Metagenome-Wide Association of Microbial Determinants of Host Phenotype in Drosophila melanogaster

Abstract

J.M.C. and P.D.N. contributed equally to this article. ABSTRACT Animal-associated bacteria (microbiota) affect host behaviors and physiological traits. To identify bacterial genetic determinants of microbiota-responsive host traits, we employed a metagenome-wide association (MGWA) approach in two steps. First, we measured twomicrobiota-responsive host traits, development time and triglyceride (TAG) content, inDrosophila melanogaster flies monoassociated with each of 41 bacterial strains. The effects of monoassociation on host traits were not con-fined to particular taxonomic groups. Second, we clustered protein-coding sequences of the bacteria by sequence similarity de novo and statistically associated the magnitude of the host trait with the bacterial gene contents. The animals had beenmonoas-sociated with genome-sequenced bacteria, so the metagenome content was unambiguous. This analysis showed significant ef-fects of pyrroloquinoline quinone biosynthesis genes on development time, confirming the results of a published transposon mutagenesis screen, thereby validating theMGWA; it also identified multiple genes predicted to affect host TAG content, includ-ing extracellular glucose oxidation pathway components. To test the validity of the statistical associations, we expressed candi-date genes in a strain that lacks them. Monoassociation with bacteria that ectopically expressed a predicted oxidoreductase or gluconate dehydrogenase conferred reducedDrosophila TAG contents relative to the TAG contents in empty vector controls. Consistent with the prediction that glucose oxidation pathway gene expression increased bacterial glucose utilization, the glu-cose content of the host diet was reduced when flies were exposed to these strains. Our findings indicate that microbiota affec