The airway microbiota in cystic fibrosis: a complex and dynamic biological community and implications for therapeutic management
Bacteria
Polymicrobial infections are increasingly recognized as clinically important in cystic fibrosis (CF), which is a human autosomal recessive disease resulting in decreased clearance of mucus from the lungs with concomitant microbial pulmonary infections conducing to lung damage and death of patients. Here, we developed a pyrosequencing approach to extensively explore, for the first time, the diversity and dynamics of fungal and bacterial populations (microbiota) in CF lower airways. We clearly demonstrated that the diversity and microbial species richness were lower in patients with decreased lung function, and we interpreted our results to highlight the potential interactions between microorganisms and the role of fungi in the context of improving CF management.  High-throughput sequencing, due to its potential for massive direct sequencing after a single run of DNA amplification and automation, appears to be the most promising approach to access the CF lung microbiota. The present study should stimulate a debate over the best way to combine new technology (deep-sequencing), ecological tools (to analyze community interactions), and clinically relevant information.   A better knowledge of sputum microbiota would represent a major advance in our understanding of the disease, and has the potential to dramatically improve survival in CF patients.