Seasonal life stage changes contribute to gut bacterial community profiles of high-altitude birds

Abstract Understanding the impact of life stages in avian gut microbiota diversity and community assembly in high-altitude habitats is an innovative viewpoint for comprehending adaptation strategies of birds to extreme environments. This study investigates the difference of gut microbiota composition, co-occurrence network and community assembly between breeding and overwintering life stages in high-altitude avian species, Bar-headed geese (Anser indicus) and Ruddy shelducks (Tadorna ferruginea). Using 16S rRNA sequencing, we found striking seasonal convergence in core phyla: Proteobacteria (~35%) and Firmicutes (~21%) dominated overwintering communities in both species, contrasting with divergent breeding-stage profiles (e.g., A. indicus: 64.87% Proteobacteria vs. T. ferruginea: 66.29% Cyanobacteria). Alpha diversity surged in overwintering stage, with overwintering populations harboring 24.5% unique amplicon sequence variants (ASVs) versus 2.5% in breeding groups. Beta diversity differed significantly between stages, driven by shifts in Proteobacteria, Cyanobacteria, and Actinobacteria. Co-occurrence networks exhibited higher complexity (nodes/edges) and competition (15.9–16.4% negative edges) in winter. The phylogenetic bin-based null modeling results suggested that stochastic processes dominated assembly (90–99% contribution), yet dispersal limitation intensified in winter, reflecting environmental constraints. Functional profiling highlighted winter-enriched energy metabolism (3.62–6.40% relative abundance, RA), xenobiotic degradation (1.16–2.76% RA), and immune pathways (0.12–0.22% RA), aligning with cold adaptation. Species differences diminished in winter (e.g., Actinobacteria: 14.17% vs. 23.24%), while altitude-controlled linear model analysis confirmed seasonal effects as primary drivers. These results demonstrate that seasonal life stages reconfigure gut microbiomes toward energy efficiency, stress resilience, and stochastic assembly, overriding species-specific traits in high-altitude birds. These findings highlight that life stages may play an important role in shaping gut microbiota patterns in high-altitude habitats, with tailoring microbial profiles to meet specific physiological and ecological needs for crucial seasonal environmental adaptation.