Longitudinal Multi-omics Reveals Persistent Gut Microbial and Metabolic Dysbiosis Following Anti-Tuberculosis Therapy

Pulmonary tuberculosis (TB) is associated with systemic alterations extending beyond the lungs, yet the longitudinal impact of anti-tuberculosis therapy (ATT) on gut ecosystem recovery remains poorly understood. Here, we performed a longitudinal multi-omics analysis of gut microbial and metabolic dynamics in pulmonary TB patients (n=8) followed at baseline, 1, 6, and 8 months of ATT, compared with healthy household contacts (HHCs; n=8). Shotgun metagenomics, functional profiling, untargeted fecal metabolomics, resistome, plasmidome, virome, and microbiome-metabolome integration analyses were performed to characterize disease-associated alterations and treatment-associated recovery. Active, treatment-naive TB was characterized by reduced microbial diversity, altered community structure, depletion of beneficial commensals, and disruption of microbial functional pathways and metabolic profiles. During ATT, microbial diversity and functional/metabolic features progressively recovered; however, post-treatment profiles remained distinct from HHCs, indicating incomplete ecological restoration after microbiological cure. Microbiome-metabolome analysis revealed associations between altered bacterial taxa and metabolites involved in amino acid metabolism, bile acid transformation, oxidative stress, and host-microbial metabolic interactions. In contrast, resistome and mobile genetic element profiles demonstrated greater stability throughout treatment. HHCs exposed to index TB cases maintained relative gut ecosystem stability over time. Bacterial-AMR correlation analysis identified taxon-specific resistance associations among gut bacteria. Together, these findings provide a longitudinal systems-level view of gut ecosystem remodeling during TB and highlight that restoration of microbial homeostasis extends beyond pathogen clearance.