Data from: Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next-generation sequencing

Few studies have applied NGS methods to investigate the microbiome of
vertebrates in their natural environment and in freshwater fishes in
particularly. Here, we used pyrosequencing of the 16S gene rRNA to (i)
test for differences in kidney bacterial communities (i.e. microbiota) of
dwarf and normal whitefish found as sympatric pairs, (ii) test the
hypothesis of higher bacterial diversity in normal compared with dwarf
whitefish and (iii) test for the occurrence of parallelism with the
presence and composition of bacterial communities across species pairs
inhabiting different lakes. The kidney microbiota of 253 dwarf and normal
whitefish from five lakes was analysed combining a double-nested PCR
approach with 454 pyrosequencing. Bacteria were detected in 52.6% of the
analysed whitefish. There was no overall significant difference among
lakes and forms, although the lake × form interaction was found
significant. We identified 579 bacterial genera, which is substantially
more than previous descriptions using less sensitive techniques of fish
bacterial diversity in kidney, pathogenic or not. Ten of these genera
contained eighteen pathogenic species. Differences in bacteria composition
between whitefish forms were not parallel among lakes. In accordance with
the higher diversity of prey types, normal whitefish kidney tissue
consistently had a more diverse bacterial community and this pattern was
parallel among lakes. These results add to building evidence from previous
studies on this system that the adaptive divergence of dwarf, and normal
whitefish has been driven by both parallel and nonparallel ecological
conditions across lakes.