Evidence that host identity drives differences in A.
mexicanus microbiome composition
We next tested whether the identity of the host population impacts
microbiome composition independent of habitat by comparing the
intestinal microbiome of six-month-old fish from the Río Choy River,
Pachón Cave, Tinaja Cave, and Molino Cave that have been bred in the
laboratory for generations, were surface sterilized as embryos, and were
raised on the same recirculating water system and diet. In this
controlled setting, we found that Tinaja and Molino cavefish had
significantly lower microbial species richness compared to surface fish
suggesting that host genetics alone can impact alpha diversity, the
number and distribution of microbial species in the intestine
(Figure 3A : Shannon Index, Figure S2B : Inverse Simpson
Index).
In addition to impacting microbial species richness, we found that
morphotype identity had a significant impact on microbiome composition
(Table 1 , Beta Diversity Permanova, p=0.002). To visualize the
differences in microbiome composition we summarized ASV abundances into
Bray-Curtis dissimilarities and performed principle coordination
analysis (PCoA, Figure 3B ). In the PCoA plot comparing
laboratory raised fish, the centroid of Tinaja cavefish samples is
furthest from surface fish samples and the ellipses estimating
covariance overlap except for Pachón and Tinaja cavefish samples
(Figure 3B ). PCoA plots of unweighted unifrac and Jaccard
distances differently show that the Pachón centroid is ordinated
furthest from surface fish and that ellipses estimating covariances
overlap in all samples (Figure S3 ). To determine which
laboratory-reared morphotypes harbored significantly different
microbiomes, we performed a pairwise post-hoc test (Table 2 ).
We found that the microbiome of surface fish was significantly different
from Pachón and Tinaja cavefish (p.adj = 0.025 and 0.020) but not Molino
cavefish (p.adj = 0.075). These results suggest that Tinaja and Pachón
cavefish have acquired genetic changes that result in establishment of a
different microbiome from surface fish despite being raised in the same
habitat. We also found that samples from Pachón and Tinaja cavefish were
significantly different from each other suggesting distinct cavefish
populations have genetic differences that impact microbiome composition
(p.adj = 0.006). Since the fish were all raised under identical
conditions, these results suggest that morphotype identity alone
accounts for differences in microbiome composition in A.
mexicanus .