| legionella maceachernii | 7 | species | bacteria | bacteria | 466 |
| legionella longbeachae | 16 | species | bacteria | bacteria | 450 |
| legionella lansingensis | 1 | species | bacteria | bacteria | 45067 |
| legionella jordanis | 7 | species | bacteria | bacteria | 456 |
| legionella hackeliae | 3 | species | bacteria | bacteria | 449 |
| legionella feeleii | 8 | species | bacteria | bacteria | 453 |
| legionella cincinnatiensis | 4 | species | bacteria | bacteria | 28085 |
| legionella cherrii | 1 | species | bacteria | bacteria | 28084 |
| legionella birminghamensis | 1 | species | bacteria | bacteria | 28083 |
| legionella anisa | 11 | species | bacteria | bacteria | 28082 |
| lechiguanas virus | 1 | no rank | viruses | viruses | 69245 |
| lebombo virus | -3 | species | | viruses | 40057 |
| lassa mammarenavirus | 41 | species | viruses | viruses | 11620 |
| lasiodiplodia theobromae | 20 | no rank | plants | fungi | 502207 |
| lanjan virus | 1 | species | | viruses | 1564119 |
| lagochilascaris minor | 8 | species | | helminths | 1783269 |
| lactobacillus sp. | 36 | species | bacteria | bacteria | 1591 |
| lachnoanaerobaculum saburreum | 14 | species | bacteria | bacteria | 467210 |
| kyasanur forest disease virus | 13 | species | viruses | viruses | 33743 |
| koutango virus | 3 | species | viruses | viruses | 44025 |
| kokobera virus | 4 | species | viruses | viruses | 44024 |
| kluyveromyces marxianus | 50 | species | plants | fungi | 4911 |
| kluyvera cryocrescens | 24 | species | bacteria | bacteria | 580 |
| kluyvera ascorbata | 18 | species | bacteria | bacteria | 51288 |
| klebsiella pneumoniae | 146 | species | bacteria | bacteria | 573 |
| klebsiella oxytoca | 66 | species | bacteria | bacteria | 571 |
| klebsiella granulomatis | 16 | species | bacteria | bacteria | 39824 |
| kingella kingae | 27 | species | bacteria | bacteria | 504 |
| kingella denitrificans | 9 | species | bacteria | bacteria | 502 |
| kemerovo virus | 8 | no rank | viruses | viruses | 40064 |
| kedougou virus | 2 | species | viruses | viruses | 64311 |
| kasokero virus | 1 | species | | viruses | 1712570 |
| kairi virus | 4 | species | viruses | viruses | 80939 |
| juquitiba virus | 2 | species | viruses | viruses | 430511 |
| junin mammarenavirus | 31 | species | viruses | viruses | 11619 |
| jc polyomavirus | 89 | species | viruses | viruses | 10632 |
| japanese encephalitis virus | 83 | species | viruses | viruses | 11072 |
| issyk-kul virus | 2 | species | | viruses | 1453408 |
| isoparorchis hypselobagri | 5 | species | invertebrates | helminths | 36663 |
| isaria javanica | 5 | species | plants | fungi | 43265 |
| isaria farinosa | 25 | species | plants | fungi | 89141 |
| influenza c virus | 48 | species | viruses | viruses | 11552 |
| influenza b virus | 57 | species | viruses | viruses | 11520 |
| influenza a virus | 135 | species | viruses | viruses | 11320 |
| inermicapsifer madagascariensis | 8 | species | | helminths | |
| ilheus virus | 6 | species | viruses | viruses | 59563 |
| igbo ora virus | 5 | no rank | viruses | viruses | 79899 |
| hypoderaeum conoideum | 7 | species | invertebrates | helminths | 220810 |
| hymenolepis nana | 28 | species | invertebrates | helminths | 102285 |
| hymenolepis diminuta | 45 | species | invertebrates | helminths | 6216 |
| hydatigera taeniaeformis | 33 | species | invertebrates | helminths | 6205 |
