Environment impacts gut microbiome richness in hybridizing chickadees, while ancestry influences community composition

Abstract Among closely related species, host phylogenetic relationships are typically a stronger predictor of gut microbiome composition than environmental variation. However, the relative impact of genetic admixture caused by hybridization versus environmental variation on gut microbiome communities is poorly understood. To explore this knowledge gap, we used fecal metabarcoding to characterize chickadee gut microbiomes along a hybrid zone transect in natural environments and after transfer to a common, controlled environment. We collected fecal samples from nestling black‐capped ( Poecile atricapillus ), Carolina ( Poecile carolinensis ), and hybrid chickadees immediately after removal from their nests and twice after entering captivity and experiencing common diet and environmental conditions. To characterize gut microbiome communities, we extracted fecal DNA and sequenced the V3–V4 region of the 16S rRNA gene using Illumina MiSeq. Overall, Firmicutes and Proteobacteria were the major microbial phyla present across host species groups. Our analysis of alpha diversity showed that the transition to common environmental conditions significantly impacted host gut microbiome richness. In contrast, the change in host environment did not impact the community composition (i.e., beta diversity) of the gut microbiomes. Although not statistically significant, host ancestry may influence the microbiome composition more than host environment. Additional analyses suggest chloroplast 16S rRNA sequences accurately characterized host diets in captivity. In certain cases, 16S rRNA sequences can provide reliable characterization of habitat and dietary variation in wild birds. Although environment more strongly shapes microbiome richness and evenness, host ancestry may have a greater influence on the specific microbes present in the microbiome.