| prevotella buccae | 17 | species | bacteria | bacteria | 28126 |
| prevotella buccalis | 4 | species | bacteria | bacteria | 28127 |
| prevotella corporis | 6 | species | bacteria | bacteria | 28128 |
| prevotella dentalis | 7 | species | bacteria | bacteria | 52227 |
| prevotella denticola | 18 | species | bacteria | bacteria | 28129 |
| prevotella disiens | 8 | species | bacteria | bacteria | 28130 |
| prevotella enoeca | 2 | species | bacteria | bacteria | 76123 |
| prevotella intermedia | 65 | species | bacteria | bacteria | 28131 |
| prevotella loescheii | 21 | species | bacteria | bacteria | 840 |
| prevotella melaninogenica | 28 | species | bacteria | bacteria | 28132 |
| prevotella nigrescens | 37 | species | bacteria | bacteria | 28133 |
| prevotella oralis | 18 | species | bacteria | bacteria | 28134 |
| prevotella oris | 13 | species | bacteria | bacteria | 28135 |
| prevotella oulorum | 4 | species | bacteria | bacteria | 28136 |
| prevotella ruminicola | 39 | species | bacteria | bacteria | 839 |
| prevotella veroralis | 7 | species | bacteria | bacteria | 28137 |
| procerovum calderoni | 1 | species | | helminths | |
| prohemistomum vivax | 1 | species | | helminths | |
| propionibacterium acnes | 77 | species | bacteria | bacteria | 1747 |
| propionibacterium avidum | 11 | species | bacteria | bacteria | 33010 |
| propionibacterium granulosum | 18 | species | bacteria | bacteria | 33011 |
| propionibacterium propionicum | 18 | species | bacteria | bacteria | 1750 |
| prosthodendrium molenkampi | 5 | species | | helminths | |
| proteus mirabilis | 80 | species | bacteria | bacteria | 584 |
| proteus penneri | 16 | species | bacteria | bacteria | 102862 |
| proteus vulgaris | 53 | species | bacteria | bacteria | 585 |
| prototheca wickerhamii | 26 | species | plants | | 3111 |
| prototheca zopfii | 23 | species | plants | | 3112 |
| providencia alcalifaciens | 15 | species | bacteria | bacteria | 126385 |
| providencia rettgeri | 31 | species | bacteria | bacteria | 587 |
| providencia stuartii | 41 | species | bacteria | bacteria | 588 |
| pseudamphistomum aethiopicum | -3 | species | | helminths | |
| pseudamphistomum truncatum | 5 | species | invertebrates | helminths | 524295 |
| pseudocowpox virus | 10 | species | viruses | viruses | 129726 |
| pseudomonas aeruginosa | 243 | species | bacteria | bacteria | 287 |
| pseudomonas alcaligenes | 25 | species | bacteria | bacteria | 43263 |
| pseudomonas fluorescens | 122 | species | bacteria | bacteria | 294 |
| pseudomonas pseudoalcaligenes | 41 | species | bacteria | bacteria | 330 |
| pseudomonas putida | 133 | species | bacteria | bacteria | 303 |
| pseudomonas stutzeri | 76 | species | bacteria | bacteria | 316 |
| pseudonocardia autotrophica | 10 | species | bacteria | bacteria | 2074 |
| pseudoramibacter alactolyticus | 13 | species | bacteria | bacteria | 113287 |
| pseudoterranova decipiens | 28 | species | invertebrates | helminths | 6271 |
| psilorchis hominis | -3 | species | | helminths | |
| psychrobacter phenylpyruvicus | 11 | species | bacteria | bacteria | 29432 |
| punta toro virus | 28 | species | viruses | viruses | 11587 |
| purpureocillium lilacinum | 30 | species | plants | fungi | 33203 |
| pygidiopsis summa | 4 | species | invertebrates | helminths | 104472 |
