Pre- and Post-treatment Lung Microbiota, Metabolome and Immune Signatures at the Site of Disease in Patients With Active Pulmonary Tuberculosis

Inclusion Criteria: * 18-60 years old. * Agree to undergo CXR and/or CT scan. * Has unilateral TB disease defined as one lung with extensive evidence of TB disease (non-applicable to healthy controls; sick controls will require an alternative diagnosis). * No evidence of prior TB treatment and/or CXR/CT does not have obvious evidence of prior TB. * Willing to undergo a research bronchoscopy at baseline, 6 months and 18 months and likely to remain in the area for the study period. * If HIV-positive, must be stable on antiretroviral therapy (ART) for ≥1 year. * Able and willing to return for follow-up visits, with no plans to move in the near future. * Willing to comply with study requirements i.e. provision of contact details and written, informed consent prior to enrolment. Exclusion Criteria: * Less than 18 years or older than 60 years of age. * Has already initiated TB treatment. * Rifampicin resistant. * Has a previous history of TB. * Bilateral TB disease defined as both lungs with extensive TB disease * Has received probiotics, antibiotics or inhaled steroids within three months prior to enrolment (not applicable to sick controls) * Has diabetes mellitus, which affects TB disease, treatment response, and the microbiome * Has a contraindication for bronchoscopy (e.g., FEV1 \<70%), as determined by bronchoscopists according to best practice guidelines * Has a daily alcohol intake of more than 6 beers or 4 mixed drinks * Is pregnant (a commercial human chorionic gonadotropin determination assay will be performed in accordance with manufacturer's guidance on urine) or pregnancy planned for follow-up period * Recent hospitalization for any reason