| spirometra mansonoides | 19 | species | invertebrates | helminths | 46899 |
| spironema | 5 | genus | bacteria | | 109459 |
| spirosoma | 6 | genus | bacteria | | 107 |
| spirulina | 60 | genus | bacteria | | 1154 |
| spongiibacter | 1 | genus | bacteria | | 630749 |
| spongiobacter | 3 | genus | bacteria | | 314672 |
| spongitalea | -3 | genus | bacteria | | 499058 |
| sporacetigenium | 2 | genus | bacteria | | 360541 |
| sporanaerobacter | 2 | genus | bacteria | | 165812 |
| sporidiobolus salmonicolor | 26 | species | plants | fungi | 5005 |
| sporobacter | 4 | genus | bacteria | | 44748 |
| sporobacterium | 2 | genus | bacteria | | 100132 |
| sporohalobacter | 4 | genus | bacteria | | 973 |
| sporolactobacillus | 13 | genus | bacteria | | 2077 |
| sporomusa | 27 | genus | bacteria | | 2375 |
| sporopachydermia lactativora | 3 | species | plants | fungi | 45794 |
| sporotalea | 1 | genus | bacteria | | 380083 |
| sporothrix stenoceras | 8 | species | plants | fungi | 5173 |
| sporotomaculum | 3 | genus | bacteria | | 68034 |
| stackebrandtia | 3 | genus | bacteria | | 283810 |
| stanieria | 3 | genus | bacteria | | 102115 |
| staphylococcus capitis | 20 | species | bacteria | bacteria | 29388 |
| staphylococcus hominis | 23 | species | bacteria | bacteria | 1290 |
| staphylococcus lugdunensis hku09-01 | 1 | no rank | bacteria | bacteria | 698737 |
| staphylococcus pseudintermedius | 14 | species | bacteria | bacteria | 283734 |
| staphylococcus rostri | 1 | species | bacteria | bacteria | 522262 |
| staphylococcus sciuri | 28 | species | bacteria | bacteria | 1296 |
| staphylococcus simulans | 30 | species | bacteria | bacteria | 1286 |
| staphylothermus | 16 | genus | bacteria | | 2279 |
| stappia | 9 | genus | bacteria | | 152161 |
| starkeya | 13 | genus | bacteria | | 152053 |
| starria | 1 | genus | bacteria | | 241429 |
| stella | 39 | genus | bacteria | | 93 |
| stemphylium | 26 | genus | plants | | 95729 |
| stenothermobacter | 1 | genus | bacteria | | 331644 |
| stenoxybacter | 2 | genus | bacteria | | 422440 |
| sterigmatomyces halophilus | 3 | species | plants | fungi | 5617 |
| steroidobacter | 2 | genus | bacteria | | 469322 |
| sterolibacterium | 6 | genus | bacteria | | 157591 |
| stetteria | 4 | genus | bacteria | | 52130 |
| stigmatella | 41 | genus | bacteria | | 40 |
| stigonema | 9 | genus | bacteria | | 221292 |
| stilesia hepatica | 2 | species | | helminths | |
| streptacidiphilus | 3 | genus | bacteria | | 228398 |
| streptoalloteichus | 18 | genus | bacteria | | 2016 |
| streptococcus merionis | 1 | species | bacteria | bacteria | 400065 |
| streptococcus oralis | 43 | species | bacteria | bacteria | 1303 |
| streptococcus parasanguinis | 28 | species | bacteria | bacteria | 1318 |
| streptococcus porcinus | 8 | species | bacteria | bacteria | 1340 |
| streptofusia | -3 | genus | bacteria | | 42688 |
| streptomonospora | 5 | genus | bacteria | | 104204 |
| streptosporangium | 19 | genus | bacteria | | 2000 |
| strongyloides avium | 4 | species | | helminths | |
| strongyloides tumefaciens | 1 | species | | helminths | |
| stygiolobus | 9 | genus | bacteria | | 41674 |
| subaequorebacter | -3 | genus | bacteria | | 395928 |
| subsaxibacter | 3 | genus | bacteria | | 291181 |
| subsaximicrobium | 2 | genus | bacteria | | 291178 |
| subtercola | 6 | genus | bacteria | | 120212 |
| subulura brumpti | 3 | species | | helminths | |
| subulura differens | 1 | species | | helminths | |
| subulura minetti | 1 | species | | helminths | |
| subulura strongylina | 2 | species | | helminths | |
| subulura suctoria | 2 | species | | helminths | |
| succiniclasticum | 6 | genus | bacteria | | 40840 |
| succinimonas | 3 | genus | bacteria | | 83768 |
| succinispira | 1 | genus | bacteria | | 78119 |
| succinivibrio | 9 | genus | bacteria | | 83770 |
| sufflavibacter | 1 | genus | bacteria | | 399942 |
| suifilaria suis | -3 | species | | helminths | |
| sulfitobacter | 18 | genus | bacteria | | 60136 |
| sulfobacillus | 24 | genus | bacteria | | 28033 |
| sulfolobus | 103 | genus | bacteria | | 2284 |
| sulfophobococcus | 3 | genus | bacteria | | 53425 |
| sulfuricurvum | 3 | genus | bacteria | | 286130 |
| sulfurihydrogenibium | 11 | genus | bacteria | | 212790 |
| sulfurimonas | 8 | genus | bacteria | | 202746 |
| sulfurisphaera | 7 | genus | bacteria | | 69655 |
| sulfurivirga | 2 | genus | bacteria | | 364031 |
| sulfurospirillum | 47 | genus | bacteria | | 57665 |
| sulfurovum | 6 | genus | bacteria | | 265570 |
| swaminathania | 5 | genus | bacteria | | 209260 |
| symbiobacterium | 15 | genus | bacteria | | 2733 |
| symphyonema | 1 | genus | bacteria | | 221284 |
| symphyonemopsis | 1 | genus | bacteria | | 221286 |
| symploca | 20 | genus | bacteria | | 105591 |
| syncephalastrum racemosum | 15 | species | plants | fungi | 13706 |
| synechococcus | 131 | genus | bacteria | | 1129 |
| synechocystis | 113 | genus | bacteria | | 1142 |
| synergistes | 22 | genus | bacteria | | 2753 |
| syntrophobacter | 32 | genus | bacteria | | 29526 |
| syntrophobotulus | 1 | genus | bacteria | | 51196 |
| syntrophococcus | 8 | genus | bacteria | | 84036 |
| syntrophomonas | 20 | genus | bacteria | | 862 |
| syntrophorhabdus | 1 | genus | bacteria | | 513557 |
| syntrophothermus | 4 | genus | bacteria | | 129001 |
| syntrophus | 24 | genus | bacteria | | 43773 |
| syphacia muris | 12 | species | invertebrates | helminths | 451379 |
| syphacia obvelata | 18 | species | invertebrates | helminths | 412127 |
| taenia (drepanidotaenia) lanceolata | -3 | species | | helminths | |