| Rachicladosporium sp. | RD052025, RD052397, RD052727 |
| Radulidium sp. | RD051785 |
| Radulomyces sp. | RD010470, RD010474, RD010513 |
| Ragnhildiana sp. | RD052069 |
| Rahnella sp. | RD014420, RD014423, RD014424, RD014425, RD014426 |
| Ramicandelaber sp. | RD002555, RD002556, RD013427, RD013473, RD050162, RD069168, RD069169 |
| Ramichloridium sp. | RD052117, RD052483, RD052593, RD052659, RD052816, RD052843, RD054555, RD054576, RD054797, RD057871, RD058137, RD059078, RD060286 |
| Ramlibacter sp. | RD001728, RD001729 |
| Ramophialophora sp. | RD053457, RD053680, RD053917, RD058506, RD059281 |
| Ramularia sp. | RD003348, RD003383, RD053149, RD055918, RD056740, RD056904, RD057979, RD059263 |
| Raoultibacter sp. | RD014181, RD014912 |
| Rasamsonia sp. | RD015083, RD015084, RD015085, RD015086, RD015087, RD057267, RD059637 |
| Reinekea sp. | RD002588, RD002625, RD002717 |
| Remersonia sp. | RD015050, RD015051, RD015071 |
| Repetophragma sp. | RD051478, RD051479 |
| Resinicium sp. | RD057892, RD061162 |
| Reticulascus sp. | RD053141 |
| Rhamphoria sp. | RD052453, RD052487, RD053937 |
| Rhamphoriopsis sp. | RD003320 |
| Rheinheimera sp. | RD000138 |
| Rhexoacrodictys sp. | RD052075, RD052451, RD052510, RD054241 |
| Rhexocercosporidium sp. | RD052312, RD052340 |
| Rhexodenticula sp. | RD057829, RD060934 |
| Rhexothecium sp. | RD057410 |
| Rhinocladiella sp. | RD050588, RD051222, RD051955, RD052916, RD052923, RD057940 |
| Rhizobium sp. | RD000159, RD003567, RD003569, RD006346, RD006348, RD008761, RD011392, RD011397, RD011408, RD011411, RD011412, RD011423, RD011437, RD011452, RD012986, RD013351, RD013362, RD013372 |
| Rhizoctonia sp. | RD000502 |
| Rhizomucor sp. | RD011309, RD014154, RD015057, RD015058, RD015075, RD015123, RD015124, RD015125, RD015966, RD015976, RD015981, RD015982, RD015992, RD069088, RD069151 |
| Rhizopus sp. | RD012368, RD013421, RD013425, RD013426, RD013440, RD014144, RD015100, RD015126, RD015127, RD015975, RD015991, RD056082, RD056405, RD056864, RD057733, RD059830, RD059956 |
| Rhizoscyphus sp. | RD013246 |
| Rhizosphaera sp. | RD010054, RD058115 |
| Rhodanobacter sp. | RD000739, RD000744, RD000758, RD000759, RD000779, RD000795, RD000796, RD000798, RD000817, RD000818, RD000821, RD000828, RD000842, RD001746, RD001775, RD001776, RD001778, RD001784, RD001786, RD001787, RD001789, RD001791, RD001811, RD001812, RD001813, RD001818, RD001850, RD001893, RD002413, RD002442, RD002444, RD002456, RD004390, RD004391 |
| Rhodobacter sp. | RD002626 |
| Rhodoblastus sp. | RD000088 |
| Rhodococcus sp. | RD001249, RD002480, RD003100, RD003243, RD003954, RD004021, RD004063, RD004064, RD004065, RD004078, RD004080, RD004081, RD004107, RD004184, RD004192, RD004725, RD004839, RD005357, RD006118, RD006175, RD006177, RD007114, RD007455, RD007510, RD008836, RD008959, RD009038, RD010794, RD010849, RD010860, RD010875, RD010922, RD010999, RD011026, RD011078, RD011080, RD011110, RD011116, RD011135, RD011153, RD011223, RD011225, RD011387, RD012553, RD012609, RD012619, RD012624, RD012627, RD013323, RD013328, RD013329, RD013332, RD013333, RD013334, RD013335, RD013337, RD015140, RD015786, RD015794, RD015811, RD015812, RD054907, RD054909, RD054911, RD054982, RD055460, RD055502, RD055550, RD066212, RD066612, RD066613, RD066614, RD066615, RD066616, RD066617, RD066631, RD066632, RD066633, RD066635, RD066636, RD066637 |
| Rhodophyticola sp. | RD000144, RD002068 |
| Rhodosporidiobolus sp. | RD009903, RD051103 |
| Rhodotorula sp. | RD008842, RD008847, RD008882, RD011881, RD011891, RD011918, RD012207, RD012209, RD012460, RD012482, RD012488, RD012489, RD012495, RD012496, RD013271, RD015466, RD015471, RD015529, RD015533, RD050886, RD055019, RD055076 |
| Rhodoveronaea sp. | RD052785, RD052788, RD053172 |
| Rhopalostroma sp. | RD054585 |
| Rhytidhysteron sp. | RD053711 |
| Rigidoporus sp. | RD009310, RD010585, RD010586 |
| Robertkochia sp. | RD003089, RD003090 |
| Robillarda sp. | RD009906, RD050547, RD051905, RD051914, RD052733, RD054011, RD054048, RD054565, RD057335, RD057337, RD057752, RD057756, RD057817, RD058946, RD060499, RD060672 |
| Roseiarcus sp. | RD002418 |
| Roseivirga sp. | RD000636, RD000637, RD002635, RD003053 |
| Roseivivax sp. | RD003167 |
| Rosellinia sp. | RD000381, RD000382, RD000383, RD000384, RD001061, RD002266, RD015281, RD015292, RD015307, RD015326, RD057765, RD058656 |
| Roseobacter sp. | RD002013, RD002047, RD003483 |
| Roseomonas sp. | RD013349, RD016000, RD016001 |
| Roseovarius sp. | RD000898, RD002019, RD002751, RD002770, RD002773, RD003530 |
| Rothia sp. | RD012185, RD012470, RD012632, RD014593, RD014944, RD055490 |
| Roussoella sp. | RD003309, RD009112, RD009558, RD009615, RD009875, RD010142, RD053658, RD053967, RD055205 |
| Rouxiella sp. | RD014429 |
| Rubidimonas sp. | RD002806 |
| Rubneribacter sp. | RD014182, RD014183, RD014184 |
| Rubritepida sp. | RD003572 |
| Rubrivirga sp. | RD003137, RD003518, RD006380 |
| Rudaibacter sp. | RD001829 |
| Ruegeria sp. | RD000881, RD000890, RD001999, RD002000, RD002002, RD002003, RD002005, RD002008, RD002009, RD002010, RD002011, RD002012, RD002014, RD002023, RD002024, RD002046, RD002785, RD003490, RD003497, RD003500, RD003535, RD003536, RD003539, RD003547, RD003548, RD003549, RD003554, RD003557, RD003559, RD003561, RD006138, RD006141 |
| Rugamonas sp. | RD000812, RD001877 |
| Rugosimonospora sp. | RD001907 |
| Ruinenia sp. | RD051115 |
| Ruminococcus sp. | RD014898, RD014899, RD015179 |
| Rummeliibacillus sp. | RD013388 |
| Ruthenibacterium sp. | RD014228, RD014229, RD014230, RD014231 |
