Investigators will examine temporal and regional dynamic changes in the microbiome of Cystic Fibrosis patients to explore microbiome features that are associated with an inflammatory phenotype. Investigators hypothesize that temporal and spatial differences in lung microbiome are associated with host inflammatory responses.

While chronic and polymicrobial airway colonization are commonly recognized in cystic fibrosis (CF), it is unclear what factors of the microbial environment lead to infection with pathogenic microorganism. This is a multi center, longitudinal cohort of adult Cystic Fibrosis subjects recruit4ed from NYU and Columbia to understand how changes in the airway microbiome may affect the host inflammatory responses in Cystic Fibrosis (CF). There will be three approaches to understanding inflammatory responses; 1) a longitudinal assessment of temporal changes in the microbiome over a 6-month period of clinical stability; 2) comparison of the regional differences in airway microbiome between lung segments with more versus less disease; 3) evaluation of functional aspects of the lung microbiome.

Inclusion Criteria:

• CF diagnosis
• able to produce sputum
• no recent (one month) exacerbation defined as physician treatment with antibiotics for ≥ 7days
• FEV1 ≥ 30% of predicted.

Exclusion Criteria:

• Initiation of any new chronic therapy (e.g., ibuprofen, aerosolized rhDNase, hypertonic saline, azithromycin, tobramycin inhalation solution, aztreonam inhalation solution, ivacaftor) within 8 weeks prior to enrolment
• introduction of vitamins or proton pump inhibitors within 8 weeks prior to enrolment
• use of new investigational therapy within 4 weeks
• current smoker; use of oral corticosteroids
• Initiation of treatment or change in regimen for allergic bronchopulmonary aspergillosis or nontuberculous mycobacteria within 8 weeks.
• liver enzymes > 3 times the upper limit
• pregnancy

Additional Exclusion Criteria for Bronchoscopy Subgroup (Aims 2 and 3):

• FEV1 < 50% of predicted.
• Significant cardiovascular disease defined as abnormal EKG, known or suspected coronary artery disease or congestive heart failure.
• Significant renal disease (Creatinine Clearance < 30%).
• Severe malnutrition (BMI <18kg/m2)

Multicenter study to create a longitudinal cohort of adult CF subjects recruited from NYU and Columbia. A subgroup of subjects will be selected for a more invasive assessment of the lung microbiome with research bronchoscopy.