Experimental evolution has a long history of uncovering fundamental insights into evolutionary processes but has largely neglected one underappreciated component--the microbiome. As eukaryotic hosts evolve, the microbiome may also evolve in response. However, the microbial contribution to host evolution remains poorly understood. Here, we analyzed the metagenomes from 10 E&R experiments in Drosophila melanogaster to determine how the microbiome changes in response to host selection. Bacterial diversity was significantly different in 5/10 studies in traits associated with metabolism or immunity. Additionally, we find that excluding reads from a facultative symbiont, Wolbachia, in the analysis of bacterial diversity changes the inference, raising important questions for future E&R experiments in D. melanogaster. Our results suggest the microbiome often responds to host selection but highlights the need for more work to understand how the microbiome changes the host response to selection.

The microbiome responds to Evolve and Resequence experiments in Drosophila melanogaster