There is an increasing recognition that the airways of persons with cystic fibrosis (CF) typically harbor complex polymicrobial communities that include numerous bacterial species. It is unknown, however, how changes in these communities relate to the progression of lung disease. More specifically, how changes in the structure and/or activity of airway bacterial communities are associated with the intermittent pulmonary exacerbations (PExs) that characterize CF has not been systematically investigated. The lack of respiratory specimens and granular clinical data from periods of time preceding PExs has been a critical barrier to progress in this area. The scientific premise for this project is that a better understanding of airway microbial community dynamics with respect to PExs will provide new opportunities to better care to persons with CF. The overarching hypothesis is that changes in the structure and/or activity of these communities drive the pathophysiology of PExs. In the short term, this study will identify targets of immediate translational clinical interest. In the longer term, this project will elucidate the mechanisms governing microbial community and host changes associated with PExs.
The specific aims of this project are to (i) characterize microbial community and host inflammatory changes that occur with PEx, (ii) develop predictive models of PEX resolution, and (iii) develop dynamic models that predict microbe-microbe and host-microbe interactions during PEx. The feasibility of this project is supported by a pilot project in which we prospectively collected daily sputum samples from a cohort of CF patients during the course of up to two years. The prospective collection of daily samples and clinical metadata proposed in the current project incorporates several improvements that will yield more robust results. Next- generation DNA sequencing and analysis of bacterial metabolites will be used to characterize the structure and activity of the bacterial communities in samples obtained around the time of pulmonary exacerbations. Microbial community changes that correlate with exacerbation onset, severity and recovery will be identified. Modeling of these changes will describe the microbial-microbial and host-microbial interactions associated with transitions in clinical state throughout the PEx cycle. This information will form the basis of follow on studies to better understand the pathophysiologic mechanisms of PEx in CF.

Public Health Relevance

Respiratory failure is the cause of death in 95% of persons with cystic fibrosis (CF). Despite the prominent role that exacerbations of pulmonary illness play in the course of CF, our understanding of pulmonary exacerbation etiology and pathophysiology is remarkably limited. This project will use a unique collection of more than 10,000 CF sputum samples to characterize the dynamic structure and activity of the airway microbiome, particularly around the time of pulmonary exacerbations. In the short term, this study will identify targets of immediate translational clinical interest; in the longer term, we aim to elucidate the mechanisms underlying the microbial determinants of CF lung disease.

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
Research Project (R01)
Project #
Application #
Study Section
Lung Cellular, Molecular, and Immunobiology Study Section (LCMI)
Program Officer
Lachowicz-Scroggins, Marrah Elizabeth
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Michigan Ann Arbor
Schools of Medicine
Ann Arbor
United States
Zip Code