A biomarker cohort study design is proposed to study whether specific airway microbiota alterations are associated with pulmonary Non-tuberculous mycobacteria (NTM) disease. In a cohort of 200 subjects suspected of having pulmonary NTM disease, the investigators will evaluate the airway microbiome using an aliquot of the induced sputum and upper airway samples. Since induced sputum may reflect different regions of the upper/lower airways, the investigators will evaluate the upper and lower airway microbiome in a subgroup (case-control group) of patients using samples obtained through upper airway sampling and bronchoscopy, respectively.

Inclusion Criteria:

• History of pulmonary symptoms: cough, fatigue, malaise, fever, weight loss, dyspnea, hemoptysis, or chest discomfort
• Imaging abnormalities (within 2 years): defined as nodular or cavitary opacities on chest radiograph, or a computed tomography scan that shows bronchiectasis or bronchial wall thickening with associated multiple small nodules.

Definition of NTM case:

• Subjects that meet inclusion criteria and have culture positivity for NTM: at least two separate expectorated induced sputum samples or from one bronchoalveolar lavage (BAL) or lung biopsy

Definition of NTM control:

• Subjects that meet inclusion criteria and have less than two separate expectorated induced sputum samples culture negative or culture negative bronchoalveolar lavage (BAL) or lung biopsy.

Exclusion Criteria for cohort study (Aim 1-2):

• Recent (<1 months prior) oral antibiotic or steroid use. (Continuous treatment with macrolides and inhaled steroids are acceptable >1 month prior)
• Recent smoking history

Exclusion Criteria for bronchoscopic study (Aims 3-4):

• Forced expiratory volume at one second (FEV1) < 70%of predicted.
• Significant cardiovascular disease defined as abnormal EKG, known or suspected coronary artery disease or congestive heart failure.
• Diabetes mellitus
• Significant liver or renal disease
• Severe coagulopathy (INR > 1.4, Partial Thromboplastin Time (PTT) > 40 seconds and platelet count < 150x103 cells).
• Pregnancy
• Ethanol (ETOH) use of more than >6 beers or >4 mixed drinks daily
• Lack of capacity to provide informed consent.

Utilizing cohorts built at NYU over the last several years, this project is uniquely positioned to investigate the microbiome signatures among subjects with NTM disease.