| zucchini yellow mosaic virus | 32 | species | viruses | viruses | 12232 |
| zaire ebolavirus | 20 | species | viruses | viruses | 186538 |
| yersinia pseudotuberculosis | 99 | species | bacteria | bacteria | 633 |
| yersinia pestis | 105 | species | bacteria | bacteria | 632 |
| yersinia enterocolitica | 126 | species | bacteria | bacteria | 630 |
| yellow fever virus | 83 | species | viruses | viruses | 11089 |
| xylella fastidiosa | 46 | species | bacteria | bacteria | 2371 |
| xanthomonas oryzae pv. oryzicola | 12 | no rank | bacteria | bacteria | 129394 |
| xanthomonas oryzae pv. oryzae | 48 | no rank | bacteria | bacteria | 64187 |
| xanthomonas citri subsp. malvacearum | 22 | subspecies | bacteria | bacteria | 86040 |
| wheat yellow mosaic virus | 8 | species | viruses | viruses | 75746 |
| wheat dwarf virus | 42 | species | viruses | viruses | 10834 |
| western equine encephalitis virus | 30 | species | viruses | viruses | 11039 |
| west nile virus | 97 | species | viruses | viruses | 11082 |
| volepox virus | 1 | species | viruses | viruses | 28874 |
| vibrio vulnificus | 73 | species | bacteria | bacteria | 672 |
| vibrio parahaemolyticus | 74 | species | bacteria | bacteria | 670 |
| vibrio mimicus | 28 | species | bacteria | bacteria | 674 |
| vibrio cholerae | 145 | species | bacteria | bacteria | 666 |
| vesicular stomatitis virus | 177 | species | viruses | viruses | 11276 |
| venezuelan equine encephalitis virus | 54 | species | viruses | viruses | 11036 |
| veillonella dispar | 17 | species | bacteria | bacteria | 39778 |
| variola virus | 80 | species | viruses | viruses | 10255 |
| vaccinia virus | 197 | species | viruses | viruses | 10245 |
| ustilago tritici | 9 | species | plants | fungi | 117174 |
| unidentified influenza virus | 240 | species | viruses | viruses | 11309 |
| trypanosoma cruzi | 130 | species | invertebrates | protozoa | 5693 |
| trypanosoma brucei rhodesiense | 45 | subspecies | invertebrates | protozoa | 31286 |
| trypanosoma brucei gambiense | 41 | subspecies | invertebrates | protozoa | 31285 |
| trichinella spiralis | 78 | species | invertebrates | helminths | 6334 |
| trichinella pseudospiralis | 28 | species | invertebrates | helminths | 6337 |
| trichinella nelsoni | 14 | species | invertebrates | helminths | 6336 |
| trichinella nativa | 22 | species | invertebrates | helminths | 6335 |
| trichinella britovi | 23 | species | invertebrates | helminths | 45882 |
| treponema pallidum | 87 | species | bacteria | bacteria | 160 |
| toxoplasma gondii | 148 | species | invertebrates | protozoa | 5811 |
| tomato spotted wilt virus | 48 | species | viruses | viruses | 11613 |
| tilletia indica | 22 | species | plants | fungi | 43049 |
| tick-borne encephalitis virus (strain sofjin) | -1 | no rank | viruses | viruses | 11087 |
| tick-borne encephalitis virus | 55 | species | viruses | viruses | 11084 |
| tatlockia micdadei | 25 | species | bacteria | bacteria | 451 |
| taenia solium | 55 | species | invertebrates | helminths | 6204 |
| synchytrium endobioticum | 12 | species | plants | fungi | 286115 |
| swine vesicular disease virus | 23 | no rank | viruses | viruses | 12075 |
| sugarcane mosaic virus | 23 | species | viruses | viruses | 12224 |
| sudan ebolavirus | 8 | species | viruses | viruses | 186540 |
| strongyloides stercoralis | 48 | species | invertebrates | helminths | 6248 |
| streptococcus viridans | 35 | species | bacteria | bacteria | 78535 |
| streptococcus uberis | 41 | species | bacteria | bacteria | 1349 |
| streptococcus suis | 50 | species | bacteria | bacteria | 1307 |
