Comparison of the intestinal microbiome between wild and
laboratory-reared A. mexicanus
To understand how similar the microbiome of A. mexicanus in their
wild habitat is to those raised in the laboratory, we compared the
microbiomes of field collected surface fish and Pachón cavefish to their
laboratory-reared counterparts that had been bred in the laboratory for
generations and were raised on the same diet and in the same water. The
laboratory habitat is different from both the cave and river habitats.
In the laboratory, the fish experience lower temperature and pH, higher
conductance and dissolved oxygen, an invariable light cycle, more
crowded growth conditions, and a consistent high-nutrient diet
(Table S1 ). We found that laboratory-raised fish had greater
richness of microbial species in the intestinal microbiome compared to
fish in the wild habitat (Figure 3A , Shannon Index,Figure S2 , total observed species, phylogenetic index);
alpha-diversity was significantly different in samples from surface fish
and Pachón cavefish collected in the field compared to surface fish and
Pachón cavefish raised in the lab (Shannon Diversity Tukey’s post-hoc
test, wild surface vs lab surface FDR p.adj = 0.001, wild Pachón vs lab
Pachón FDR p.adj = 0.008). Since fish are colonized with microbes after
hatching, our results suggest the laboratory supports a richer microbial
diversity than either natural environment.
To obtain a graphical representation of the differences in microbiome
composition between the wild and the laboratory-reared fish we
summarized ASV abundances into Bray-Curtis dissimilarities and performed
principle coordination analysis (PCoA, Figure 3B ). In the PCoA
plot, wild surface fish and wild Pachón cavefish form two partially
overlapping clusters that are separate from laboratory-raised fish. We
found that habitat (wild versus lab) significantly impacted microbiome
composition (Table 1, adonis R function, or Permanova, p
=0.002,); beta-diversity was significantly different in samples from
surface fish and Pachón cavefish collected in the wild compared to
surface fish and Pachón cavefish raised in the lab (Table 2,pairwise post-hoc test, wild surface vs lab surface FDR p.adj = 0.005,
wild Pachón vs lab Pachón FDR p.adj = 0.006). In summary, the intestinal
microbiome of A. mexicanus in the laboratory has increased
richness and altered composition compared to A. mexicanus in
their natural habitat. These results have implications for researchers
investigating the evolution of cavefish traits that may be influenced by
microbiome composition.