Urbanization shapes gut bacterial communities and metabolic functions in migratory wild birds across Bangladesh

Abstract Background Understanding the association between birds, zoonotic infections, and urban environments is increasingly important due to industrialization and emerging zoonoses. Investigating the diversity, structure, and metabolic potential of the gut bacteriome of migratory wild birds can uncover recurring biological patterns across species, particularly in those that serve as reservoirs of zoonotic microorganisms. Methods This study investigated the fecal bacteriomes of migratory wild birds across three locations in Chattogram, Bangladesh. Wi-Fi–enabled miniature digital cameras were deployed at each site to monitor feeding activity and support the assessment of gut microbiota diversity among different bird species using 16S rR NA gene (V3–V4 region) sequencing. Nine pooled fecal samples were collected from birds feeding at provisioned stations, including four from urban (URB1–URB4), three from semi-urban (SURB1–SURB3), and two from rural sites (RUR1–RUR2). Results Fecal bacteriomes of wild birds showed habitat-specific diversity and functional patterns. Alpha diversity did not differ significantly by Shannon index (p > 0.05), but dominant species evenness differed by Simpson index (p < 0.05). Beta diversity revealed clustering of urban and semi-urban samples, while rural samples formed a distinct group (Bray–Curtis P < 0.05; PC1 = 52.8%, PC2 = 18.3%). Firmicutes dominated all samples (> 70%). Urban samples had higher Proteobacteria (21.2%), semi-urban had higher Bacteroidetes (4.2%), and rural had higher Actinomycetota (9.9%). Pathogenic genera comprised 26% of taxa, including Escherichia, Salmonella, and Staphylococcus. KEGG analysis showed urban enrichment of methane metabolism (5.34%) and photosynthesis (5.20%), semi-urban enrichment of ribosomal pathways (11.30%) and ABC transporters (4.18%), and rural enrichment of bacterial secretion systems (2.61%) and flagellar assembly (1.11%). Conclusions Urbanization structured wild bird gut bacteriomes, producing habitat-specific taxonomic and functional signatures. Urban and semi-urban communities clustered together, whereas rural bacteriomes were distinct. Shifts in dominant taxa, pathogenic genera, and KEGG pathways indicate ecological adaptation with health implications.