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 .