| rhodoblastus | 5 | genus | bacteria | | 168658 |
| rhodocista | 8 | genus | bacteria | | 34023 |
| rhodocyclus | 35 | genus | bacteria | | 1064 |
| rhodocytophaga | 1 | genus | bacteria | | 455076 |
| rhodoferax | 25 | genus | bacteria | | 28065 |
| rhodoglobus | 3 | genus | bacteria | | 193383 |
| rhodoluna | 1 | genus | bacteria | | 529883 |
| rhodomicrobium | 19 | genus | bacteria | | 1068 |
| rhodonellum | 2 | genus | bacteria | | 336827 |
| rhodopila | 12 | genus | bacteria | | 1070 |
| rhodopirellula | 12 | genus | bacteria | | 265488 |
| rhodoplanes | 4 | genus | bacteria | | 29407 |
| rhodopseudomonas | 150 | genus | bacteria | | 1073 |
| rhodospira | 3 | genus | bacteria | | 69959 |
| rhodospirillum | 96 | genus | bacteria | | 1081 |
| rhodothalassium | 2 | genus | bacteria | | 85273 |
| rhodothermus | 32 | genus | bacteria | | 29548 |
| rhodovarius | 1 | genus | bacteria | | 268408 |
| rhodovastum | 1 | genus | bacteria | | 504465 |
| rhodovibrio | 2 | genus | bacteria | | 85274 |
| rhodovulum | 22 | genus | bacteria | | 34008 |
| richelia | 18 | genus | bacteria | | 98443 |
| rikenella | 8 | genus | bacteria | | 28138 |
| rivularia | 16 | genus | bacteria | | 373984 |
| robiginitalea | 3 | genus | bacteria | | 252306 |
| robiginitomaculum | 2 | genus | bacteria | | 437506 |
| robinsoniella | 1 | genus | bacteria | | 588605 |
| ronia | 1 | genus | | | |
| roseateles | 7 | genus | bacteria | | 93681 |
| roseburia | 23 | genus | bacteria | | 841 |
| roseburia intestinalis xb6b4 | 1 | no rank | bacteria | bacteria | 718255 |
| roseburia inulinivorans dsm 16841 | 1 | no rank | bacteria | bacteria | 622312 |
| roseibacillus | 1 | genus | bacteria | | 518755 |
| roseibacterium | 1 | genus | bacteria | | 159345 |
| roseibium | 5 | genus | bacteria | | 150830 |
| roseicyclus | 1 | genus | bacteria | | 336277 |
| roseiflexus | 10 | genus | bacteria | | 120961 |
| roseinatronobacter | 3 | genus | bacteria | | 121820 |
| roseisalinus | 3 | genus | bacteria | | 289239 |
| roseivirga | 4 | genus | bacteria | | 290180 |
| roseivivax | 6 | genus | bacteria | | 93682 |
| roseobacter | 50 | genus | bacteria | | 2433 |
| roseococcus | 9 | genus | bacteria | | 35812 |
| roseospira | 4 | genus | bacteria | | 86671 |
| roseospirillum | 4 | genus | bacteria | | 83400 |
| rothia dentocariosa | 19 | species | bacteria | bacteria | 2047 |
| rothia mucilaginosa | 19 | species | bacteria | bacteria | 43675 |
| ruania | 2 | genus | bacteria | | 626119 |
| rubellimicrobium | 2 | genus | bacteria | | 295418 |
| rubidibacter | 1 | genus | bacteria | | 582491 |
| rubrimonas | 2 | genus | bacteria | | 89523 |
| rubritalea | 5 | genus | bacteria | | 361050 |
| rubritepida | 1 | genus | bacteria | | 182402 |
| rubrivivax | 26 | genus | bacteria | | 28067 |
| rubrobacter | 17 | genus | bacteria | | 42255 |
| rudanella | 2 | genus | bacteria | | 451373 |
| ruegeria | 23 | genus | bacteria | | 97050 |
| ruminobacillus | -3 | genus | bacteria | | 344734 |
| ruminobacter | 13 | genus | bacteria | | 866 |
| ruminococcus | 58 | genus | bacteria | | 1263 |
| ruminococcus flavefaciens | 44 | species | bacteria | bacteria | 1265 |
| ruminofilibacter | 1 | genus | bacteria | | 340117 |
| rummeliibacillus | 1 | genus | bacteria | | 648802 |
| runella | 5 | genus | bacteria | | 105 |
| saccharibacillus | 1 | genus | bacteria | | 456492 |
| saccharibacter | 5 | genus | bacteria | | 231052 |
| saccharococcus | 14 | genus | bacteria | | 29395 |
| saccharomonospora | 15 | genus | bacteria | | 1851 |
| saccharophagus | 8 | genus | bacteria | | 316625 |
| saccharospirillum | 3 | genus | bacteria | | 231683 |
| saccharothrix | 26 | genus | bacteria | | 2071 |
| saccharothrixopsis | -3 | genus | bacteria | | 104593 |
| sagittula | 10 | genus | bacteria | | 58842 |
| salana | 3 | genus | bacteria | | 120376 |
| salegentibacter | 7 | genus | bacteria | | 143222 |
| salibacter | -3 | genus | bacteria | | 444513 |
| salicola | 3 | genus | bacteria | | 332339 |
| salimicrobium | 1 | genus | bacteria | | 351195 |
| salinibacillus | 3 | genus | bacteria | | 320933 |
| salinibacter | 19 | genus | bacteria | | 146918 |
| salinibacterium | 3 | genus | bacteria | | 235888 |
| salinicoccus | 13 | genus | bacteria | | 45669 |
| salinicola | 5 | genus | bacteria | | 404432 |
| salinimicrobium | 2 | genus | bacteria | | 561367 |
| salinimonas | 2 | genus | bacteria | | 288793 |
| salinisphaera | 3 | genus | bacteria | | 180541 |
| salinispora | 30 | genus | bacteria | | 168694 |
| salinivibrio | 10 | genus | bacteria | | 51366 |
| salipiger | 5 | genus | bacteria | | 263377 |
| salirhabdus | 1 | genus | bacteria | | 394505 |
| salsuginibacillus | 1 | genus | bacteria | | 427077 |
| samsonia | 2 | genus | bacteria | | 160433 |
| sandaracinobacter | 8 | genus | bacteria | | 56358 |
| sandarakinorhabdus | 1 | genus | bacteria | | 362865 |
| sandarakinotalea | 1 | genus | bacteria | | 319234 |
| saprospira | 18 | genus | bacteria | | 1007 |
| sarcina | 30 | genus | bacteria | | 1266 |
| sarcocystis bertrami | 1 | species | | protozoa | |
| sarcocystis cuniculi | 2 | species | | protozoa | |
| sarcocystis fayeri | 5 | species | | protozoa | 1073925 |