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.