Gut microbime always have big impacts on health of wild animals,while habitat pollution and human activities could threaten their survival by switching intestinal microbiome.Here,we satellite-tracked same group of swan geese (Ansercygnoides) migrating from their breeding area (Khukh Lake,Mongolia) with rare human activities to wintering area (Poyang Lake,China) with high level of human activities and fisheries aquaculture.Twenty fecal samples were collected from each site without hurting the wild geese.High-throughput sequencing of 16S and ITS was employed to depict bacteria and fungi composition and diversity of their gut microbiome.The dominant bacterial phyla were Firmicutes,Proteobacteria,and Actinobacteria,and the dominant fungal phyla were Basidiomycota,Ascomycota,and Zygomycota.Although general composition,alpha-diversity,functional prediction,and the central taxa in phylogenetic networks showed some similarities in geese gut between two habitats,significant divergences were also detected in terms of beta-diversity,species abundances and interaction network topologies.In addition,disease-related and xenobiotics biodegradation pathways,and pathogenic bacteria were significantly increased in bacteria communities from samples in the Poyang Lake.Our results revealed the convergence and divergence of wild swan geese during their migration.We also indicated that habitat environments could alter the gut microbial communities of wild animals intestines,suggesting that polluted habitats could indirectly threaten wild animals by switching their gut microbiome.