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Here, we assembled 340 metagenomes from 52 bird species covering 11 provincial administrative districts in China, presenting a specialized migratory microbial genome and gene catalog to archive the genomic and functional diversity of gut microbiomes in wild birds. This comprehensive migratory bird microbial genome and gene (MBGG) catalog includes 5823 metagenome\u2010assembled genomes (MAGs), 13\u00a0072 plasmid sequences, and 44\u00a0974 viral genomes, which represent 1709 candidate species spanning 36 phyla. The catalog also contains over 20 million non\u2010redundant protein\u2010encoding genes, the use of which is confirmed by the mining of 15\u00a0678 secondary metabolite biosynthetic gene clusters, 1814 known antibiotic resistance genes, and 7219 virulence factors. The number of clinically critical ARGs identified in\n                    <jats:italic>Grus japonensis<\/jats:italic>\n                    was the highest, followed by\n                    <jats:italic>Cygnus cygnus<\/jats:italic>\n                    and\n                    <jats:italic>Sibirionetta formosa<\/jats:italic>\n                    , which indicated that these species are hotspot species of clinically critical AMR dissemination. Moreover, we mapped the profile of bacterial zoonotic\/opportunistic pathogens carried by wild birds and evaluated their associations with publicly available genomes. Finally, the precise migratory movements for 10 bird species using a global positioning system tracking system help to assess the movement of microorganisms and AMR risk. Collectively, this valuable resource provides the basis for the integration and unification of global wild bird microbiomes, timely sharing, and assessing the uncertainty of migratory microbiomes in the future.\n                  <\/jats:p>","DOI":"10.1002\/advs.74581","type":"journal-article","created":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T12:23:16Z","timestamp":1772972596000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats"],"prefix":"10.1002","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7461-2195","authenticated-orcid":false,"given":"Yanan","family":"Wang","sequence":"first","affiliation":[{"name":"International Joint Research Center of National Animal Immunology College of Veterinary Medicine Henan Agricultural University  Zhengzhou China"},{"name":"CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences (CAS)  Beijing China"},{"name":"Longhu Laboratory of Advanced Immunology Zhengzhou China"},{"name":"Beijing Key Laboratory of Antimicrobial\u2010Resistant Pathogen Microbiology and AI\u2010Empowered Containment Institute of Microbiology Chinese Academy of Sciences (CAS) Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heqi","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Evolution &amp; Animal Models Kunming Institute of Zoology Chinese Academy of Sciences Kunming China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengqi","family":"Qu","sequence":"additional","affiliation":[{"name":"International Joint Research Center of National Animal Immunology College of Veterinary Medicine Henan Agricultural University  Zhengzhou 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