Altered airway microbiota and microbial biomarkers across respiratory diseases: insights from 16S rDNA sequencing

Objective The airway microbiota plays an important role in respiratory health and disease, yet comprehensive comparisons of microbial alterations across different respiratory disorders remain limited. Methods We performed 16S rDNA sequencing to characterize the airway microbiota in patients with chronic obstructive pulmonary disease (COPD, n = 53), bronchial asthma (BA, n = 38), pneumonia (PNE, n = 25), chronic cough (CC, n = 21), bronchitis (BRO, n = 4), and lung cancer (CA, n = 3), alongside healthy controls (NC, n = 9). Microbial richness, alpha and beta diversity, taxonomic composition, and disease-specific microbial biomarkers were systematically analyzed. Results Microbial richness and diversity were significantly reduced in respiratory diseases compared with controls, particularly in CA and BRO. Beta diversity analysis revealed distinct clustering, with COPD, BA, and PNE forming Firmicutes-dominated clusters, while CA and BRO clustered separately with Proteobacteria dominance. CC and NC shared similar profiles. MetaStat analysis showed enrichment of Firmicutes in COPD and PNE, Proteobacteria in CA, and unclassified taxa in CC. Linear discriminant analysis identified biomarkers like Rothia in COPD, Veillonella in PNE, Haemophilus in BA, Neisseria in CA, and Neisseria subflava in BRO, with healthy controls enriched in Clostridia. Conclusion Our findings reveal that airway microbial communities are profoundly altered in respiratory diseases, characterized by reduced diversity, disease-specific clustering, and distinct microbial biomarkers. These results highlight the potential of airway microbiota as diagnostic indicators and provide insights into the pathophysiological roles of microbial dysbiosis in respiratory diseases.