The Microbiota of the Pediatric CF Airway: What Role Does It Play?

Progressive, obstructive lung disease remains the biggest cause of morbidity and early mortality in cystic fibrosis (CF). Early detection and treatment of pulmonary decline is key to optimal long-term outcome; however, physiologic measures of lung function and radiologic outcomes fail to capture the inflammation and infection that begin in infancy, which are often asymptomatic.

Mucus stasis and impaired bacterial killing provide the optimal environment for chronic bacterial infection in the CF airway. Culture-independent approaches using next-generation sequencing techniques have revealed a more complex, polymicrobial community in the CF airway than previously identified using traditional culture. Interestingly, a large number of these communities are anaerobes, known to inhabit the oral cavity and thought to be non-pathogenic. Recently, anaerobes in CF sputum were found to generate a nutritional environment through fermentative metabolism and mucin degradation that facilitates the growth and persistence of bacterial pathogens like Pseudomonas aeruginosa, a known contributor to lung function decline in CF.

Surprisingly, Dr. Laguna has found that anaerobes are already present in higher relative abundance compared to traditional CF pathogens in the lower airways of infants with CF; however, we do not yet understand their contribution in the development of early lung disease. The key question remains whether the early presence of anaerobic bacteria in the lower airways of CF infants predisposes them to a more rapid decline in lung function, more frequent pulmonary exacerbations or structural lung damage.

Therefore, the central hypothesis of this proposal is that anaerobic bacteria in the lower airways of infants and children with CF is associated with fermentative metabolism and will have a unique metabolic and metaproteomic biosignature that incites inflammation and contributes to the development of early CF lung disease. This research takes advantage of the team’s expertise and established collaborations with experts in the field as well as a unique and valuable resource: a collection of bronchoalveolar lavage fluid (BALF) samples from children with/without CF available for immediate analysis.

The aims of this project are three-fold:

• First, through the measurement of fermentation and mucin products, to determine if anaerobic communities in BALF associate with a fermentative environment in the CF airway.
• Second, to determine if the lower airway microbiota is associated with the metabolomic profile measured in BALF from young children with/without CF.
• Third, through innovative metaproteomics technology, to characterize the metaproteome to determine the metabolic activity of the microbial communities in the CF airway.

The knowledge gained upon completion of this project would allow healthcare providers to consider anaerobic specific antibiotics or encourage the development of new antimicrobials targeting bacterial fermentative processes as a new treatment for CF lung disease.