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Ornelas-García P, Pajares S, Sosa-Jiménez VM, Rétaux S, Miranda-Gamboa RA.2018. Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853)PeerJ Preprints6:e27058v1https://doi.org/10.7287/peerj.preprints.27058v1
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 locally contrasting environmental conditions and physiological adaptations of the host. Stomach biopsies were 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 Betaprotobacteria 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 (caves vs surface rivers). Rather, we observed a consistent association between β-diversity and dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota of A. mexicanus is not linked with the habitat but results from water conditions.
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Rarefaction curves of observed species of 16S rDNA genes for the different fish samples. Symbol abbreviations: R, Rascón; M, Micos; P, Pachón; M, male; F, female.
Venn diagrams showing the numbers of shared and unique genus OTUs (at 97% of similarity) from stomach microbiome among fish samples from the same population: a) Rascón, b) Micos, and c) Pachón. Symbol abbreviations: R, Rascón; M, Micos; P, Pachón; M, male; F, female.
Distribution of bacterial taxonomic groups from mapped reads among the different hypervariable regions of 16S rRNA for each fish sample. The number of reads for each region is indicated in parentheses. Symbol abbreviations: R, Rascón; M, Micos; P, Pachón; M, male; F, female.