| marihabitans | 1 | genus | bacteria | | 568214 |
| marichromatium | 8 | genus | bacteria | | 85076 |
| maricaulis | 7 | genus | bacteria | | 74317 |
| maribius | 1 | genus | bacteria | | 387095 |
| maribacter | 4 | genus | bacteria | | 252356 |
| margalefia | 1 | genus | bacteria | | 306266 |
| mangrovibacter | 1 | genus | bacteria | | 451512 |
| mandrillus sphinx foamy virus | -3 | no rank | viruses | viruses | 288117 |
| mammalian orthoreovirus 1 | 25 | no rank | viruses | viruses | 538120 |
| malonomonas | 10 | genus | bacteria | | 57039 |
| malikia | 1 | genus | bacteria | | 263066 |
| mahella | 1 | genus | bacteria | | 252965 |
| magnetospirillum | 39 | genus | bacteria | | 13134 |
| magnetococcus | 10 | genus | bacteria | | 162171 |
| macromonas | 2 | genus | bacteria | | 183669 |
| macrococcus | 9 | genus | bacteria | | 69965 |
| lysobacter | 24 | genus | bacteria | | 68 |
| lysinibacillus | 4 | genus | bacteria | | 400634 |
| lyngbya | 65 | genus | bacteria | | 28073 |
| lutimonas | 2 | genus | bacteria | | 449810 |
| lutimaribacter | 1 | genus | bacteria | | 490828 |
| lutiella | -3 | genus | bacteria | | 549168 |
| lutibacterium | 2 | genus | bacteria | | 179836 |
| lutibacter | 3 | genus | bacteria | | 358023 |
| luteolibacter | 1 | genus | bacteria | | 518753 |
| luteococcus | 6 | genus | bacteria | | 33983 |
| luteimonas | 4 | genus | bacteria | | 83614 |
| luteibacter | 6 | genus | bacteria | | 242605 |
| lutaonella | 1 | genus | bacteria | | 488548 |
| luedemannella | 1 | genus | bacteria | | 349314 |
| longispora | 10 | genus | bacteria | | 203522 |
| longilinea | 2 | genus | bacteria | | 475961 |
| lonepinella | 3 | genus | bacteria | | 53416 |
| loktanella | 9 | genus | bacteria | | 245186 |
| litoricola | 4 | genus | bacteria | | 418700 |
| listeria innocua | 58 | species | bacteria | bacteria | 1642 |
| lishizhenia | 1 | genus | bacteria | | 559293 |
| linmingia | 1 | genus | bacteria | | 188918 |
| limnothrix | 20 | genus | bacteria | | 132605 |
| limnobacter | 4 | genus | bacteria | | 131079 |
| limibacter | 1 | genus | bacteria | | 518746 |
| lichtheimia ramosa | 2 | species | plants | fungi | 688394 |
| lewinella | 3 | genus | bacteria | | 70994 |
| levilinea | 3 | genus | bacteria | | 475965 |
| leucothrix | 15 | genus | bacteria | | 45247 |
| leuconostoc fallax | 10 | species | bacteria | bacteria | 1251 |
| leuconostoc citreum | 21 | species | bacteria | bacteria | 33964 |
| leuconostoc | 89 | genus | bacteria | | 1243 |
| leptothrix | 41 | genus | bacteria | | 88 |
| leptospirillum | 49 | genus | bacteria | | 179 |
| leptonema | 20 | genus | bacteria | | 32205 |
| leptomonas | 32 | genus | invertebrates | | 5683 |
| leptolyngbya | 19 | genus | bacteria | | 47251 |
| leptolinea | 2 | genus | bacteria | | 475966 |
| leptobacterium | 1 | genus | bacteria | | 472054 |
| lentzea | 8 | genus | bacteria | | 165301 |
| lentisphaera | 2 | genus | bacteria | | 256846 |
| lentimonas | -3 | genus | bacteria | | 417293 |
| lentibacillus | 8 | genus | bacteria | | 175304 |
| leisingera | 5 | genus | bacteria | | 191028 |
| leiperenia leiperi | -3 | species | | helminths | |
| leiperenia galebi | -3 | species | | helminths | |
| leeuwenhoekiella | 2 | genus | bacteria | | 283735 |
| leeia | 1 | genus | bacteria | | 650341 |
| lechevalieria | 15 | genus | bacteria | | 166974 |
| lebetimonas | 1 | genus | bacteria | | 267989 |
| leahibacter | -3 | genus | bacteria | | 197884 |
| leadbetterella | 1 | genus | bacteria | | 319458 |
| lautropia | 4 | genus | bacteria | | 47670 |
| larkinella | 2 | genus | bacteria | | 332157 |
| lapillicoccus | 2 | genus | bacteria | | 402170 |
| lampropedia | 9 | genus | bacteria | | 198705 |
| lamprocystis | 9 | genus | bacteria | | 53452 |
| laminosioptes cysticola | 2 | species | | | |
| lactonifactor | 1 | genus | bacteria | | 420345 |
| lactococcus lactis | 120 | species | bacteria | bacteria | 1358 |
| lactobacillus salivarius | 36 | species | bacteria | bacteria | 1624 |
| lactobacillus rhamnosus | 71 | species | bacteria | bacteria | 47715 |
| lactobacillus plantarum | 92 | species | bacteria | bacteria | 1590 |
| lactobacillus paracasei | 44 | species | bacteria | bacteria | 1597 |
| lactobacillus oris | 7 | species | bacteria | bacteria | 1632 |
| lactobacillus mucosae | 9 | species | bacteria | bacteria | 97478 |
| lactobacillus jensenii | 14 | species | bacteria | bacteria | 109790 |
| lactobacillus iners | 10 | species | bacteria | bacteria | 147802 |
| lactobacillus helveticus | 64 | species | bacteria | bacteria | 1587 |
| lactobacillus gasseri | 37 | species | bacteria | bacteria | 1596 |
| lactobacillus fermentum | 47 | species | bacteria | bacteria | 1613 |
| lactobacillus crispatus | 27 | species | bacteria | bacteria | 47770 |
| lactobacillus casei | 97 | species | bacteria | bacteria | 1582 |
| lactobacillus acidophilus | 95 | species | bacteria | bacteria | 1579 |
| lacticigenium | 1 | genus | bacteria | | 633405 |
| lacinutrix | 2 | genus | bacteria | | 291183 |
| lacibacter | 1 | genus | bacteria | | 649461 |
| lachnospira | 13 | genus | bacteria | | 28050 |
| lachnobacterium | 1 | genus | bacteria | | 140625 |
| laceyella | 3 | genus | bacteria | | 292635 |
| labrys | 6 | genus | bacteria | | 204476 |
| labrenzia | 1 | genus | bacteria | | 478070 |
| labedella | 1 | genus | bacteria | | 390250 |
| kutzneria | 6 | genus | bacteria | | 43356 |