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The Cystic Fibrosis Pulmonary Microbiome

In this podcast Dr. Lindsay Caverly, Dr. Robert Quinn and Dr. Ryan Thomas discuss the pulmonary microbiome in cystic fibrosis. This wide-ranging discussion begins with a conversation of the microbiome in the normal lung and then moves to the alterations of the microbiome in cystic fibrosis and the tools and techniques used in the discovery of these changes. They cover how antibiotics and other chronic treatments of cystic fibrosis alter the microbiome in CF as well as how the new CFTR modulators maybe having an effect both clinically and on future research. They finish by discussing the potential benefits of gaining better understanding of the microbiome and areas for future research.



Contact Information: 

Ryan Thomas, MD:

Robert Quinn, PhD:

ATS Peds:


Selected Relevant References:

Lindsay Caverly:

  • Caverly LJ et al. Measures of Cystic Fibrosis Airway Microbiota During Periods of Clinical Stability. Ann Am Thorac Soc. 2019 Dec;16(12):1534-1542.
  • Caverly LJ, Zhao J, LiPuma JJ. Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection. Pediatr Pulmonol . 2015 Oct;50 Suppl 40:S31-8.
  • Caverly LJ, Huang YJ, Sze MA. Past, Present, and Future Research on the Lung Microbiome in Inflammatory Airway Disease. Chest . 2019 Aug;156(2):376-382.
  • Caverly LJ, LiPuma JJ. Cystic fibrosis respiratory microbiota: unraveling complexity to inform clinical practice. Expert Rev Respir Med. 2018 Oct;12(10):857-865.
  • Carmody et al. Fluctuations in airway bacterial communities associated with clinical states and disease stages in cystic fibrosis. PLoS One. 2018 Mar 9;13(3):e0194060.

Robert Quinn: 

  • Quinn RA et al. Microbial, host and xenobiotic persity in the cystic fibrosis sputum metabolome. ISME J. 2016 Jun; 10(6): 1483–1498. 
  • Quinn RA et al. A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. The ISME Journal volume 9, pages1024–1038. ISME J. 2015 Mar 17;9(4):1024-38.
  • Quinn RA et al. Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease. PeerJ. 2016 Aug 11;4:e2174.
  • Raghunashi R et al. High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy. mSystems. 2020 Jun 23;5(3):e00292-20.
  • Quinn RA et al. Ecological networking of cystic fibrosis lung infections. NPJ Biofilms Microbiomes. 2016 Dec 2;2:4.


Other Referenced Works:

  • Muhlebach MS et al. Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children. PLoS Pathog. 2018 Jan 18;14(1):e1006798.
  • Sly PD et al. Lung disease at diagnosis in infants with cystic fibrosis detected by newborn screening. Am J Respir Crit Care Med 2009; 180: pp. 146-152
  • JM Flynn et al. Disruption of Cross-Feeding Inhibits Pathogen Growth in the Sputa of Patients with Cystic Fibrosis. 
  • Muhlebach MS et al.  Anaerobic bacteria cultured from cystic fibrosis airways correlate to milder disease: a multisite study. Eur Respir J. 2018 Jul 11;52(1):1800242. mSphere. 2020 Apr 29;5(2):e00343-20.
  • Pittman JE et al. Association of Antibiotics, Airway Microbiome, and Inflammation in Infants with Cystic Fibrosis. Ann Am Thorac Soc. 2017 Oct;14(10):1548-1555.
  • Nelso MT et al. Maintenance tobramycin primarily affects untargeted bacteria in the CF sputum microbiome. Thorax. 2020 Jul 6
  • Cowley SC et al. Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation. mBio. 2015 Jul 28;6(4):e00767.
  • Heltshe SL et al. Pseudomonas aeruginosa in cystic fibrosis patients with G551D-CFTR treated with ivacaftor. Clin Infect Dis. 2015 Mar 1;60(5):703-12.
  • Singh SB. Pathogen acquisition in patients with cystic fibrosis receiving ivacaftor or lumacaftor/ivacaftor. Pediatr Pulmonol. 2019 Aug;54(8):1200-1208.
  • Hisert KB et al. Restoring Cystic Fibrosis Transmembrane Conductance Regulator Function Reduces Airway Bacteria and Inflammation in People with Cystic Fibrosis and Chronic Lung Infections. Am J Respir Crit Care Med. 2017 Jun 15;195(12):1617-1628.