| phyllobates terribilis | 2 | species | vertebrates | | 111132 |
| pichia kudriavzevii | 67 | species | plants | fungi | 4909 |
| plasmodium falciparum | 209 | species | invertebrates | protozoa | 5833 |
| plasmodium vivax | 80 | species | invertebrates | protozoa | 5855 |
| plum pox virus | 57 | species | viruses | viruses | 12211 |
| pneumocystis jirovecii | 34 | species | plants | fungi | 42068 |
| potato virus x | 71 | species | viruses | viruses | 12183 |
| potato virus y | 52 | species | viruses | viruses | 12216 |
| powassan virus | 11 | species | viruses | viruses | 11083 |
| propionibacterium acnes | 77 | species | bacteria | bacteria | 1747 |
| proteus mirabilis | 80 | species | bacteria | bacteria | 584 |
| proteus vulgaris | 53 | species | bacteria | bacteria | 585 |
| providencia stuartii | 41 | species | bacteria | bacteria | 588 |
| pseudoalteromonas tetraodonis | 9 | species | bacteria | bacteria | 43659 |
| pseudomonas aeruginosa | 243 | species | bacteria | bacteria | 287 |
| pseudomonas alcaligenes | 25 | species | bacteria | bacteria | 43263 |
| pseudomonas fluorescens | 122 | species | bacteria | bacteria | 294 |
| pseudomonas putida | 133 | species | bacteria | bacteria | 303 |
| pseudomonas savastanoi pv. glycinea | 35 | no rank | bacteria | bacteria | 318 |
| pseudomonas stutzeri | 76 | species | bacteria | bacteria | 316 |
| pyrodinium bahamense | 16 | species | plants | protozoa | 73915 |
| rabbit hemorrhagic disease virus | 37 | species | viruses | viruses | 11976 |
| rabbitpox virus | 31 | no rank | viruses | viruses | 32606 |
| rabies virus | 96 | species | viruses | viruses | 11292 |
| ralstonia mannitolilytica | 9 | species | bacteria | bacteria | 105219 |
| ralstonia pickettii | 44 | species | bacteria | bacteria | 329 |
| ralstonia solanacearum | 79 | species | bacteria | bacteria | 305 |
| recombinant sars coronavirus | 3 | species | synthetic | | 575560 |
| reston ebolavirus | 9 | species | viruses | viruses | 186539 |
| rhinovirus a | 7 | species | viruses | viruses | 147711 |
| rhinovirus b | 8 | species | viruses | viruses | 147712 |
| rhizopus oryzae | 86 | species | plants | fungi | 64495 |
| rhodococcus equi | 50 | species | bacteria | bacteria | 43767 |
| rice black streaked dwarf virus | 14 | species | viruses | viruses | 10990 |
| rice dwarf virus | 29 | species | viruses | viruses | 10991 |
| rice gall dwarf virus | 11 | species | viruses | viruses | 10986 |
| rice ragged stunt virus | 15 | species | viruses | viruses | 42475 |
| rice stripe virus | 118 | species | viruses | viruses | 12331 |
| rice tungro bacilliform virus | 21 | species | viruses | viruses | 10654 |
| rice yellow mottle virus | 23 | species | viruses | viruses | 31744 |
| ricinus communis | 104 | species | plants | | 3988 |
| rickettsia conorii | 40 | species | bacteria | bacteria | 781 |
| rickettsia felis | 29 | species | bacteria | bacteria | 42862 |
| rickettsia prowazekii | 51 | species | bacteria | bacteria | 782 |
| rickettsia rickettsii | 53 | species | bacteria | bacteria | 783 |
| rickettsia typhi | 36 | species | bacteria | bacteria | 785 |
| rift valley fever virus | 41 | species | viruses | viruses | 11588 |
| rinderpest virus | 39 | species | viruses | viruses | 11241 |
| 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 |
| rothia dentocariosa | 19 | species | bacteria | bacteria | 2047 |
| rubella virus | 64 | species | viruses | viruses | 11041 |
| russian spring-summer encephalitis virus | 7 | species | viruses | viruses | 64316 |
| sabia mammarenavirus | 9 | species | viruses | viruses | 45709 |
| 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 paratyphi a | 22 | no rank | bacteria | bacteria | 54388 |
| 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 |
| sapporo virus | 16 | species | viruses | viruses | 95342 |
| seoul virus | 27 | species | viruses | viruses | 11608 |
| serratia marcescens | 100 | species | bacteria | bacteria | 615 |
| sheeppox virus | 10 | species | viruses | viruses | 10266 |
| 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 |
| skunkpox virus | 1 | species | viruses | viruses | 160796 |
| soil-borne cereal mosaic virus | 8 | species | viruses | viruses | 100887 |
| soil-borne wheat mosaic virus | 21 | species | viruses | viruses | 28375 |
| southern bean mosaic virus | 29 | species | viruses | viruses | 12139 |
| soybean dwarf virus | 12 | species | viruses | viruses | 12049 |
| soybean mosaic virus | 32 | species | viruses | viruses | 12222 |
| span 232 virus | -1 | no rank | viruses | viruses | 262397 |
| spirillum minus | 5 | species | | bacteria | |
| 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 intermedius | 37 | species | bacteria | bacteria | 1285 |
| staphylococcus saprophyticus | 42 | species | bacteria | bacteria | 29385 |
| stenotrophomonas maltophilia | 80 | species | bacteria | bacteria | 40324 |
| streptobacillus moniliformis | 20 | species | bacteria | bacteria | 34105 |
| streptococcus acidominimus | 6 | species | bacteria | bacteria | 1326 |
| streptococcus agalactiae | 62 | species | bacteria | bacteria | 1311 |
| streptococcus canis | 16 | species | bacteria | bacteria | 1329 |
| streptococcus criceti | 10 | species | bacteria | bacteria | 1333 |
| streptococcus equi | 30 | species | bacteria | bacteria | 1336 |
| streptococcus equinus | 52 | species | bacteria | bacteria | 1335 |
| streptococcus intermedius | 31 | species | bacteria | bacteria | 1338 |
| streptococcus milleri | 39 | species | bacteria | bacteria | 33040 |
| streptococcus pneumoniae | 199 | species | bacteria | bacteria | 1313 |
| streptococcus pyogenes | 113 | species | bacteria | bacteria | 1314 |
| streptococcus suis | 50 | species | bacteria | bacteria | 1307 |