Selection for stress tolerance and longevity in Drosophila melanogaster have strong impacts on microbiome profiles

There is experimental evidence that microbiomes have strong influence on a range of host traits. This has led to a debate whether the holobiont, i.e., the host and its associated microbiota, constitute a distinct biological entity, on which selection can act. This idea has so far received limited empirical validation. In our project we used Drosophila melanogaster lines from a large-scale artificial selection experiment to investigate whether the microbiota differ in lines selected for different stress resistance traits and longevity. Such findings would provide indirect support for the hologenome hypothesis. Lines were selected for a range of stress resistance traits and longevity and following multiple generations of artificial selection all selection regimes and corresponding controls had their microbiomes assessed. The microbiome was interrogated based on 16S rRNA sequencing. We found that the microbiome of flies from the different selection regimes differed markedly from that of the unselected control regime, and microbial diversity was consistently higher in selected relative to control regimes. Several common Drosophila bacterial species showed differentially abundance in the different selection regimes despite flies being exposed to similar environmental conditions.