| rocio virus | 8 | species | viruses | viruses | 64315 |
| ross river virus | 48 | species | viruses | viruses | 11029 |
| rotavirus a | 58 | species | viruses | viruses | 28875 |
| rotavirus b | 22 | species | viruses | viruses | 28876 |
| rotavirus c | 33 | species | viruses | viruses | 36427 |
| rotavirus d | -3 | species | viruses | viruses | 335100 |
| rotavirus e | 4 | species | | viruses | |
| rotavirus f | -3 | species | viruses | viruses | 183405 |
| rothia dentocariosa | 19 | species | bacteria | bacteria | 2047 |
| royal farm virus | 1 | species | viruses | viruses | 64288 |
| rubella virus | 64 | species | viruses | viruses | 11041 |
| sabia mammarenavirus | 9 | species | viruses | viruses | 45709 |
| saccharomonospora viridis | 11 | species | bacteria | bacteria | 1852 |
| saccharomyces cerevisiae | 584 | species | plants | fungi | 4932 |
| saccharopolyspora rectivirgula | 29 | species | bacteria | bacteria | 28042 |
| saimiriine herpesvirus 1 | 9 | species | viruses | viruses | 10353 |
| saksenaea vasiformis | 20 | species | plants | fungi | 90258 |
| salehabad virus | -3 | no rank | viruses | viruses | 904699 |
| salmonella bongori | 18 | species | bacteria | bacteria | 54736 |
| salmonella enterica | 107 | species | bacteria | bacteria | 28901 |
| salmonella enterica subsp. enterica serovar enteritidis | 87 | no rank | bacteria | bacteria | 149539 |
| salmonella enterica subsp. enterica serovar typhi | 85 | no rank | bacteria | bacteria | 90370 |
| salmonella enterica subsp. enterica serovar typhimurium | 77 | no rank | bacteria | bacteria | 90371 |
| sandfly fever naples virus | 4 | species | viruses | viruses | 206160 |
| sandfly fever virus group | -3 | species | | viruses | |
| sarcinomyces phaeomuriformis | 6 | species | plants | fungi | 66227 |
| sarcocystis hominis | 10 | species | invertebrates | protozoa | 61650 |
| sarcocystis lindemanni | -3 | species | | protozoa | |
| sarcocystis suihominis | 8 | species | invertebrates | protozoa | 102713 |
| sarocladium kiliense | 11 | species | plants | fungi | 45277 |
| sarocladium strictum | 17 | species | plants | fungi | 5046 |
| saumarez reef virus | 1 | species | viruses | viruses | 40012 |
| scedosporium boydii | 48 | species | plants | fungi | 5597 |
| schistocephalus solidus | 32 | species | invertebrates | helminths | 70667 |
| schistosoma bovis | 24 | species | invertebrates | helminths | 6184 |
| schistosoma haematobium | 56 | species | invertebrates | helminths | 6185 |
| schistosoma intercalatum | 22 | species | invertebrates | helminths | 6187 |
| schistosoma japonicum | 53 | species | invertebrates | helminths | 6182 |
| schistosoma malayensis | 4 | species | invertebrates | helminths | 53353 |
| schistosoma mansoni | 138 | species | invertebrates | helminths | 6183 |
| schistosoma mattheei | 17 | species | invertebrates | helminths | 31246 |
| schistosoma mekongi | 12 | species | invertebrates | helminths | 38744 |
| schistosoma rodhaini | 11 | species | invertebrates | helminths | 6188 |
| schistosoma spindale | 9 | species | invertebrates | helminths | 6189 |
| schistosomatium douthitti | 18 | species | invertebrates | helminths | 38741 |
| schizophyllum commune | 74 | species | plants | fungi | 5334 |
| scopulariopsis acremonium | 4 | species | plants | fungi | 186355 |
| scopulariopsis asperula | -3 | species | plants | fungi | 186356 |
| scopulariopsis brumptii | 5 | species | plants | fungi | 40376 |
