| candidatus endoriftia | 1 | genus | bacteria | | 393764 |
| candidatus endoecteinascidia | 2 | genus | bacteria | | 330062 |
| candidatus endobugula | 24 | genus | bacteria | | 62100 |
| candidatus desulforudis | 1 | genus | bacteria | | 471826 |
| candidatus contubernalis | 8 | genus | bacteria | | 338648 |
| candidatus competibacter | 14 | genus | bacteria | | 221279 |
| candidatus cloacimonas | 1 | genus | bacteria | | 456826 |
| candidatus clavichlamydia | 2 | genus | bacteria | | 469811 |
| candidatus chlorothrix | 5 | genus | bacteria | | 257502 |
| candidatus catenimonas | -3 | genus | bacteria | | 356787 |
| candidatus carsonella | 10 | genus | bacteria | | 114185 |
| candidatus cardinium | 14 | genus | bacteria | | 273135 |
| candidatus brocadia | 20 | genus | bacteria | | 380240 |
| candidatus blochmannia | 20 | genus | bacteria | | 203804 |
| candidatus bacilloplasma | 2 | genus | bacteria | | 467747 |
| candidatus azobacteroides | -3 | genus | bacteria | | 511434 |
| candidatus aquirestis | 1 | genus | bacteria | | 526862 |
| candidatus aquiluna | 1 | genus | bacteria | | 529881 |
| candidatus anammoxoglobus | 3 | genus | bacteria | | 363278 |
| candidatus amoebophilus | 4 | genus | bacteria | | 281119 |
| candidatus amoebinatus | 1 | genus | bacteria | | 216387 |
| candidatus alysiosphaera | 2 | genus | bacteria | | 356778 |
| candidatus accumulibacter | 22 | genus | bacteria | | 327159 |
| candida galli | 3 | species | plants | fungi | 197054 |
| candida dubliniensis | 43 | species | plants | fungi | 42374 |
| campanulotes bidentatus compar | 5 | subspecies | invertebrates | | 135595 |
| caminicella | 3 | genus | bacteria | | 166484 |
| caminibacter | 6 | genus | bacteria | | 191301 |
| camelostrongylus mentulatus | 7 | species | invertebrates | helminths | 53334 |
| calothrix | 39 | genus | bacteria | | 1186 |
| caloranaerobacter | 4 | genus | bacteria | | 171003 |
| caloramator | 11 | genus | bacteria | | 44258 |
| calhevirus 1 | 12 | species | viruses | viruses | 870710 |
| caldococcus | 5 | genus | bacteria | | 57173 |
| caldivirga | 5 | genus | bacteria | | 76886 |
| caldithrix | 3 | genus | bacteria | | 187144 |
| calditerrivibrio | 1 | genus | bacteria | | 545865 |
| calditerricola | 1 | genus | bacteria | | 373053 |
| caldisphaera | 3 | genus | bacteria | | 200414 |
| caldimonas | 6 | genus | bacteria | | 196013 |
| caldimicrobium | 19 | genus | bacteria | | 444090 |
| caldilinea | 2 | genus | bacteria | | 233191 |
| caldicellulosiruptor | 39 | genus | bacteria | | 44000 |
| caldibacillus | 9 | genus | bacteria | | 74585 |
| caldanaerovirga | 1 | genus | bacteria | | 591374 |
| caldanaerocella | 1 | genus | bacteria | | 265002 |
| caldanaerobius | 1 | genus | bacteria | | 862261 |
| caldanaerobacter | 8 | genus | bacteria | | 249529 |
| caldalkalibacillus | 2 | genus | bacteria | | 379065 |
| caenispirillum | 1 | genus | bacteria | | 414051 |
| byssovorax | 8 | genus | bacteria | | 224459 |
| butyrivibrio hungatei | 6 | species | bacteria | bacteria | 185008 |
| butyrivibrio fibrisolvens | 49 | species | bacteria | bacteria | 831 |
| butyrivibrio | 49 | genus | bacteria | | 830 |
| butyricimonas | 1 | genus | bacteria | | 574697 |
| butyricicoccus | 1 | genus | bacteria | | 580596 |
| buttiauxella | 9 | genus | bacteria | | 82976 |
| burzellia | -3 | genus | bacteria | | 470491 |
| burkholderia stabilis | 13 | species | bacteria | bacteria | 95485 |
| burkholderia multivorans | 21 | species | bacteria | bacteria | 87883 |
| burkholderia dolosa | 7 | species | bacteria | bacteria | 152500 |
| burkholderia cenocepacia | 30 | species | bacteria | bacteria | 95486 |
| bulleidia | 5 | genus | bacteria | | 118747 |
| budvicia | 4 | genus | bacteria | | 82978 |
| buchnera | 60 | genus | bacteria | | 32199 |
| brumimicrobium | 3 | genus | bacteria | | 200473 |
| brooklawnia | 1 | genus | bacteria | | 369926 |
| brochothrix | 42 | genus | bacteria | | 2755 |
| brevibacterium sanguinis | 1 | species | bacteria | bacteria | 232444 |
| brasilonema | 1 | genus | bacteria | | 383614 |
| bradyrhizobium | 100 | genus | bacteria | | 374 |
| brackiella | 1 | genus | bacteria | | 124224 |
| brachyspira murdochii | 8 | species | bacteria | bacteria | 84378 |
| brachymonas | 6 | genus | bacteria | | 28219 |
| brachybacterium | 12 | genus | bacteria | | 43668 |
| boyliae | -3 | genus | bacteria | | 196614 |
| bowmanella | 2 | genus | bacteria | | 366580 |
| bovine foamy virus | 18 | species | viruses | viruses | 207343 |
| bovine adenovirus 10 | 5 | no rank | viruses | viruses | 39788 |
| bosea | 19 | genus | bacteria | | 85413 |
| borreliella andersonii | 8 | species | bacteria | bacteria | 42109 |
| bogoriella | 2 | genus | bacteria | | 56054 |
| blepharocorys uncinata | -3 | species | invertebrates | protozoa | 686991 |
| blennothrix | 5 | genus | bacteria | | 483695 |
| blautia | 2 | genus | bacteria | | 572511 |
| blattabacterium | 9 | genus | bacteria | | 34098 |
| blastopirellula | 4 | genus | bacteria | | 265487 |
| blastomonas | 7 | genus | bacteria | | 150203 |
| blastococcus | 7 | genus | bacteria | | 38501 |
| blastochloris | 14 | genus | bacteria | | 59282 |
| bizionia | 7 | genus | bacteria | | 283785 |
| bisgaardia | 1 | genus | bacteria | | 109471 |
| biostraticola | 1 | genus | bacteria | | 466108 |
| bifissio | -3 | genus | bacteria | | 174924 |
| bifidobacterium thermophilum | 12 | species | bacteria | bacteria | 33905 |
| bifidobacterium longum | 58 | species | bacteria | bacteria | 216816 |
| bifidobacterium catenulatum | 14 | species | bacteria | bacteria | 1686 |
| bifidobacterium breve | 39 | species | bacteria | bacteria | 1685 |
| bifidobacterium bifidum | 53 | species | bacteria | bacteria | 1681 |
| bifidobacterium animalis | 32 | species | bacteria | bacteria | 28025 |