| streptococcus equi | 30 | species | bacteria | bacteria | 1336 |
| streptococcus equinus | 52 | species | bacteria | bacteria | 1335 |
| streptococcus gordonii | 61 | species | bacteria | bacteria | 1302 |
| streptococcus intermedius | 31 | species | bacteria | bacteria | 1338 |
| streptococcus milleri | 39 | species | bacteria | bacteria | 33040 |
| streptococcus mitis | 45 | species | bacteria | bacteria | 28037 |
| streptococcus mutans | 104 | species | bacteria | bacteria | 1309 |
| streptococcus pneumoniae | 199 | species | bacteria | bacteria | 1313 |
| streptococcus pyogenes | 113 | species | bacteria | bacteria | 1314 |
| streptococcus salivarius | 53 | species | bacteria | bacteria | 1304 |
| streptococcus sanguinis | 74 | species | bacteria | bacteria | 1305 |
| streptococcus sobrinus | 43 | species | bacteria | bacteria | 1310 |
| streptococcus suis | 50 | species | bacteria | bacteria | 1307 |
| streptococcus uberis | 41 | species | bacteria | bacteria | 1349 |
| streptomyces somaliensis | 10 | species | bacteria | bacteria | 78355 |
| strongyloides fuelleborni | 12 | species | invertebrates | helminths | 44441 |
| strongyloides papillosus | 14 | species | invertebrates | helminths | 174720 |
| strongyloides ransomi | 12 | species | invertebrates | helminths | 553534 |
| strongyloides stercoralis | 48 | species | invertebrates | helminths | 6248 |
| strongyloides westeri | 12 | species | invertebrates | helminths | 174724 |
| sudan ebolavirus | 8 | species | viruses | viruses | 186540 |
| suid herpesvirus 1 | 106 | species | viruses | viruses | 10345 |
| sutterella wadsworthensis | 7 | species | bacteria | bacteria | 40545 |
| suttonella indologenes | 6 | species | bacteria | bacteria | 13276 |
| swine vesicular disease virus | 23 | no rank | viruses | viruses | 12075 |
| syphacea obvelata | -3 | species | | helminths | |
| tacaiuma virus | 2 | species | viruses | viruses | 611707 |
| taenia crassiceps | 36 | species | invertebrates | helminths | 6207 |
| taenia multiceps | 14 | species | invertebrates | helminths | 94034 |
| taenia saginata | 31 | species | invertebrates | helminths | 6206 |
| taenia solium | 55 | species | invertebrates | helminths | 6204 |
| taeniolella exilis | -3 | species | | fungi | 1891693 |
| taeniolella stilbospora | 1 | species | plants | fungi | 306689 |
| talaromyces marneffei | 43 | species | plants | fungi | 37727 |
| talaromyces purpureogenus | 25 | species | plants | fungi | 1266744 |
| tamdy virus | 1 | species | | viruses | 1453410 |
| tanapox virus | 9 | species | viruses | viruses | 99000 |
| tannerella forsythia | 56 | species | bacteria | bacteria | 28112 |
| tatlockia micdadei | 25 | species | bacteria | bacteria | 451 |
| tatumella ptyseos | 2 | species | bacteria | bacteria | 82987 |
| teladorsagia circumcincta | 53 | species | invertebrates | helminths | 45464 |
| ternidens deminutus | 4 | species | invertebrates | helminths | 317882 |
| tetraploa aristata | 4 | species | plants | fungi | 682077 |
| thelazia californiensis | 6 | species | | helminths | |
| thelazia callipaeda | 11 | species | invertebrates | helminths | 103827 |
| thelazia rhodesi | 4 | species | invertebrates | helminths | 150477 |
| thermomyces lanuginosus | 49 | species | plants | fungi | 5541 |
| thielavia terrestris | 10 | species | plants | fungi | 35720 |
| thogoto virus | 37 | species | viruses | viruses | 11569 |
| tick-borne encephalitis virus | 55 | species | viruses | viruses | 11084 |
