On the influence of gut bacteria on host biology: insights from ecological and evolutionary studies on Drosophila melanogaster

Abstract

Gut microbes are increasingly implicated in modulating host biology. The ability of the microbiome to contribute to diverse host phenotypes and, in turn, alter host fitness, raises the possibility that the presence of such microbes can influence the host’s evolution. However, empirical studies on the evolutionary aspects of host-microbe relationships are rare. We used experimental evolution on laboratory populations of D. melanogaster to understand how a host can evolve without its microbiome. For this, we compared replicate Drosophila populations reared without the microbes (labeled as MBL1-4, for “Microbiota-less”) for 54 host generations with their corresponding controls (labeled as MB1-4), whose microbiome was reconstituted every generation. This comparison was done in two common-garden assay environments: with microbes and microbe-free. We found that contrary to what we expected, only modest adaptations were seen in MBL populations. When looking at the phenotypic plasticity of MB-MBLs across with-microbe and microbe-free environments, we saw that MBLs had lesser plasticity than MBs. This might hint at MBLs reducing their dependence on microbes. We performed RNA-Seq on MBL1 and MB1 populations to see if there were changes in gene expression patterns. We found that a cluster of anti-microbial peptides (AMPs) was up-regulated, and another cluster of heat shock proteins (HSPs) was down-regulated in MBL1 compared to MB1. The RNA-Seq results also hinted that the peritrophic matrix could be a site of interest for further investigations related to these populations. These results show that while the host’s homeostasis is perturbed by microbiome manipulation on short timescales, the host-microbiome integration seems more labile on longer timescales, with hosts showing potential for adaptation without the microbes. While most of the studies on Drosophila-microbiome interactions are done on inbred host strains (i.e., strains with reduced genetic variation than the outbred strains), our results on short timescales were obtained on outbred strains. Therefore, we asked if the reduced genetic variation of the host through inbreeding affects the extent of microbiome modulation of the host phenotypes. We found that the overall modulation of the host by microbiome was less pronounced in the inbred flies than in their outbred counterparts. Inbred populations had more variation in the traits than the outbred populations. The traits with higher variation in outbred flies further increased their variation in inbred flies. Also, while both males and females showed microbiome modulation in outbred flies, only female inbred flies showed modulation by microbiome. These results reveal that outbred strains of Drosophila might differ in their response to microbiome than the inbred strains.