DISCUSSION
We characterized the intestinal microbiome of A. mexicanussurface fish and cavefish morphotypes in their natural habitat and reared under identical conditions in the laboratory to understand 1) if wild cavefish and surface fish have different microbiomes, 2) if the wild microbiomes are represented in the laboratory-reared fish, and 3) if host evolutionary history alone drives differences in microbiome composition. Our results show that in their natural habitat, surface fish and cavefish are dominated by only a few phyla that differ between river-dwelling and cave-dwelling fish. We found that the laboratory environment supports growth of a richer microbial community that contains more of the wild surface fish taxa compared to the wild cavefish taxa. By comparing the microbiomes of surface fish and multiple cavefish morphotypes that were reared in the laboratory, we discovered that host genetics drives differences in microbiome richness and composition and that the microbial community relationships recapitulate the phylogeny of the host. Our study shows that phylosymbiosis can occur within the same species consisting of populations that have adapted to dramatically different habitats. Furthermore, we found consistent and readily quantifiable differences in taxa between A. mexicanusmorphotypes that can be used to investigate the genetic basis of microbial community structure and how it impacts the development, physiology, metabolism, and behavior of the host.