Table 3.
Lifestyles exhibited by the closest relatives of fish gut microbes. These categories are referred to in Fig. 4
| Category | Description |
|---|---|
| 1 | Vertebrate gut generalists: fish gut associates cluster within clades consisting of all or mostly (≥85% with n ≥ 10 clade members) bacteria from vertebrate guts |
| 2 | Animal and vertebrate gut generalists: fish gut associates belonged to clades containing some bacteria, but <85%, from mammalian or bird guts. All other bacteria within these clades were derived from nonvertebrate animals or nongut tissues from vertebrates |
| 3 | Fish gut generalists: fish gut associates belonged to lineages consisting only of microbes from the guts of fish. Each clade harboured bacteria from multiple host species |
| 4 | Fish gut specialists—multi-host population: fish gut associates belonged to lineages consisting only of microbes from the guts of fish. Each clade harboured bacteria from multiple host populations of a single species |
| 5 | Fish gut specialists—single-host population: fish gut associates belonged to lineages consisting only of microbes from the guts of fish. Each clade harboured bacteria from just one host population from one species |
| 6 | Animal generalists: fish gut associates grouped into lineages for which animals (e.g. invertebrates such as insects and corals; nongut habitats from fish and mammals) and fish guts were the only source habitats |
| 7 | Terrestrial environmental microbes: fish gut associates were most closely related to bacteria from terrestrial environments. |
| 8 | Terrestrial freshwater microbes: fish gut associates were most closely related to bacteria from freshwater environments |
| 9 | Marine environmental microbes: fish gut associates were most closely related to bacteria from marine or estuarine environments |
| 10 | Miscellaneous environmental microbes: fish gut associates were most closely related to bacteria from other types of environments (e.g. snow, ice, air) |
| 11 | Plant-associated microbes: fish gut associates were most closely related to bacteria isolated from plants |
| 12 | Microbes from artificial habitats: fish gut associates were most closely related to bacteria from a human-made or human-altered environment |
| 13 | Undefined, basal clade members: fish gut associates were basal to clades with mixed habitat sources |
| 14 | Microbes with unspecified habitats: fish gut associates were most closely related to bacteria with unspecified isolation sources |