| zymophilus | 7 | genus | bacteria | | 39949 |
| zymomonas | 77 | genus | bacteria | | 541 |
| zymobacter | 12 | genus | bacteria | | 33073 |
| zunongwangia | 2 | genus | bacteria | | 417127 |
| zooshikella | 3 | genus | bacteria | | 202771 |
| zoogloea | 50 | genus | bacteria | | 349 |
| zobellia | 9 | genus | bacteria | | 112040 |
| zobellella | 3 | genus | bacteria | | 347533 |
| zhouia | 2 | genus | bacteria | | 561555 |
| zhihengliuella | 3 | genus | bacteria | | 370735 |
| zeaxanthinibacter | 2 | genus | bacteria | | 561554 |
| zavarzinella | 1 | genus | bacteria | | 600332 |
| yonghaparkia | 2 | genus | bacteria | | 355929 |
| yersinia aleksiciae | 1 | species | bacteria | bacteria | 263819 |
| yeosuana | 2 | genus | bacteria | | 288018 |
| yaniella | 5 | genus | bacteria | | 225447 |
| yangia | 1 | genus | bacteria | | 354203 |
| xylanimonas | 5 | genus | bacteria | | 186188 |
| xylanimicrobium | 1 | genus | bacteria | | 289244 |
| xylanibacterium | 3 | genus | bacteria | | 228972 |
| xylanibacter | 3 | genus | bacteria | | 558436 |
| xenophilus | 3 | genus | bacteria | | 151754 |
| xenococcus | 8 | genus | bacteria | | 52607 |
| xanthobacter | 56 | genus | bacteria | | 279 |
| woronichinia | 7 | genus | bacteria | | 283819 |
| woodsholea | 2 | genus | bacteria | | 240236 |
| wohlfahrtiimonas | 1 | genus | bacteria | | 582472 |
| winogradskyella | 4 | genus | bacteria | | 286104 |
| williamsia | 7 | genus | bacteria | | 85043 |
| wigglesworthia | 24 | genus | bacteria | | 51228 |
| westiellopsis | 12 | genus | bacteria | | 221285 |
| wenxinia | 1 | genus | bacteria | | 653686 |
| weissella confusa | 18 | species | bacteria | bacteria | 1583 |
| weissella cibaria | 12 | species | bacteria | bacteria | 137591 |
| weeksella virosa dsm 16922 | -3 | no rank | bacteria | bacteria | 865938 |
| wautersiella | 2 | genus | bacteria | | 343873 |
| vulcanithermus | 3 | genus | bacteria | | 206044 |
| vulcanisaeta | 4 | genus | bacteria | | 164450 |
| vulcanibacillus | 1 | genus | bacteria | | 551771 |
| volucribacter | 2 | genus | bacteria | | 256730 |
| vogesella | 5 | genus | bacteria | | 57739 |
| vitreoscilla | 47 | genus | bacteria | | 59 |
| vitellibacter | 3 | genus | bacteria | | 171193 |
| viridibacillus | 2 | genus | bacteria | | 496496 |
| virgisporangium | 1 | genus | bacteria | | 65504 |
| virgibacillus | 21 | genus | bacteria | | 84406 |
| victivallis | 2 | genus | bacteria | | 172900 |
| verticillium leptobactrum | 1 | species | plants | fungi | 93594 |
| verrucosispora | 17 | genus | bacteria | | 84593 |
| verrucomicrobium | 18 | genus | bacteria | | 2735 |
| verminephrobacter | 2 | genus | bacteria | | 364316 |
| venteria | -3 | genus | bacteria | | 335967 |
| venenivibrio | 1 | genus | bacteria | | 407997 |
| variovorax | 34 | genus | bacteria | | 34072 |
| varibaculum cambriense | 2 | species | bacteria | bacteria | 184870 |
| varibaculum | 2 | genus | bacteria | | 184869 |
| ustilago | 92 | genus | plants | | 5269 |
| uruburuella | 1 | genus | bacteria | | 299568 |
| ureibacillus | 7 | genus | bacteria | | 160795 |
| undibacterium | 1 | genus | bacteria | | 401469 |
| umezawaea | 1 | genus | bacteria | | 583360 |
| umezakia | 25 | genus | bacteria | | 198592 |
| ulvibacter | 3 | genus | bacteria | | 237444 |
| ultramicrobacter | -3 | genus | bacteria | | 388394 |
| uliginosibacterium | 1 | genus | bacteria | | 392735 |
| tyzzeria anseris | -3 | species | | protozoa | |
| tychonema | 8 | genus | bacteria | | 54312 |
| turneriella | 7 | genus | bacteria | | 338321 |
| turicibacter | 3 | genus | bacteria | | 191303 |
| tumebacillus | 1 | genus | bacteria | | 432330 |
| tuberoidobacter | -3 | genus | bacteria | | 131 |
| tuberibacillus | 1 | genus | bacteria | | 340096 |
| trypanosoma theodori | -3 | species | | protozoa | |
| trypanosoma theileri | 13 | species | invertebrates | protozoa | 67003 |
| trypanosoma rangeli | 28 | species | invertebrates | protozoa | 5698 |
| trypanosoma nabiasi | 2 | species | invertebrates | protozoa | 296053 |
| trypanosoma melophagium | 4 | species | invertebrates | protozoa | 715481 |
| trypanosoma lewisi | 30 | species | invertebrates | protozoa | 5695 |
| trypanosoma gallinarum | 2 | species | invertebrates | protozoa | 393991 |
| trypanosoma calmetti | -3 | species | | protozoa | |
| trypanosoma avium | 18 | species | invertebrates | protozoa | 43998 |
| truepera | 2 | genus | bacteria | | 332248 |
| tropicimonas | 1 | genus | bacteria | | 599652 |
| tropicibacter | 1 | genus | bacteria | | 599653 |
| tritrichomonas muris | 7 | species | invertebrates | protozoa | 5726 |
| tritrichomonas minuta | -3 | species | | protozoa | |
| tritrichomonas equi | -3 | species | | protozoa | |
| tritrichomonas enteris | -3 | species | | protozoa | |
| tritrichomonas eberthi | 1 | species | | protozoa | |
| tritrichomonas caviae | -3 | species | | protozoa | |
| trigonala | -3 | genus | bacteria | | 386607 |
| trichuris muris | 44 | species | invertebrates | helminths | 70415 |
| trichotomospora | -3 | genus | bacteria | | 65518 |
| trichothecium roseum | 17 | species | plants | fungi | 47278 |
| trichosporon faecale | 3 | species | plants | fungi | 82510 |
| trichosporon coremiiforme | 1 | species | plants | fungi | 82509 |
| trichormus | 6 | genus | bacteria | | 264688 |
| trichophyton terrestre | 12 | species | plants | fungi | 81845 |
| trichomonas vaginalis virus | 16 | species | viruses | viruses | 29256 |
| trichomonas felistomae | -3 | species | | protozoa | |