| Origin | Code | Comment | Supplementary Taxo |
|---|
| Macrococcus canis | ISMaca | | |
| Magasanikbacteria bacterium | ISMaba | | Candidatus Magasanikbacteria bacterium |
| Magnetococcus marinus | ISMama | | |
| Magnetococcus sp. | ISMasp | | |
| Magnetoglobus multicellularis | ISMamu | | Candidatus Magnetoglobus multicellularis |
| Magnetomorum sp. | ISMags | | Candidatus Magnetomorum sp. |
| Magnetospirillum gryphiswaldense | ISMgr | | |
| Magnetospirillum magneticum | ISMamg | | |
| Magnetospirillum magnetotacticum | ISMmg | | |
| Magnetospirillum moscoviense | ISMmo | | |
| Magnetovibrio blakemorei | ISMbl | | |
| Mahella australiensis | ISMaau | | |
| Mannheimia haemolytica | ISMha | | |
| Marine actinobacterium | ISMaa | | |
| Marine psychrotrophic bacterium | ISMps | | |
| Marinobacter aquaeolei | ISMaq | | |
| Marinobacter hydrocarbonoclasticus | ISMahy | | |
| Marinobacter salarius | ISMsa | | |
| Marinobacter salinus | ISMasa | | |
| Marinobacter sp. | ISMrsp | | |
| Marinomonas sp. | ISMisp | | |
| Marinomonas spartinae | ISMspa | | |
| Marinospirillum insulare | ISMain | | |
| Mariprofundus ferrooxydans | ISMafe | | |
| Massilia sp | ISMass | | |
| Massilimicrobiota sp. | ISMssp | | |
| Meiothermus silvanus | ISMesi | | |
| Melainabacteria bacterium | ISMeba | | Candidatus Melainabacteria bacterium |
| Mesorhizobium alhagi | ISMal | | |
| Mesorhizobium loti | ISMlo | | |
| Mesorhizobium metallidurans | ISMme | | |
| Mesorhizobium sp. | ISMesp | | |
| Metagenomic data from CARNOULES | ISCAR | | |
| Metagenomic data from Diamante Lake | ISDIAL | Plasmidome from a microbial community of Diamante Lake | |
| Metallosphaera yellowstonensis | ISMye | | |
| Methanobacterium formicicum | ISMefo | | |
| Methanobrevibacter millerae | ISMmi | | |
| Methanobrevibacter ruminantium | ISMru | | |
| Methanobrevibacter smithii | ISMesm | | |
| Methanocaldococcus jannaschii | ISMja | | |
| Methanocella conradii | ISMeco | | |
| Methanococcoïdes burtonii | ISMbu | | |
| Methanococcoides methylutens | ISMeme | | |
| Methanoculleus bourgensis | ISMebo | | |
| Methanohalobium evestigatum | ISMev | | |
| Methanohalophilus mahii | ISMem | | |
| Methanolinea tarda | ISMta | | |
| Methanoperedens sp. | ISMeth | | |
| Methanoplasma termitum | ISMte | | |
| Methanosaeta concilii | ISMco | | |
| Methanosaeta thermophila | ISMth | | |
| Methanosarcina acetivorans | ISMac | | |
| Methanosarcina barkeri | ISMba | | |
| Methanosarcina mazei | ISMma | | |
| Methanosarcina sp. | ISMets | | |
| Methanosarcina vacuolata | ISMeva | | |
| Methanosphaera stadtmanae | ISMst | | |
| Methanosphaerula palustris | ISMepa | | |
| Methanospirillum hungatei | ISMhu | | |
| Methanotorris igneus | ISMig | | |
| Methylibium petroleiphilum | ISMpe | | |
| Methylobacter tundripaludum | ISMetu | | |
| Methylobacterium chloromethanicum | ISMch | | |
| Methylobacterium dichloromethanicum | ISMdi | | |
| Methylobacterium extorquens | ISMex | | |
