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.