Cystic Fibrosis Sputum and Saliva Microbiome

Cystic fibrosis is an inherited disease characterized by chronic respiratory tract infection and progressive lung disease. Studies of cystic fibrosis lung microbiology often rely on expectorated sputum to reflect the microbiota present in the lower airways. Passage of sputum through the oropharynx during collection, however, contributes microbes present in saliva to the sample, which could produce misleading results. Using culture-independent DNA sequencing-based analyses, we characterized the bacterial communities in pairs of expectorated sputum and saliva samples to generate a model for decontaminating sputum in silico. Our results suggest that salivary contamination of expectorated sputum does not have a large effect on most sputum samples, and that observations of high bacterial diversity likely accurately reflect taxa present in cystic fibrosis lower airways.