| Methylobacterium nodulans | ISMno | | |
| Methylobacterium phyllosphaerae | ISMph | | |
| Methylobacterium populi | ISMpo | | |
| Methylobacterium radiotolerans | ISMra | | |
| Methylobacterium sp. | ISMtsp | | |
| Methylocaldum szegediense | ISMsz | | |
| Methylocella silvestris | ISMsi | | |
| Methylococcus capsulatus | ISMca | | |
| Methylocystis sp. | ISMet | | |
| Methyloglobulus morosus | ISMemo | | |
| Methylomicrobium alcaliphilum | ISMeal | | |
| Methylomonas koyamae | ISMko | | |
| Methylomonas methanica | ISMmet | | |
| Methylosinus sp. | ISMetp1 | | |
| Micrococcus luteus | ISMlu | | |
| Micrococcus terreus | ISMcte | | |
| Microcoleus chthonoplastes | ISMich | | |
| Microcoleus sp. | ISMic | | |
| Microcoleus vaginatus | ISMiva | | |
| Microcystis aeruginosa | ISMae | | |
| Micromonospora aurantiaca | ISMau | | |
| Micromonospora sp. | ISMicsp | | |
| Microscilla sp. | ISMsp | | |
| Microthrix parvicella | ISMipa | | |
| Mimivirus | ISvMimi | | |
| Mitsuokella multacida | ISMmu | | |
| Moorea producens | ISMpr | | |
| Moorella mulderi | ISMomu | | |
| Moorella thermoacetica | ISMoth | | |
| Moraxella bovis | ISMobo | | |
| Moraxella bovoculi | ISMobv | | |
| Moraxella lacunata | ISMla | | |
| Moraxella ovis | ISMov | | |
| Morganella morganii | ISMomo | | |
| Moritella viscosa | ISMvi | | |
| Mucilaginibacter rubuse | ISMuru | | |
| Mycobacterium abscessus | ISMab | | |
| Mycobacterium avium | ISMav | | |
| Mycobacterium bovis | ISMbo | | |
| Mycobacterium branderi | ISMbr | | |
| Mycobacterium canettii | ISMyca | | |
| Mycobacterium celatum | ISMce | | |
| Mycobacterium flavescens | ISMfl | | |
| Mycobacterium fortuitum | ISMfo | | |
| Mycobacterium gilvum | ISMgi | | |
| Mycobacterium hyopneumoniae | ISMhp | | |
| Mycobacterium indicus | ISMyin | | |
| Mycobacterium intracellulare | ISMin | | |
| Mycobacterium kansasii | ISMka | | |
| Mycobacterium marinum | ISMyma | | |
| Mycobacterium paratuberculosis | ISMpa | | |
| Mycobacterium rhodesiae | ISMrh | | |
| Mycobacterium scrofulaceum | ISMsc | | |
| Mycobacterium smegmatis | ISMsm | | |
| Mycobacterium sp. | ISMysp | | |
| Mycobacterium tuberculosis | ISMt | Predefined common nomenclature | |
| Mycobacterium tusciae | ISMtu | | |
| Mycobacterium ulcerans | ISMul | | |
| Mycobacterium vanbaalenii | ISMva | | |
| Mycobacterium xenopi | ISMxe | | |
| Mycobacterium yongonense | ISMyo | | |
| Mycolicibacterium psychrotolerans | ISMyps | | |
| Mycoplasma agalactiae | ISMag | | |
| Mycoplasma arginini | ISMar | | |
| Mycoplasma bovis | ISMbov | | |
| Mycoplasma fermentans | ISMfe | | |
| Mycoplasma hyopneumoniae | ISMhp | | |
| Mycoplasma hyorhinis | ISMhy | | |
| Mycoplasma incognitus | ISMyin | | |
| Mycoplasma mycoides | ISMmy | | |
| Mycoplasma pulmonis | ISMpu | | |
| Mycoplasma synoviae | ISMsy | | |
| Myroides odoratimimus | ISMod | | |
| Myroides sp. | ISMyr | | |
| Myxococcales bacterium | ISMyba | | |
| Myxococcus fulvus | ISMfu | | |
| Myxococcus xanthus | ISMxa | | |