| scopulariopsis candida | 3 | species | | fungi | 186344 |
| scopulariopsis flava | 1 | species | plants | fungi | 186360 |
| scopulariopsis fusca | -3 | species | plants | fungi | 186361 |
| scytalidium infestans | -3 | species | | fungi | |
| seal parapoxvirus | 6 | no rank | viruses | viruses | 187984 |
| sebaldella termitidis | 2 | species | bacteria | bacteria | 826 |
| selenomonas artemidis | 6 | species | bacteria | bacteria | 671224 |
| selenomonas dianae | 3 | species | bacteria | bacteria | 135079 |
| selenomonas flueggei | 5 | species | bacteria | bacteria | 135080 |
| selenomonas infelix | 6 | species | bacteria | bacteria | 135082 |
| selenomonas noxia | 11 | species | bacteria | bacteria | 135083 |
| semliki forest virus | 119 | species | viruses | viruses | 11033 |
| seoul virus | 27 | species | viruses | viruses | 11608 |
| sepik virus | 2 | species | viruses | viruses | 44026 |
| serratia ficaria | 10 | species | bacteria | bacteria | 61651 |
| serratia marcescens | 100 | species | bacteria | bacteria | 615 |
| serratia odorifera | 11 | species | bacteria | bacteria | 618 |
| serratia plymuthica | 24 | species | bacteria | bacteria | 82996 |
| serratia proteamaculans | 17 | species | bacteria | bacteria | 28151 |
| serratia rubidaea | 10 | species | bacteria | bacteria | 61652 |
| setaria equina | 4 | species | invertebrates | helminths | 221942 |
| setosphaeria rostrata | 2 | species | plants | fungi | 45150 |
| shigella boydii | 21 | species | bacteria | bacteria | 621 |
| shigella dysenteriae | 80 | species | bacteria | bacteria | 622 |
| shigella flexneri | 142 | species | bacteria | bacteria | 623 |
| shigella sonnei | 53 | species | bacteria | bacteria | 624 |
| sindbis virus | 107 | species | viruses | viruses | 11034 |
| sphingomonas paucimobilis | 56 | species | bacteria | bacteria | 13689 |
| spirillum minus | 5 | species | | bacteria | |
| spirocerca lupi | 19 | species | invertebrates | helminths | 304461 |
| sporothrix schenckii | 40 | species | plants | fungi | 29908 |
| st. louis encephalitis virus | 38 | species | viruses | viruses | 11080 |
| staphylococcus aureus | 271 | species | bacteria | bacteria | 1280 |
| staphylococcus epidermidis | 114 | species | bacteria | bacteria | 1282 |
| staphylococcus haemolyticus | 36 | species | bacteria | bacteria | 1283 |
| staphylococcus hyicus | 37 | species | bacteria | bacteria | 1284 |
| staphylococcus intermedius | 37 | species | bacteria | bacteria | 1285 |
| staphylococcus lugdunensis | 24 | species | bacteria | bacteria | 28035 |
| staphylococcus saprophyticus | 42 | species | bacteria | bacteria | 29385 |
| staphylococcus warneri | 25 | species | bacteria | bacteria | 1292 |
| stellantchasmus falcatus | 8 | species | invertebrates | helminths | 104478 |
| stenella araguata | 4 | species | plants | fungi | 93486 |
| stenotrophomonas maltophilia | 80 | species | bacteria | bacteria | 40324 |
| stictodora fuscata | 1 | species | | helminths | |
| streptobacillus moniliformis | 20 | species | bacteria | bacteria | 34105 |
| streptococcus acidominimus | 6 | species | bacteria | bacteria | 1326 |
| streptococcus agalactiae | 62 | species | bacteria | bacteria | 1311 |
| streptococcus anginosus | 29 | species | bacteria | bacteria | 1328 |
| streptococcus canis | 16 | species | bacteria | bacteria | 1329 |
| streptococcus constellatus | 25 | species | bacteria | bacteria | 76860 |
| streptococcus criceti | 10 | species | bacteria | bacteria | 1333 |