The microbial communities living on and in vertebrate hosts have myriad effects on their hosts, potentially including fitness and speciation. Microbiomes are influenced by both intrinsic (from the host) and extrinsic (from the environment) factors, but the relative contributions of each are unknown for most non-model species. Abiotic environmental factors can influence the microbiome directly but it is less clear how abiotic gradients shape microbiome communities in the wild. Here, we captured eight wild Anna’s hummingbirds from three different elevations along their elevational distribution in California and moved them directly to a middle (“Within Range”) elevation. After some time at this elevation, the birds were moved in captivity to an “Above Range” elevation, and two birds were later moved back to the Within Range elevation. Fecal and food samples were collected longitudinally and the V4 region of the 16S rRNA gene analyzed. The most abundant phyla in all samples were Fusobacteria, Firmicutes, Actinobacteria, and Proteobacteria. Individual Bird ID explained the greatest amount of microbiome variation at 27.5%, signifying some amount of stability in the Anna’s hummingbird fecal microbiome. Sample elevation explained 19.6% (p = 0.001) of the variation using weighted UniFrac, but only 2.0% (p = 0.047) using unweighted UniFrac, implying a change in abundance of bacterial lineages in the microbiome but not in the presence or absence of the microbes. Additionally, Fusobacteria were 7.0x more abundant in the Above Range elevation samples while Firmicutes were 0.3x lower. A thorough understanding of how the environment can shape the microbiome may assist in conservation efforts and a general understanding of host-microbiome relationships in an era of rapid and global environmental change.

The extent to which the avian microbiome is shaped by host phylogeny relative to other factors is largely unknown. In this study, we examine microbial biodiversity across multiple body sites of 211 bird species sampled in Malawi. Microbial community dissimilarity differed significantly across body sites, which included blood, buccal cavity, gizzard, intestine, cloaca, liver, and spleen. With these data, we tested the hypothesis that the avian microbiota follow a Species-Area Relationship by using a comparative phylogenetic method to examine the correlation between microbiota richness and host weight. Using Pagel’s lambda, we confirmed that bird mass is significantly correlated with host phylogeny but found that few microbial diversity metrics showed such a correlation. Phylogenetic Generalized Least Squares identified a significant but weak negative correlation between host weight and microbial richness of the blood and a similarly significant but weak positive correlation between the cloacal microbiota and host weight among birds within the order Passeriformes. Taken together, these results suggest that the avian microbiome does not follow a traditional species-area relationship when phylogenetic relatedness is considered, rather, microbial diversity is influenced by factors beyond host phylogeny and size.

All animals coexist and interact with microorganisms, including bacteria, archaea, microscopic eukaryotes, and viruses. These microorganisms can have an enormous influence on the biology and health of macro-organisms.