Variation in cloacal microbiota of Canada goose (Branta canadensis) across rural and urban areas in Illinois, USA

Introduction: The cloacal microbiota of birds is shaped by host factors, diet, environmental exposure, and increasing overlap between wild bird habitats and human development may influence these communities. However, the effects of urbanization on herbivorous waterfowl in Illinois remain poorly understood. Methods: ) sampled from rural and urban areas in Illinois using 16S rRNA gene V4 amplicon sequencing, and evaluated associations between host age, host sex, and human population density and microbial community structure. Alpha diversity metrics did not differ significantly across host age or sex, although ASV richness was significantly higher in rural compared to urban samples. In contrast, beta-diversity analyses indicated that host age was the strongest factor associated with differences in microbial community composition, with additional but weaker effects of human population density, while host sex had comparatively little influence. Discussion: Overall, these results suggest that ecological context, including habitat type and environmental exposure, were associated with variation in the cloacal microbiota of Canada goose, although additional unmeasured environmental and spatial factors may also contribute to observed patterns. This study provides a baseline characterization of microbiota variation across age classes and habitats in Illinois Canada goose and highlights the importance of considering ecological context when interpreting wildlife-associated microbial communities.