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.