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Gut microbiota is increasingly linked to the development of various pulmonary diseases through a gut–lung axis. However, the mechanisms by which gut commensal microbes impact trafficking and functional transition of immune cells remain largely unknown. Using integrated microbiota dysbiosis approaches, we uncover that the gut microbiota directs the migration of group 2 innate lymphoid cells (ILC2s) from the gut to the lung through a gut–lung axis. We identify Proteobacteria as a critical species in the gut microbiome to facilitate natural ILC2 migration, and increased Proteobacteria induces IL-33 production. Mechanistically, IL-33–CXCL16 signaling promotes the natural ILC2 accumulation in the lung, whereas IL-25–CCL25 signals augment inflammatory ILC2 accumulation in the intestines upon abdominal infection, pa…