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Relevant literature on respiratory tract microbiota and immune and respiratory disease published in PubMed, SpringerLink and Web of Science up to June 2026 was narratively reviewed. This review aims to elucidate the interactions between the commensal microbiota of the respiratory tract and the host immune system and reveal how these interactions evolve from homeostasis to disease pathogenesis. We also analyze how dysbiosis can promote chronic airway inflammation by changing microbial metabolites, destroying the integrity of epithelial barrier, and activating abnormal immune and inflammatory pathways, thus playing a key driving role in chronic obstructive pulmonary disease (COPD), asthma, cystic fibrosis (CF), bronchiectasis and other diseases. Additionally, the potential and challenges of current treatment strategies based on microbiota regulation, such as herbal medicines and probiotics, in the prevention and treatment of respiratory diseases are discussed. This review provides a new perspective for revealing the etiology of respiratory diseases and lays a solid theoretical foundation for the development of microbial intervention therapy.<\/jats:p>","DOI":"10.3390\/pathogens15090883","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T14:49:34Z","timestamp":1787582974000},"page":"883","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Beyond Pathogens: Modulating the Commensal Microbiota to Reshape Immunity for Respiratory Disease Intervention"],"prefix":"10.3390","volume":"15","author":[{"given":"Yang","family":"Yang","sequence":"first","affiliation":[{"name":"Ministry of Education Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Tianjin 301617, China"},{"name":"State Key Laboratory of Chinese Medicine Modernization, Tianjin University of 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