses | viruses | 35304 |
| bunostomum phlebotomum | 10 | species | invertebrates | helminths | 577651 |
| buffalopox virus | 7 | no rank | viruses | viruses | 32605 |
| brugia timori | 10 | species | invertebrates | helminths | 42155 |
| brugia pahangi | 53 | species | invertebrates | helminths | 6280 |
| brugia malayi | 68 | species | invertebrates | helminths | 6279 |
| brugia guyanensis | 2 | species | | helminths | |
| brugia beaveri | 2 | species | | helminths | |
| brucella melitensis | 52 | species | bacteria | bacteria | 29459 |
| brevundimonas vesicularis | 15 | species | bacteria | bacteria | 41276 |
| brevundimonas diminuta | 54 | species | bacteria | bacteria | 293 |
| brevibacillus brevis | 57 | species | bacteria | bacteria | 1393 |
| bovine spongiform encephalopathy agent | 101 | species | | | |
| bovine papular stomatitis virus | 10 | species | viruses | viruses | 129727 |
| bovine ephemeral fever virus | 14 | species | viruses | viruses | 11303 |
| borreliella burgdorferi | 144 | species | bacteria | bacteria | 139 |
| borrelia turicatae | 21 | species | bacteria | bacteria | 142 |
| borrelia recurrentis | 21 | species | bacteria | bacteria | 44449 |
| borrelia persica | 5 | species | bacteria | bacteria | 44448 |
| borrelia parkeri | 13 | species | bacteria | bacteria | 141 |
| borrelia hispanica | 4 | species | bacteria | bacteria | 40835 |
| borrelia hermsii | 44 | species | bacteria | bacteria | 140 |
| borrelia duttonii | 13 | species | bacteria | bacteria | 40834 |
| borrelia crocidurae | 13 | species | bacteria | bacteria | 29520 |
| borna disease virus | 65 | species | viruses | viruses | 12455 |
| bordetella pertussis | 122 | species | bacteria | bacteria | 520 |
| bordetella parapertussis | 37 | species | bacteria | bacteria | 519 |
| bordetella bronchiseptica | 55 | species | bacteria | bacteria | 518 |
| bordetella avium | 21 | species | bacteria | bacteria | 521 |
| bolbosoma | 8 | genus | | | 1155702 |
| blautia producta | 23 | species | bacteria | bacteria | 33035 |
| blastomyces dermatitidis | 50 | species | plants | fungi | 5039 |
| blastocystis hominis | 41 | species | plants | | 12968 |
| bilophila wadsworthia | 21 | species | bacteria | bacteria | 35833 |
| bilharziella polonica | 6 | species | invertebrates | helminths | 100590 |
| bifidobacterium dentium | 13 | species | bacteria | bacteria | 1689 |
| biatriospora mackinnonii | 1 | species | plants | fungi | 1489893 |
| bhanja virus | 9 | species | | viruses | 1213620 |
| bertiella studeri | 4 | species | invertebrates | helminths | 578852 |
| bertiella mucronata | 1 | species | | helminths | |
| bergeyella zoohelcum | 13 | species | bacteria | bacteria | 1015 |
| bebaru virus | 1 | species | viruses | viruses | 59305 |
| baylisascaris procyonis | 22 | species | invertebrates | helminths | 6259 |
| batken virus | 2 | no rank | viruses | viruses | 53017 |
| basidiobolus ranarum | 18 | species | plants | fungi | 34480 |
| bartonella quintana | 54 | species | bacteria | bacteria | 803 |
| bartonella henselae | 77 | species | bacteria | bacteria | 38323 |