Experimental evolution of Drosophila without its microbiome

Abstract

In single-generation experiments, microbiome removal often affects multiple host traits. However, relatively little is understood about the long-term implications of living in a microbe-free environment. To address this question, we evolved four replicate laboratory populations of Drosophila melanogaster without microbes and compared their traits with corresponding control populations that were reared with microbiota. This comparison was done under two assay environments: with-microbes and microbe-free. Prior single-generation experiments on our populations had revealed that microbiota removal significantly affects multiple traits, which suggested that the flies were under strong selection pressure to adapt to the absence of microbes. However, contrary to our expectations, the selected populations underwent very modest changes even after 54-57 generations of selection. Moreover, the magnitude of change in trait values across the with- and without- microbe environments was less for the selected populations than for the controls. RNA-Seq on one of the evolutionary replicates revealed that compared to the control, some anti-microbial peptides (AMPs) in the selected population were up-regulated, while several heat shock proteins (HSPs) were down-regulated. These results suggest that robust host-microbiome integrations on short timescales can nevertheless be labile on longer timescales. We situate these results in the context of the "evolutionary addiction hypothesis" and the "hygiene hypothesis".