Increased host diversity limits bacterial generalism but may promote microbe-microbe interactions.

Host-associated bacteria vary in the number of host species they occupy. By colonizing many host species, host generalists can have disproportionate ecological impacts and should gain an evolutionary advantage when host species availability varies. However, past work has shown that many bacterial lineages are host specific. We hypothesized that constraints on bacterial host generalism will differ depending on ecological context. To test this, we assessed patterns of diversity and specialization in the cloacal microbiomes of reptile communities from the temperate zone to the tropics, a 10-fold increase in host species richness. We found that some host-specific lineages increased in richness along with their hosts, while generalist lineages did not. Generalist lineages were able to attain their highest host prevalence when host diversity was lower. In our highest diversity host communities, we found that the successful generalists, typically Proteobacteria, were disproportionately likely to co-occur with one another across evolutionarily disparate hosts. Our data indicated that bacterial lineages may adapt to the evolutionary pressures of high diversity host communities either by specializing on hosts or by forming cohorts of co-occurring bacterial lineages. Previous research across vertebrate gut microbiomes has shown that mutually beneficial relationships between bacterial lineages are widespread. Our work further supports that finding and contextualizes it within a range of host community diversity.