| saccharibacter | 5 | genus | bacteria | | 231052 |
| saccharibacillus | 1 | genus | bacteria | | 456492 |
| runella | 5 | genus | bacteria | | 105 |
| rummeliibacillus | 1 | genus | bacteria | | 648802 |
| ruminofilibacter | 1 | genus | bacteria | | 340117 |
| ruminococcus flavefaciens | 44 | species | bacteria | bacteria | 1265 |
| ruminococcus | 58 | genus | bacteria | | 1263 |
| ruminobacter | 13 | genus | bacteria | | 866 |
| ruminobacillus | -3 | genus | bacteria | | 344734 |
| ruegeria | 23 | genus | bacteria | | 97050 |
| rudanella | 2 | genus | bacteria | | 451373 |
| rubrobacter | 17 | genus | bacteria | | 42255 |
| rubrivivax | 26 | genus | bacteria | | 28067 |
| rubritepida | 1 | genus | bacteria | | 182402 |
| rubritalea | 5 | genus | bacteria | | 361050 |
| rubrimonas | 2 | genus | bacteria | | 89523 |
| rubidibacter | 1 | genus | bacteria | | 582491 |
| rubellimicrobium | 2 | genus | bacteria | | 295418 |
| ruania | 2 | genus | bacteria | | 626119 |
| rothia mucilaginosa | 19 | species | bacteria | bacteria | 43675 |
| rothia dentocariosa | 19 | species | bacteria | bacteria | 2047 |
| roseospirillum | 4 | genus | bacteria | | 83400 |
| roseospira | 4 | genus | bacteria | | 86671 |
| roseococcus | 9 | genus | bacteria | | 35812 |
| roseobacter | 50 | genus | bacteria | | 2433 |
| roseivivax | 6 | genus | bacteria | | 93682 |
| roseivirga | 4 | genus | bacteria | | 290180 |
| roseisalinus | 3 | genus | bacteria | | 289239 |
| roseinatronobacter | 3 | genus | bacteria | | 121820 |
| roseiflexus | 10 | genus | bacteria | | 120961 |
| roseicyclus | 1 | genus | bacteria | | 336277 |
| roseibium | 5 | genus | bacteria | | 150830 |
| roseibacterium | 1 | genus | bacteria | | 159345 |
| roseibacillus | 1 | genus | bacteria | | 518755 |
| roseburia inulinivorans dsm 16841 | 1 | no rank | bacteria | bacteria | 622312 |
| roseburia intestinalis xb6b4 | 1 | no rank | bacteria | bacteria | 718255 |
| roseburia | 23 | genus | bacteria | | 841 |
| roseateles | 7 | genus | bacteria | | 93681 |
| ronia | 1 | genus | | | |
| robinsoniella | 1 | genus | bacteria | | 588605 |
| robiginitomaculum | 2 | genus | bacteria | | 437506 |
| robiginitalea | 3 | genus | bacteria | | 252306 |
| rivularia | 16 | genus | bacteria | | 373984 |
| rikenella | 8 | genus | bacteria | | 28138 |
| richelia | 18 | genus | bacteria | | 98443 |
| rhodovulum | 22 | genus | bacteria | | 34008 |
| rhodovibrio | 2 | genus | bacteria | | 85274 |
| rhodovastum | 1 | genus | bacteria | | 504465 |
| rhodovarius | 1 | genus | bacteria | | 268408 |
| rhodothermus | 32 | genus | bacteria | | 29548 |
| rhodothalassium | 2 | genus | bacteria | | 85273 |
| rhodospirillum | 96 | genus | bacteria | | 1081 |
| rhodospira | 3 | genus | bacteria | | 69959 |
| rhodopseudomonas | 150 | genus | bacteria | | 1073 |
| rhodoplanes | 4 | genus | bacteria | | 29407 |
| rhodopirellula | 12 | genus | bacteria | | 265488 |
| rhodopila | 12 | genus | bacteria | | 1070 |
| rhodonellum | 2 | genus | bacteria | | 336827 |
| rhodomicrobium | 19 | genus | bacteria | | 1068 |
| rhodoluna | 1 | genus | bacteria | | 529883 |
| rhodoglobus | 3 | genus | bacteria | | 193383 |
| rhodoferax | 25 | genus | bacteria | | 28065 |
| rhodocytophaga | 1 | genus | bacteria | | 455076 |
| rhodocyclus | 35 | genus | bacteria | | 1064 |
| rhodocista | 8 | genus | bacteria | | 34023 |
| rhodoblastus | 5 | genus | bacteria | | 168658 |
| rhodobium | 12 | genus | bacteria | | 34016 |
| rhodobacter | 151 | genus | bacteria | | 1060 |
| rhodobaca | 4 | genus | bacteria | | 119541 |
| rhodanobacter | 10 | genus | bacteria | | 75309 |
| rhinocladiella basitona | 2 | species | plants | fungi | 215248 |
| rheinheimera | 8 | genus | bacteria | | 67575 |
| rhabdoderma | 3 | genus | bacteria | | 262065 |
| rhabdochromatium | 2 | genus | bacteria | | 48728 |
| rhabditis macrocerca | -3 | species | | helminths | |
| rhabditis gingivalis | -3 | species | | helminths | |
| rhabditis clavopapillata | -3 | species | | helminths | |
| rhabditis axei | 1 | species | | helminths | |
| rexia | 2 | genus | bacteria | | 262901 |
| retortamonas sinensis | -3 | species | | protozoa | |
| retortamonas ovis | -3 | species | | protozoa | |
| retortamonas cuniculi | -3 | species | | protozoa | |
| retortamonas caviae | -3 | species | | protozoa | |
| reinekea | 2 | genus | bacteria | | 230494 |
| reichenowia | 2 | genus | bacteria | | 237321 |
| reichenbachiella | 4 | genus | bacteria | | 156993 |
| rasamsonia argillacea | 3 | species | plants | fungi | 69808 |
| rarobacter | 9 | genus | bacteria | | 13242 |
| rapidithrix | 3 | genus | bacteria | | 413963 |
| raphidiopsis | 12 | genus | bacteria | | 244599 |
| raoultella terrigena | 16 | species | bacteria | bacteria | 577 |
| raoultella | 11 | genus | bacteria | | 160674 |
| ramlibacter | 5 | genus | bacteria | | 174951 |
| raillietina williamsi | 1 | species | | helminths | |
| raillietina ransomi | -3 | species | | helminths | |
| raillietina micracantha | 2 | species | invertebrates | helminths | 227345 |
| raillietina magninumida | -3 | species | | helminths | |
| raillietina georgiensis | 2 | species | | helminths | |
| raillietina cesticillus | 12 | species | | helminths | 246978 |
| raillietia hopkinsi | -3 | species | | | |