| streptococcus pyogenes | 113 | species | bacteria | bacteria | 1314 |
| streptococcus pneumoniae | 199 | species | bacteria | bacteria | 1313 |
| streptococcus milleri | 39 | species | bacteria | bacteria | 33040 |
| streptococcus intermedius | 31 | species | bacteria | bacteria | 1338 |
| streptococcus equinus | 52 | species | bacteria | bacteria | 1335 |
| streptococcus equi | 30 | species | bacteria | bacteria | 1336 |
| streptococcus criceti | 10 | species | bacteria | bacteria | 1333 |
| streptococcus canis | 16 | species | bacteria | bacteria | 1329 |
| streptococcus agalactiae | 62 | species | bacteria | bacteria | 1311 |
| streptococcus acidominimus | 6 | species | bacteria | bacteria | 1326 |
| streptobacillus moniliformis | 20 | species | bacteria | bacteria | 34105 |
| stenotrophomonas maltophilia | 80 | species | bacteria | bacteria | 40324 |
| staphylococcus saprophyticus | 42 | species | bacteria | bacteria | 29385 |
| staphylococcus intermedius | 37 | species | bacteria | bacteria | 1285 |
| staphylococcus haemolyticus | 36 | species | bacteria | bacteria | 1283 |
| staphylococcus epidermidis | 114 | species | bacteria | bacteria | 1282 |
| staphylococcus aureus | 271 | species | bacteria | bacteria | 1280 |
| st. louis encephalitis virus | 38 | species | viruses | viruses | 11080 |
| sporothrix schenckii | 40 | species | plants | fungi | 29908 |
| spirillum minus | 5 | species | | bacteria | |
| span 232 virus | -1 | no rank | viruses | viruses | 262397 |
| soybean mosaic virus | 32 | species | viruses | viruses | 12222 |
| soybean dwarf virus | 12 | species | viruses | viruses | 12049 |
| southern bean mosaic virus | 29 | species | viruses | viruses | 12139 |
| soil-borne wheat mosaic virus | 21 | species | viruses | viruses | 28375 |
| soil-borne cereal mosaic virus | 8 | species | viruses | viruses | 100887 |
| skunkpox virus | 1 | species | viruses | viruses | 160796 |
| sindbis virus | 107 | species | viruses | viruses | 11034 |
| shigella sonnei | 53 | species | bacteria | bacteria | 624 |
| shigella flexneri | 142 | species | bacteria | bacteria | 623 |
| shigella dysenteriae | 80 | species | bacteria | bacteria | 622 |
| shigella boydii | 21 | species | bacteria | bacteria | 621 |
| sheeppox virus | 10 | species | viruses | viruses | 10266 |
| serratia marcescens | 100 | species | bacteria | bacteria | 615 |
| seoul virus | 27 | species | viruses | viruses | 11608 |
| sapporo virus | 16 | species | viruses | viruses | 95342 |
| sandfly fever naples virus | 4 | species | viruses | viruses | 206160 |
| salmonella enterica subsp. enterica serovar typhimurium | 77 | no rank | bacteria | bacteria | 90371 |
| salmonella enterica subsp. enterica serovar typhi | 85 | no rank | bacteria | bacteria | 90370 |
| salmonella enterica subsp. enterica serovar paratyphi a | 22 | no rank | bacteria | bacteria | 54388 |
| salmonella enterica subsp. enterica serovar enteritidis | 87 | no rank | bacteria | bacteria | 149539 |
| salmonella enterica | 107 | species | bacteria | bacteria | 28901 |
| salmonella bongori | 18 | species | bacteria | bacteria | 54736 |
| sabia mammarenavirus | 9 | species | viruses | viruses | 45709 |
| russian spring-summer encephalitis virus | 7 | species | viruses | viruses | 64316 |
| rubella virus | 64 | species | viruses | viruses | 11041 |
| rothia dentocariosa | 19 | species | bacteria | bacteria | 2047 |
| rotavirus c | 33 | species | viruses | viruses | 36427 |
| rotavirus b | 22 | species | viruses | viruses | 28876 |
| rotavirus a | 58 | species | viruses | viruses | 28875 |