A. mexicanus as a model for investigating host-microbiome
interactions
Our study stands apart from other investigations on the factors that
influence the fish microbiome due to the nature and future promise of
the model system. A. mexicanus consists of multiple cavefish
populations of polyphyletic origin allowing investigations of parallel
evolution. We found that host-driven microbiome differences exist
between and within branches of the A. mexicanus phylogeny
providing multiple natural replicates to investigate evolution of
microbiome composition. In most other species it is not possible to
compare divergent populations and a representative ancestor in a
controlled laboratory setting. A. mexicanus is easy to grow and
manipulate in the lab, standardized husbandry protocols are published ,
the genome is sequenced and annotated , and there are a growing number
of resources available to examine and manipulate gene function .
Furthermore, methods for deriving germ-free zebrafish, and inoculating
them with specific microbes could be applied to A. mexicanus .
Since post-larval fish are transparent like zebrafish, the biogeography
of the A. mexicanus microbiome could be visualized in live fish
using fluorescent microbes. Perhaps most importantly, the surface fish
and cavefish are interfertile allowing hybridization of surface/cave and
cave/cave individuals to investigate the heritability and genetic basis
of traits using QTL mapping. It is possible to generate hundreds of F2
hybrids and use them to evaluate complex interactions between host
genotype, phenotype, and microbiome community structure. We showed that
proportional abundance of Fusobacteriota is very different between
surface fish and Pachón cavefish and stable within individuals
suggesting it would be a promising taxon to focus on for future QTL
studies. In addition to providing insight into the relative impacts of
environment and host in determining microbiome composition, our findings
establish A. mexicanus as an evolutionary model to investigate
the molecular mechanisms that mediate host-microbe interactions.