Urbanization and the Gut Microbiome: Insights From the Anna's Hummingbird (Calypte anna) in California

Complex environmental characteristics shape the gut microbiome of wildlife with critical implications for host health, pathogen resistance, digestion, and overall fitness. While foundational avian microbiome research has focused mainly on domestic birds and poultry due to their proximity to humans and the associated zoonotic risks from imbalanced microbiomes, studying the gut microbiome of wild birds is also essential. Wild birds fill important roles in their habitats-serving as critical pollinators and bioindicators of ecosystem health. Despite this, their gut microbiomes remain less explored, particularly concerning how urbanization affects microbiome composition and diversity, which may provide insight into the health of birds in urban habitats. This study investigates the gut microbiome of the Anna's Hummingbird (Calypte anna), a species that thrives in urban and rural environments across the West Coast. We amplified the V1-V3 region of bacterial 16S rRNA extracted from fecal samples and used the QIIME2 platform to characterize bacterial communities. By analyzing bacterial communities from birds sampled across a range of anthropogenically altered locations, we explore correlations between microbiome composition and habitat characteristics (artificial light at night, human density, air pollution, and % imperviousness). We show that air quality is an important driver of microbial diversity and offer insights into how the heterogeneity of urban landscapes impacts the microbiome composition of wild birds.