title: The airway microbiota in cystic fibrosis: a complex fungal and bacterial community--implications for therapeutic management.
abstract: BACKGROUND
  Given the polymicrobial nature of pulmonary infections in patients with cystic fibrosis (CF), it is essential to enhance our knowledge on the composition of the microbial community to improve patient management. In this study, we developed a pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in CF lower airways.
  
  
  RESULTS
  Fungi and bacteria diversity in eight sputum samples collected from four adult CF patients was investigated using conventional microbiological culturing and high-throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene. The unveiled microbial community structure was compared to the clinical profile of the CF patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera were not detected by cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function and poor clinical status. Values of Chao1 richness estimator were statistically correlated with values of the Shwachman-Kulczycki score, body mass index, forced vital capacity, and forced expiratory volume in 1 s (p = 0.046, 0.047, 0.004, and 0.001, respectively for fungal Chao1 indices, and p = 0.010, 0.047, 0.002, and 0.0003, respectively for bacterial Chao1 values). Phylogenetic analysis showed high molecular diversities at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans than with Aspergillus fumigatus.
  
  
  CONCLUSIONS
  In light of the recent concept of CF lung 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 CF.
authors.affiliation: Center for Infection and Immunity of Lille (CIIL), Institut Pasteur de Lille, Biology and Diversity of Emerging Eukaryotic Pathogens (BDEEP), BP 245, Lille, France. Laurence.delhaes@pasteur-lille.fr
authors.forename: Laurence
authors.initials: L
authors.lastname: Delhaes
authors.forename: Sébastien
authors.initials: S
authors.lastname: Monchy
authors.forename: Emilie
authors.initials: E
authors.lastname: Fréalle
authors.forename: Christine
authors.initials: C
authors.lastname: Hubans
authors.forename: Julia
authors.initials: J
authors.lastname: Salleron
authors.forename: Sylvie
authors.initials: S
authors.lastname: Leroy
authors.forename: Anne
authors.initials: A
authors.lastname: Prevotat
authors.forename: Frédérick
authors.initials: F
authors.lastname: Wallet
authors.forename: Benoit
authors.initials: B
authors.lastname: Wallaert
authors.forename: Eduardo
authors.initials: E
authors.lastname: Dei-Cas
authors.forename: Telesphore
authors.initials: T
authors.lastname: Sime-Ngando
authors.forename: Magali
authors.initials: M
authors.lastname: Chabé
authors.forename: Eric
authors.initials: E
authors.lastname: Viscogliosi
mesh_terms: D000328:Adult; D001419:Bacteria / Q000145:classification / Q000235:genetics; D044822:Biodiversity; D003550:Cystic Fibrosis / Q000382:microbiology* / Q000628:therapy*; D004269:DNA, Bacterial / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005260:Female; D005658:Fungi / Q000145:classification / Q000235:genetics; D006801:Humans; D008297:Male; D054892:Metagenome / Q000235:genetics*; D012137:Respiratory System / Q000382:microbiology*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer