Gut microbiota variation and trophic niche differentiation among sympatric birds in a forest-farmland mosaic

The abundance and diversity of gut microbiota influence avian health, nutrient assimilation, and overall physiological performance. However, the extent to which variation in gut microbial composition corresponds to resource use and niche differentiation among sympatric bird species remains poorly understood. We characterized the gut microbiota of three bird species inhabiting a forest–farmland mosaic in suburban Harbin, China: Oriental Turtle-dove ( Streptopelia orientalis ), Hoopoe ( Upupa epops ), and Grey-backed Thrush ( Turdus hortulorum ), using 16S rRNA V3–V4 sequencing. Proteobacteria were predominant in Streptopelia and Turdus , whereas Firmicutes were more abundant in Upupa . LEfSe analysis identified species-specific microbial biomarkers, including Pseudomonas in Upupa , Tyzzerella in Turdus , and Paracoccus in Streptopelia . KEGG-based functional predictions revealed that lipoic acid metabolism was enriched in Streptopelia . Thiamine metabolism and carbon fixation were enriched in Turdus , while pyruvate metabolism was more abundant in Streptopelia and Upupa . Pianka index analyses indicated greater overlap in gut microbial composition than in dietary ASVs, with notable differences between Turdus and Upupa . These patterns suggest that gut microbial composition corresponds with species-specific trophic tendencies and dietary characteristics, potentially reflecting mechanisms of resource partitioning. Overall, taxonomic and functional differentiation of gut microbiota among the three species provides insights into the potential role of microbes in facilitating coexistence within heterogeneous habitats and informs conservation strategies for urban and peri-urban bird communities.