Intestinal microbiome of A. mexicanus cavefish and
surface fish in their natural habitats
We first analyzed the microbiome of A. mexicanus surface fish and
cavefish morphotypes by comparing fish that were captured in the Rio
Choy River and Pachón Cave, respectively. The Pachón Cave is perpetually
dark, and previous studies analyzing gut contents of field caught fish
indicate that adults are opportunistic generalists with a seasonally
variable diet of mostly detritus and bat guano . In contrast, surface
fish have a normal day/night cycle and consumes insects, crustaceans,
and annelids . In addition to consuming distinct diets, the fish reside
in water with dissimilar chemical qualities; water in the Pachón cave at
the time of collection was lower in temperature, dissolved oxygen,
conductance, copper, and phosphate (Table S1 ). Despite these
distinct habitats, we did not observe significant differences in the
richness or composition of the intestinal microbiome between fish
collected at each site (Shannon Index one-way ANOVA with Tukey’s post
hoc test p.adj = 0.84, Beta diversity Permanova with pairwise post hoc
test p.adj = 0.098). However, when we examined the proportional
abundance of taxa, we found that the fish were dominated by only one or
two phyla and the dominant phyla differed between morphotypes
(Figure 2 ). Firmicutes were the most abundant phylum in surface
fish while Proteobacteria and Bacteroidota were the most abundant phyla
in Pachón cavefish (Figure 2A,B , average proportional abundance
(APA) of Firmicutes = 0.15 Pachón, 0.64 surface, Proteobacteria = 0.62
Pachón, 0.03 surface, Bacteroidota = 0.12 Pachón, 0.09 surface). We also
observed differences in pathogenic classifications; one of the Pachón
cavefish samples (p11) had mostly Spirochaetota of the genusBrevinema which was not found in wild surface fish samples and is
likely a pathogen . Unlike Pachón cavefish samples, Surface fish samples
were dominated by the genus Clostridium (APA = 0.008 Pachón, 0.52
surface). In addition, two surface fish samples (s3, s4) had a high
proportion of the genus Cetobacterium which was found at very low
abundance in only one Pachón cavefish (APA = 0.07 Pachón, 0.20 surface).
The data suggests that in their natural habitat, A. mexicanussurface fish and cavefish gut microbiomes are dominated by only a few
microbes and that the most abundant phyla differ between populations.