| modestobacter | 5 | genus | bacteria | | 88138 |
| modicisalibacter | 3 | genus | bacteria | | 574347 |
| moellerella | 6 | genus | bacteria | | 158848 |
| mogibacterium | 9 | genus | bacteria | | 86331 |
| mojavia | 5 | genus | bacteria | | 287846 |
| monocercomonas caviae | -3 | species | | protozoa | |
| monocercomonas cuniculi | -3 | species | | protozoa | |
| monocercomonas gallinarum | -3 | species | | protozoa | |
| monocercomonas minuta | -3 | species | | protozoa | |
| monocercomonas pistillum | -3 | species | | protozoa | |
| monocercomonas ruminantium | 1 | species | | protozoa | |
| moorella | 23 | genus | bacteria | | 44260 |
| morococcus | 2 | genus | | | 212742 |
| moryella | 1 | genus | bacteria | | 437755 |
| mucilaginibacter | 3 | genus | bacteria | | 423349 |
| mucispirillum | 2 | genus | bacteria | | 248038 |
| muricauda | 4 | genus | bacteria | | 111500 |
| murid herpesvirus 1 | 105 | species | viruses | viruses | 10366 |
| murid herpesvirus 2 | 28 | species | viruses | viruses | 28304 |
| myceligenerans | 2 | genus | bacteria | | 253183 |
| mycetocola | 3 | genus | bacteria | | 76634 |
| mycobacterium arupense | 4 | species | bacteria | bacteria | 342002 |
| mycobacterium austroafricanum | 16 | species | bacteria | bacteria | 39687 |
| mycobacterium colombiense | 4 | species | bacteria | bacteria | 339268 |
| mycobacterium conceptionense | 2 | species | bacteria | bacteria | 451644 |
| mycobacterium cookii | 4 | species | bacteria | bacteria | 1775 |
| mycobacterium elephantis | 2 | species | bacteria | bacteria | 81858 |
| mycobacterium flavescens | 12 | species | bacteria | bacteria | 1776 |
| mycobacterium insubricum | 1 | species | bacteria | bacteria | 444597 |
| mycobacterium mantenii | 1 | species | bacteria | bacteria | 560555 |
| mycobacterium monacense | 3 | species | bacteria | bacteria | 85693 |
| mycobacterium noviomagense | 1 | species | bacteria | bacteria | 459858 |
| mycobacterium parascrofulaceum | 3 | species | bacteria | bacteria | 240125 |
| mycobacterium paraseoulense | 1 | species | bacteria | bacteria | 590652 |
| mycobacterium senuense | 1 | species | bacteria | bacteria | 386913 |
| mycobacterium seoulense | 1 | species | bacteria | bacteria | 386911 |
| mycobacterium sherrisii | 3 | species | bacteria | bacteria | 243061 |
| mycobacterium terrae | 20 | species | bacteria | bacteria | 1788 |
| mycobacterium tilburgii | 1 | species | bacteria | bacteria | 44467 |
| mycobacterium vulneris | 1 | species | bacteria | bacteria | 547163 |
| mycoplana | 15 | genus | bacteria | | 13159 |
| mycoplasma coccoides | 14 | species | bacteria | bacteria | 220926 |
| mycoplasma haemomuris | 10 | species | bacteria | bacteria | 55966 |
| mycoplasma ovis | 10 | species | bacteria | bacteria | 171632 |
| mycoplasma parvum | 2 | species | bacteria | bacteria | 984991 |
| mycoplasma wenyonii | 8 | species | bacteria | bacteria | 65123 |
| myrmecridium schulzeri | 1 | species | plants | fungi | 470091 |
| myxobacter | 14 | genus | bacteria | | 107830 |
| myxosarcina | 8 | genus | bacteria | | 52605 |
| nakamurella | 13 | genus | bacteria | | 53460 |
| nannocystis | 14 | genus | bacteria | | 53 |
| nanoarchaeum | 20 | genus | bacteria | | 193568 |
| nanobacterium | 6 | genus | bacteria | | 53023 |
| natranaerobius | 4 | genus | bacteria | | 375928 |
| natrialba | 17 | genus | bacteria | | 63742 |
| natrinema | 11 | genus | bacteria | | 88723 |
| natroniella | 3 | genus | bacteria | | 52003 |
| natronincola | 3 | genus | bacteria | | 89958 |
| natronoanaerobium | 1 | genus | bacteria | | 114261 |
| natronobacillus | 1 | genus | bacteria | | 472977 |
| natronobacterium | 49 | genus | bacteria | | 2256 |
| natronocella | 1 | genus | bacteria | | 414045 |
| natronococcus | 18 | genus | bacteria | | 29287 |
| natronohydrobacter | -3 | genus | bacteria | | 87171 |
| natronolimnobius | 3 | genus | bacteria | | 253106 |
| natronomonas | 20 | genus | bacteria | | 63743 |
| natronorubrum | 5 | genus | bacteria | | 134813 |
| nautella | 1 | genus | bacteria | | 481445 |
| nautilia | 6 | genus | bacteria | | 191291 |
| naxibacter | 3 | genus | bacteria | | 286637 |
| neoasaia | 4 | genus | bacteria | | 320496 |
| neocatenulostroma abietis | 7 | species | plants | fungi | 1434218 |
| neochlamydia | 11 | genus | bacteria | | 112987 |
| neoscytalidium dimidiatum | 13 | species | plants | fungi | 108428 |
| neptuniibacter | 2 | genus | bacteria | | 459520 |
| neptunomonas | 7 | genus | bacteria | | 75687 |
| nereida | 3 | genus | bacteria | | 282198 |
| nesiotobacter | 1 | genus | bacteria | | 500577 |
| nesterenkonia | 11 | genus | bacteria | | 57494 |
| neurospora sitophila | 11 | species | plants | fungi | 40126 |
| nevskia | 8 | genus | bacteria | | 64001 |
| niabella | 3 | genus | bacteria | | 379899 |
| niastella | 4 | genus | bacteria | | 354354 |
| nicoletella | 2 | genus | bacteria | | 271159 |
| nisaea | 1 | genus | bacteria | | 390876 |
| nitratifractor | 1 | genus | bacteria | | 269260 |
| nitratireductor | 2 | genus | bacteria | | 245876 |
| nitratiruptor | 3 | genus | bacteria | | 269258 |
| nitriliruptor | 2 | genus | bacteria | | 596499 |
| nitrincola | 2 | genus | bacteria | | 267849 |
| nitrobacter | 54 | genus | bacteria | | 911 |
| nitrobacteria | 5 | genus | bacteria | | 267929 |
| nitrococcus | 8 | genus | bacteria | | 35796 |
| nitrosococcus | 31 | genus | bacteria | | 1227 |
| nitrosomonas | 92 | genus | bacteria | | 914 |
| nitrosopumilus | 11 | genus | bacteria | | 338191 |
| nitrososphaera | 3 | genus | bacteria | | 497726 |
| nitrosospira | 53 | genus | bacteria | | 35798 |
| nitrosovibrio | 10 | genus | bacteria | | 1232 |
| nitrospina | 9 | genus | bacteria | | 35800 |