Microbiome features and their clinical associations in cavitary pulmonary tuberculosis

Abstract Introduction Tuberculosis (TB) remains a major global health threat. Cavitary pulmonary tuberculosis (cavitary PTB) is associated with more severe disease manifestations and complex clinical management. This study aimed to analyze the pulmonary microbiome in cavitary PTB, and explore its associations with clinical indicators. Methods A retrospective study was conducted in 200 PTB patients who underwent bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) between January 2021 to December 2023. After applying inclusion and exclusion criteria, 189 patients were enrolled and categorized into cavitary ( n = 30) and non-cavitary ( n = 159) groups based on imaging findings. Differences in clinical characteristics and pulmonary microbiome profiles between groups were analyzed. Results Patients with cavitary PTB showed a higher proportion of bilateral lung involvement compared to non-cavitary patients (80% vs. 56.60%, P = 0.024). mNGS demonstrated superior detection performance for Mycobacterium tuberculosis complex (MTBC) compared with conventional methods. Cavitary PTB patients exhibited significantly higher MTBC abundance but reduced microbial diversity. In the Spearman correlation analysis (FDR-adjusted), the presence of cavities was significantly positively correlated with two microbial taxa identified by Linear Discriminant Analysis Effect Size analysis - Mycobacterium tuberculosis complex and Prevotella jejuni . Conclusions Cavitary formation in PTB is associated with distinct alterations in pulmonary microbiome composition, characterized by increased MTBC dominance and reduced microbial diversity. Specific microbiome features are significantly correlated with key clinical indicators, highlighting their potential value in disease assessment and management. All relationships reported here are associations; the cross-sectional design of this study precludes any inference of causality.