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.