Conclusion
Astyanax mexicanus is a powerful model system to investigate the
genetic basis of morphological, physiological, and behavioral evolution
due to the ability to compare distinct cavefish morphotypes to their
extant surface fish ancestor. We were able to discover and define the
effects of environment and host evolutionary history on the gut
microbiome of this species due to the ability to study the morphotypes
in their natural habitat and compare them under the same controlled
conditions in the laboratory. We found that the microbiomes of cavefish
and surface fish in the wild are dominated by only a few phyla that
differ between river-dwelling and cave-dwelling individuals. Fish in the
laboratory have a more diverse microbiome that is distinct in
composition compared to their wild counterparts. In addition, there are
more shared microbes between lab versus wild surface fish compared to
lab versus wild cavefish. Importantly, we determined that host genetics
alone can drive differences in microbiome diversity and composition by
comparing the microbiomes of surface fish and multiple cavefish
morphotypes that were reared in the laboratory under identical
conditions. Moreover, our data revealed that the differences in
microbiome composition mirror the A. mexicanus phylogeny showing
that host evolutionary history within a single species can shape gut
microbial community structure.