title: The microbial community of the cystic fibrosis airway is disrupted in early life.
abstract: BACKGROUND
  Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF) airways, the clinical significance of which is yet to be determined. The aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with CF and children without CF.
  
  
  METHODS
  Bronchoalveolar lavage (BAL) fluid and paired oropharyngeal swabs from clinically stable children with CF (n = 13) and BAL from children without CF (n = 9) were collected. DNA was isolated, the 16S rRNA regions amplified, fragmented, biotinylated and hybridised to a 16S rRNA microarray. Patient medical and demographic information was recorded and standard microbiological culture was performed.
  
  
  RESULTS
  A diverse bacterial community was detected in the lower airways of children with CF and children without CF. The airway microbiome of clinically stable children with CF and children without CF were significantly different as measured by Shannon's Diversity Indices (p = 0.001; t test) and Principle coordinate analysis (p = 0.01; Adonis test). Overall the CF airway microbial community was more variable and had a less even distribution than the microbial community in the airways of children without CF. We highlighted several bacteria of interest, particularly Prevotella veroralis, CW040 and a Corynebacterium, which were of significantly differential abundance between the CF and non-CF lower airways. Both Pseudomonas aeruginosa and Streptococcus pneumoniae culture abundance were found to be associated with CF airway microbial community structure. The CF upper and lower airways were found to have a broadly similar microbial milieu.
  
  
  CONCLUSIONS
  The microbial communities in the lower airways of stable children with CF and children without CF show significant differences in overall diversity. These discrepancies indicate a disruption of the airway microflora occurring early in life in children with CF.
authors.affiliation: Department of Clinical Microbiology, Trinity College, Dublin, Ireland; The National Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland; The National Children's Hospital, Tallaght hospital, Dublin, Ireland.
authors.forename: Julie
authors.initials: J
authors.lastname: Renwick
authors.affiliation: The National Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland.
authors.forename: Paul
authors.initials: P
authors.lastname: McNally
authors.affiliation: Second Genome, South San Francisco, California, United States of America.
authors.forename: Bettina
authors.initials: B
authors.lastname: John
authors.affiliation: Second Genome, South San Francisco, California, United States of America.
authors.forename: Todd
authors.initials: T
authors.lastname: DeSantis
authors.affiliation: The National Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland; Hospital Limerick, Limerick, Ireland; Centre for Interventions in Infection, Inflammation & Immunity (4i), Graduate-Entry Medical School, University of Limerick, Limerick, Ireland.
authors.forename: Barry
authors.initials: B
authors.lastname: Linnane
authors.affiliation: Department of Clinical Microbiology, Trinity College, Dublin, Ireland; The National Children's Research Centre, Our Lady's Children's Hospital, Dublin, Ireland; The National Children's Hospital, Tallaght hospital, Dublin, Ireland.
authors.forename: Philip
authors.initials: P
authors.lastname: Murphy
mesh_terms: D001992:Bronchoalveolar Lavage Fluid / Q000382:microbiology; D002648:Child; D002675:Child, Preschool; D003352:Corynebacterium / Q000302:isolation & purification; D003550:Cystic Fibrosis / Q000382:microbiology*; D005260:Female; D006801:Humans; D007223:Infant; D008297:Male; D064307:Microbiota; D018720:Prevotella / Q000302:isolation & purification; D011550:Pseudomonas aeruginosa / Q000302:isolation & purification; D020545:Respiratory Mucosa / Q000382:microbiology*; D013296:Streptococcus pneumoniae / Q000302:isolation & purification