Differential abundance of microbial taxa in laboratory-rearedA. mexicanus
We next compared the microbial taxa between laboratory-raised A.
mexicanus morphotypes to gain insight into the potential functional
significance of host-driven microbiome differences. We found that the
four most abundant phyla were Firmicutes, Proteobacteria,
Fusobacteriota, and Bacteroidota like in other freshwater fishes
(Figure 2A,B, Table S2 ). However, the average proportional
abundance of Firmicutes was highest in surface fish compared to cavefish
which recapitulates what we observed in the natural habitat
(Figure 2A, B, APA = 0.40 surface, 0.36 Pachón, 0.21 Tinaja,
0.24 Molino). In addition, the phylum Bacteroidota and genusBacteroides made up a high proportion of ASVs in surface fish
samples compared to cavefish samples (Figure 2C, D , APA = 0.14
surface, 0.10 Pachón, 0.06 Tinaja, 0.07 Molino). We found that Pachón
cavefish samples were mostly dominated by Proteobacteria of the genusCupriavidus which was lower in the other morphotypes
(Figure 2C, D, APA = 0.19 Pachón, 0.08 surface, 0.06 Tinaja,
0.09 Molino).
The most striking difference in taxonomic composition we observed was
very low abundance of Fusobacteriota in Pachón cavefish compared to the
other morphotypes (Figure 2A: dark green bars, Figure
2B: light orange bars). We found that the Fusobacteriota phylum was
consistently present in surface fish and was the most abundant phylum in
1 out of 10 surface fish. Proportional abundance of Fusobacteriota was
greater in Molino and Tinaja cavefish samples compared to surface fish
samples; it was the most common phylum in 4 out of 9 Molino samples and
5 out of 9 Tinaja samples. In contrast, we did not observe it in most
Pachón samples (6 out of 8) or it was at very low abundance if present
(APA = 0.0005 Pachón, 0.08 surface, 0.46 Tinaja, 0.22 Molino). We found
that samples from wild Pachón cavefish also had low proportional
abundance of Fusobacteriota compared to samples from wild surface fish
(APA = 0.07 Pachón, 0.20 surface). The Fusobacteriota sequences we
identified in the A. mexicanus gut microbiome are assigned to the
genus Cetobacterium which is common in the microbiome of
freshwater fish . Our data suggest that genetic differences betweenA. mexicanus morphotypes alter the taxonomic composition of the
intestinal microbiome and that most strikingly, Pachón cavefish have
dramatically reduced abundance of Cetobacterium .