Symbiotic relationships between host and microbiome can play a major role in local
adaptation. Previous studies with freshwater organisms have shown that microbiome
performs numerous important biochemical functions for the host, playing a key role in
metabolism, physiology or health. Experimental studies in fish groups have found an
effect of enzymatic activity of gut microbiota on a variety of metabolic processes. The
goal of this study was to compare stomach microbiome from cave and surface Astyanax
mexicanus, in order to evaluate the potential response of microbiota to contrasting environmental
conditions and physiological adaptations of the host. Stomach microbiota
was obtained from three different populations: Pachón cave, and two surface rivers
(Rascón and Micos rivers). The stomach microbiome was analyzed using the Ion 16S
Metagenomic kit considering seven variable regions: V2, V3, V4, V6-7, V8 and V9.
A high diversity was observed across samples, including 16 phyla, 120 families and
178 genera. Gammaproteobacteria, Firmicutes, Bacteroidetes and Betaproteobacteria
were the most abundant phyla across the samples. Although the relative abundance
of the core OTUs at genus level were highly contrasting among populations, we did
not recover differences in stomach microbiome between contrasting habitats (cave vs.
surface rivers). Rather, we observed a consistent association between -diversity and
dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota
of A. mexicanus is not linked with the contrasting conditions of the habitat considered
here but is related to water parameters.