| human t-lymphotropic virus 1 | 137 | no rank | viruses | viruses | 11908 |
| human respiratory syncytial virus | 66 | species | viruses | viruses | 11250 |
| human parvovirus b19 | 81 | species | viruses | viruses | 10798 |
| human parechovirus 2 | 16 | no rank | viruses | viruses | 39085 |
| human parechovirus 1 | 29 | no rank | viruses | viruses | 12063 |
| human parainfluenza virus 3 | 51 | species | viruses | viruses | 11216 |
| human parainfluenza virus 2 | 37 | species | viruses | viruses | 11212 |
| human parainfluenza virus 1 | 34 | species | viruses | viruses | 12730 |
| human papillomavirus | 235 | species | viruses | viruses | 10566 |
| human mastadenovirus f | 1 | species | viruses | viruses | 130309 |
| human mastadenovirus e | 2 | species | viruses | viruses | 130308 |
| human mastadenovirus d | 5 | species | viruses | viruses | 130310 |
| human mastadenovirus c | 5 | species | viruses | viruses | 129951 |
| human mastadenovirus b | 3 | species | viruses | viruses | 108098 |
| human mastadenovirus a | 1 | species | viruses | viruses | 129875 |
| human immunodeficiency virus 2 | 399 | species | viruses | viruses | 11709 |
| human immunodeficiency virus 1 | 410 | species | viruses | viruses | 11676 |
| human herpesvirus 8 | 140 | species | viruses | viruses | 37296 |
| human herpesvirus 7 | 48 | species | viruses | viruses | 10372 |
| human herpesvirus 6 | 94 | species | viruses | viruses | 10368 |
| human herpesvirus 5 | 159 | species | viruses | viruses | 10359 |
| human herpesvirus 4 | 257 | species | viruses | viruses | 10376 |
| human herpesvirus 3 | 113 | species | viruses | viruses | 10335 |
| human herpesvirus 2 | 96 | species | viruses | viruses | 10310 |
| human herpesvirus 1 | 171 | species | viruses | viruses | 10298 |
| human coronavirus oc43 | 29 | no rank | viruses | viruses | 31631 |
| human coronavirus 229e | 39 | species | viruses | viruses | 11137 |
| hughes virus | 4 | species | viruses | viruses | 248052 |
| hu39694 virus | -3 | no rank | viruses | viruses | 69244 |
| hortaea werneckii | 16 | species | plants | fungi | 91943 |
| histoplasma capsulatum | 72 | species | plants | fungi | 5037 |
| himasthla muehlensi | -3 | species | | helminths | |
| heterophyopsis continua | 3 | species | | helminths | 1193295 |
| heterophyes nocens | 3 | species | invertebrates | helminths | 104455 |
| heterophyes heterophyes | 4 | species | | helminths | 1849833 |
| heterophyes dispar | 1 | species | | helminths | |
| heterobilharzia americana | 11 | species | invertebrates | helminths | 39320 |
| hepatovirus a | 95 | species | viruses | viruses | 12092 |
| hepatitis delta virus | 89 | species | viruses | viruses | 12475 |
| hepatitis c virus | 289 | species | viruses | viruses | 11103 |
| hepatitis b virus | 246 | species | viruses | viruses | 10407 |
| hendra virus | 43 | species | viruses | viruses | 63330 |
| helicobacter pylori | 246 | species | bacteria | bacteria | 210 |
| helicobacter pullorum | 19 | species | bacteria | bacteria | 35818 |
| helicobacter heilmannii | 37 | species | bacteria | bacteria | 35817 |
| helicobacter fennelliae | 16 | species | bacteria | bacteria | 215 |
| helicobacter cinaedi | 27 | species | bacteria | bacteria | 213 |
| hathewaya histolytica | 40 | species | bacteria | bacteria | 1498 |
| haplorchis yokogawai | 3 | species | invertebrates | helminths | 667377 |