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.