Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents

Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.