| pyramicocephalus anthocephalus | -3 | species | | helminths | |
| pyrenochaeta cava | 4 | species | plants | fungi | 798079 |
| pyrenochaeta unguis-hominis | 2 | species | plants | fungi | 555973 |
| pythium insidiosum | 26 | species | plants | | 114742 |
| quambalaria cyanescens | 7 | species | plants | fungi | 345902 |
| quaranfil virus | 3 | species | viruses | viruses | 688436 |
| rabies virus | 96 | species | viruses | viruses | 11292 |
| rahnella aquatilis | 21 | species | bacteria | bacteria | 34038 |
| raillietina celebensis | 2 | species | | helminths | |
| raillietina demerariensis | 1 | species | | helminths | |
| ralstonia pickettii | 44 | species | bacteria | bacteria | 329 |
| raoultella ornithinolytica | 8 | species | bacteria | bacteria | 54291 |
| reston ebolavirus | 9 | species | viruses | viruses | 186539 |
| retortamonas intestinalis | 1 | species | | protozoa | |
| rhabditis elongata | -3 | species | | helminths | |
| rhabditis inermis | -3 | species | | helminths | |
| rhabditis niellyi | -3 | species | | helminths | |
| rhabditis pellio | 5 | species | | helminths | |
| rhinocladiella aquaspersa | 6 | species | plants | fungi | 37936 |
| rhinocladiella obovoidea | -3 | species | | fungi | |
| rhinocladiella schulzeri | 1 | species | | fungi | |
| rhinosporidium seeberi | 14 | species | invertebrates | | 90339 |
| rhinovirus a | 7 | species | viruses | viruses | 147711 |
| rhinovirus b | 8 | species | viruses | viruses | 147712 |
| rhizomucor miehei | 59 | species | plants | fungi | 4839 |
| rhizomucor pusillus | 30 | species | plants | fungi | 4840 |
| rhizopus azygosporus | 5 | species | plants | fungi | 86630 |
| rhizopus microsporus | 25 | species | plants | fungi | 58291 |
| rhizopus oryzae | 86 | species | plants | fungi | 64495 |
| rhizopus stolonifer | 43 | species | plants | fungi | 4846 |
| rhodococcus equi | 50 | species | bacteria | bacteria | 43767 |
| rhodococcus erythropolis | 53 | species | bacteria | bacteria | 1833 |
| rhodococcus fascians | 28 | species | bacteria | bacteria | 1828 |
| rhodococcus rhodnii | 9 | species | bacteria | bacteria | 38312 |
| rhodococcus rhodochrous | 57 | species | bacteria | bacteria | 1829 |
| rhodotorula glutinis | 38 | species | plants | fungi | 5535 |
| rhodotorula mucilaginosa | 30 | species | plants | fungi | 5537 |
| rickettsia africae | 20 | species | bacteria | bacteria | 35788 |
| rickettsia akari | 26 | species | bacteria | bacteria | 786 |
| rickettsia australis | 17 | species | bacteria | bacteria | 787 |
| rickettsia conorii | 40 | species | bacteria | bacteria | 781 |
| rickettsia felis | 29 | species | bacteria | bacteria | 42862 |
| rickettsia honei | 12 | species | bacteria | bacteria | 37816 |
| rickettsia japonica | 14 | species | bacteria | bacteria | 35790 |
| rickettsia massiliae | 16 | species | bacteria | bacteria | 35791 |
| rickettsia prowazekii | 51 | species | bacteria | bacteria | 782 |
| rickettsia rickettsii | 53 | species | bacteria | bacteria | 783 |
| rickettsia sibirica | 14 | species | bacteria | bacteria | 35793 |
| rickettsia typhi | 36 | species | bacteria | bacteria | 785 |
| rictularia | 5 | genus | | | |
| rift valley fever virus | 41 | species | viruses | viruses | 11588 |
| rio bravo virus | 2 | species | viruses | viruses | 64285 |