Drivers of microbiome composition in A. mexicanuscompared to other fishes
Our study adds to the investigations of what drives microbiome diversity in fishes more broadly. We found that in A. mexicanus , evolutionary history alone can account for differences in gut microbiome composition. Most studies in other fish species have found that habitat is the main driver of microbial diversity. For example, a meta-analysis of 25 fish species revealed that trophic level and salinity was the best predictor of microbiome composition . Similarly, a study examining the microbiome of 227 individuals from 85 fish species found that host habitat most strongly shaped the microbiome . The dominant impact of habitat has also been observed when comparing closely related species; the microbiomes of Cichlids from two lakes cluster by diet . Nevertheless, a role for host phylogeny has been demonstrated in some comparisons. A recent examination of 24 freshwater species from the Yellow River found that diet, location, and host phylogeny predict microbiome composition .
The studies described above compared field caught fish and statistically analyzed the impact of habitat on microbiome composition. In contrast, we controlled the variable of habitat by comparing fish that were spawned in the laboratory, surface sterilized as embryos, consumed the same diet, and were raised in the same water. A study of similar design using threespine stickleback (Gasterosteus aculeatus) compared the microbiomes of freshwater benthic and freshwater limnetic ecotypes from three different lakes . In contrast to what we observed in A. mexicanus , the ecotypes did not develop different microbiomes when raised in the same conditions. The harsh cave environment may select for traits that have an outsized effect on microbiome composition compared to the variable environments experienced during the adaptive radiation of other fish species. An emerging theme in predicting microbiome composition is that the relative impact of habitat and evolutionary history depends on the ecological forces that shaped the clade being examined.