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The symptoms include a persistent cough, excessive production of purulent sputum, and recurrent hemoptysis. Dysbiosis of the microbiome plays a crucial role in the progression of BE. An increased abundance of pathogenic bacteria, along with viral and fungal infections, is closely associated with disease severity and clinical outcomes. Next-generation sequencing technology has significantly enhanced the sensitivity and resolution of the airway microbiome, providing powerful tools for a more detailed characterization of the microecology of BE. However, certain challenges still exist in clinical applications of this technology. In addition, extra-airway microbiomes, such as the gut and oral microbiome, may participate in airway inflammation and immune regulation through the gut-lung axis and oral-lung axis. In this review, we summarize the characteristics of microbiome dysbiosis in BE and highlight the potential value of related biomarkers in disease classification, severity assessment, and prognosis. We also provide an overview of recent treatment advancements. 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