| toxascaris leonina | 22 | species | invertebrates | helminths | 59264 |
| toxocara canis | 50 | species | invertebrates | helminths | 6265 |
| toxocara cati | 24 | species | invertebrates | helminths | 6266 |
| toxoplasma gondii | 148 | species | invertebrates | protozoa | 5811 |
| trachipleistophora hominis | 16 | species | plants | fungi | 72359 |
| trematosphaeria grisea | 8 | species | plants | fungi | 1489895 |
| treponema carateum | 1 | species | | bacteria | |
| treponema pallidum | 87 | species | bacteria | bacteria | 160 |
| trichinella britovi | 23 | species | invertebrates | helminths | 45882 |
| trichinella murrelli | 12 | species | invertebrates | helminths | 144512 |
| trichinella nativa | 22 | species | invertebrates | helminths | 6335 |
| trichinella nelsoni | 14 | species | invertebrates | helminths | 6336 |
| trichinella pseudospiralis | 28 | species | invertebrates | helminths | 6337 |
| trichinella spiralis | 78 | species | invertebrates | helminths | 6334 |
| trichobilharzia brevis | -3 | species | | helminths | |
| trichobilharzia ocellata | 30 | species | invertebrates | helminths | 100602 |
| trichobilharzia stagnicolae | 3 | species | invertebrates | helminths | 596254 |
| trichoderma pseudokoningii | 15 | species | plants | fungi | 317029 |
| trichoderma viride | 64 | species | plants | fungi | 5547 |
| trichomaris invadens | 4 | species | | fungi | |
| trichomonas tenax | 11 | species | invertebrates | protozoa | 43075 |
| trichomonas vaginalis | 87 | species | invertebrates | protozoa | 5722 |
| trichophyton concentricum | 5 | species | plants | fungi | 63419 |
| trichophyton equinum | 10 | species | plants | fungi | 63418 |
| trichophyton gourvilii | 1 | species | plants | fungi | 81477 |
| trichophyton mentagrophytes | 41 | species | plants | fungi | 523103 |
| trichophyton rubrum | 48 | species | plants | fungi | 5551 |
| trichophyton schoenleinii | 12 | species | plants | fungi | 34386 |
| trichophyton soudanense | 13 | species | plants | fungi | 69891 |
| trichophyton tonsurans | 34 | species | plants | fungi | 34387 |
| trichophyton verrucosum | 19 | species | plants | fungi | 63417 |
| trichophyton violaceum | 23 | species | plants | fungi | 34388 |
| trichosporon asahii | 20 | species | plants | fungi | 82508 |
| trichosporon beigelii | 40 | species | plants | fungi | 5553 |
| trichosporon inkin | 9 | species | plants | fungi | 82517 |
| trichosporon ovoides | 4 | species | plants | fungi | 82524 |
| trichostrongylus affinis | 2 | species | | helminths | |
| trichostrongylus axei | 22 | species | invertebrates | helminths | 40349 |
| trichostrongylus brevis | -3 | species | | helminths | |
| trichostrongylus calcaratus | 2 | species | | helminths | |
| trichostrongylus capricola | 3 | species | invertebrates | helminths | 126400 |
| trichostrongylus colubriformis | 57 | species | invertebrates | helminths | 6319 |
| trichostrongylus instabilis | -3 | species | | helminths | |
| trichostrongylus lerouxi | 1 | species | | helminths | |
| trichostrongylus orientalis | 1 | species | | helminths | |
| trichostrongylus probolurus | 3 | species | invertebrates | helminths | 53330 |
| trichostrongylus skrjabini | -3 | species | | helminths | |
| trichostrongylus vitrinus | 19 | species | invertebrates | helminths | 40352 |
| trichuris suis | 27 | species | invertebrates | helminths | 68888 |
| trichuris trichiura | 51 | species | invertebrates | helminths | 36087 |