The airway microbiota in cystic fibrosis: a complex and dynamic biological community and implications for therapeutic management

Given the polymicrobial nature of pulmonary infections in patients with cystic fibrosis, it is essential to enhance our knowledge on the composition of the microbial community to improve cystic fibrosis management. In this study, we developed a powerful pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in cystic fibrosis lower airways. Results from conventional microbiological culture and identification of fungi and bacteria in eight sputum samples from four adult cystic fibrosis patients were compared with those from throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene, and related to the clinical profile of the cystic fibrosis patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera had not been identified in cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function. Phylogenetic analysis showed high molecular diversity at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were rarely isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans. In light of the new concept of microbiota, we viewed the microbial community as a unique pathogenic entity. We thus interpreted our results to highlight the potential interactions between microorganisms and the role of fungi in the context of improving survival in cystic fibrosis.