Correlation and causation between the microbiome, Wolbachia and host functional traits in natural populations of drosophilid flies

: Resident microorganisms are known to influence the fitness and traits of animals under controlled laboratory conditions, but the relevance of these findings to wild animals is uncertain. This study investigated the host functional correlates of microbiota composition in a wild community of three sympatric species of mycophagous drosophilid flies, Drosophila falleni, Drosophila neotestacea and Drosophila putrida. Specifically, we quantified bacterial communities and host transcriptomes by parallel 16S rRNA gene amplicon sequencing and RNA-Seq of individual flies. Among-fly variation in microbiota composition did not partition strongly by sex or species, and included multiple modules, that is, sets of bacterial taxa whose abundance varied in concert across different flies. The abundance of bacteria in several modules varied significantly with multiple host transcripts, especially in females, but the identity of the correlated host transcriptional functions differed with host species, including epithelial barrier function in D. falleni, muscle function in D. putrida, and insect growth and development in D. neotestacea. In D. neotestacea, which harbours the endosymbionts Wolbachia and Spiroplasma, Wolbachia promotes the abundance of Spiroplasma, and is positively correlated with abundance of Lactobacillales and Bacteroidales. Furthermore, most correlations between host gene expression and relative abundance of bacterial modules were co-correlated with abundance of Wolbachia (but not Spiroplasma), indicative of an interdependence between host functional traits, microbiota composition and Wolbachia abundance in this species. These data suggest that, in these natural populations of drosophilid flies, different host species interact with microbial communities in functionally different ways that can vary with the abundance of endosymbionts.