Host-microbiome associations in livebearing fishes adapted to toxic streams rich in hydrogen sulfide: Code for analyzing 16S rRNA dataset

Organisms inhabiting extreme environments must tolerate a variety of
physiochemical stressors. In some cases, host-associated microbial
communities facilitate survival of their hosts in extreme environments,
but extremophile symbioses have not been identified in vertebrates. We
used 16S rRNA amplicon sequencing to investigate commonalities and
differences in the gut microbial communities of livebearing fish (Poecilia
mexicana species complex, Poeciliidae) that have repeatedly colonized
toxic sulfide streams in southern Mexico. We found shared core gut
microbiomes across habitat types and drainages, but also differences in
the microbiomes between sulfidic and nonsulfidic populations, both in
terms of patterns of diversity and community composition. Most
importantly, we documented convergent changes in microbiome composition
across evolutionarily independent sulfide spring lineages. These patterns
were consistent when we analyzed whole gut microbiomes and primarily
host-associated microbiomes that excluded taxa that are commonly found in
the environment. Our analyses also revealed several microbial taxa
associated with sulfide spring colonization that have previously been
implicated in symbioses and may influence the host’s tolerance to the
extreme environmental conditions. Further research will need to test how
host-associated microbes impact host function and fitness under extreme
environmental conditions.