Functional significance of differences in taxonomic composition between morphotypes
The taxonomic differences we observed between the microbiomes of laboratory raised A. mexicanus morphotypes have been associated with host traits in other species. For example, we observed a higher ratio Firmicutes to Bacteroidetes ratio (F/B ratio) in cavefish compared to surface fish (Table S2 ) which has been linked with obesity in mammals . Cavefish are fatter than surface fish and a role for the microbiome in underlying increased adiposity has yet to be explored. We found that Pachón cavefish samples had a high abundance ofCupriavidus , which is a genus associated with resistance to copper toxicity . Whether Pachón cavefish are resistant to copper has not been tested but copper concentrations in the Pachón cave were lower than in the surface river at the time of collection (Table S1 ). However, Cupriavidus has been found at higher abundance in human patients with type-2 diabetes compared to healthy individuals . Interestingly, Pachón cavefish have traits that model diabetes like insulin resistance and higher blood sugar and a possible connection with the microbiome has not yet been tested.
Another taxonomic difference that shows interesting alignment with Pachón cavefish traits is the near absence of Fusobacteriota of the genus Cetobacterium compared to the other morphotypes.Cetobacterium is common in the microbiome of herbivorous fish and is thought to assist in carbohydrate metabolism . One predominant species, Cetobacterium somerae , has been shown to produce vitamin B12 which provides resistance to pathogen infection . C. someraehas also been shown to improve glucose homeostasis when administered to zebrafish, Danio rerio , through the production of acetate and modulation of the gut-brain axis . Low Cetobacterium abundance in Pachón cavefish could therefore be linked with their observed increased sensitivity to infection and impaired glucose homeostasis . In humans, overabundance of microbes from the same family (Fusobacteriaceae ) play a role in progression of diseases like periodontitis, appendicitis, and gastrointestinal cancer . For example, abundance ofCetobacterium in combination with other microbes can be used as a diagnostic biomarker for colorectal cancer . Discovering the genetic basis of low Fusobacteriota abundance in Pachón cavefish may have biomedical relevance in addition to furthering our understanding of cavefish evolution and host-microbe interactions.