title: Airway microbiota and pathogen abundance in age-stratified cystic fibrosis patients.
abstract: Bacterial communities in the airways of cystic fibrosis (CF) patients are, as in other ecological niches, influenced by autogenic and allogenic factors. However, our understanding of microbial colonization in younger versus older CF airways and the association with pulmonary function is rudimentary at best. Using a phylogenetic microarray, we examine the airway microbiota in age stratified CF patients ranging from neonates (9 months) to adults (72 years). From a cohort of clinically stable patients, we demonstrate that older CF patients who exhibit poorer pulmonary function possess more uneven, phylogenetically-clustered airway communities, compared to younger patients. Using longitudinal samples collected form a subset of these patients a pattern of initial bacterial community diversification was observed in younger patients compared with a progressive loss of diversity over time in older patients. We describe in detail the distinct bacterial community profiles associated with young and old CF patients with a particular focus on the differences between respective "early" and "late" colonizing organisms. Finally we assess the influence of Cystic Fibrosis Transmembrane Regulator (CFTR) mutation on bacterial abundance and identify genotype-specific communities involving members of the Pseudomonadaceae, Xanthomonadaceae, Moraxellaceae and Enterobacteriaceae amongst others. Data presented here provides insights into the CF airway microbiota, including initial diversification events in younger patients and establishment of specialized communities of pathogens associated with poor pulmonary function in older patient populations.
authors.affiliation: Department of Medicine, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Cox
authors.forename: Martin
authors.initials: M
authors.lastname: Allgaier
authors.forename: Byron
authors.initials: B
authors.lastname: Taylor
authors.forename: Marshall S
authors.initials: MS
authors.lastname: Baek
authors.forename: Yvonne J
authors.initials: YJ
authors.lastname: Huang
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Daly
authors.forename: Ulas
authors.initials: U
authors.lastname: Karaoz
authors.forename: Gary L
authors.initials: GL
authors.lastname: Andersen
authors.forename: Ronald
authors.initials: R
authors.lastname: Brown
authors.forename: Kei E
authors.initials: KE
authors.lastname: Fujimura
authors.forename: Brian
authors.initials: B
authors.lastname: Wu
authors.forename: Diem
authors.initials: D
authors.lastname: Tran
authors.forename: Jonathan
authors.initials: J
authors.lastname: Koff
authors.forename: Mary Ellen
authors.initials: ME
authors.lastname: Kleinhenz
authors.forename: Dennis
authors.initials: D
authors.lastname: Nielson
authors.forename: Eoin L
authors.initials: EL
authors.lastname: Brodie
authors.forename: Susan V
authors.initials: SV
authors.lastname: Lynch
mesh_terms: D000293:Adolescent; D000328:Adult; D017677:Age Distribution; D000368:Aged; D001483:Base Sequence; D002648:Child; D002675:Child, Preschool; D003550:Cystic Fibrosis / Q000382:microbiology* / Q000503:physiopathology; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics; D017931:DNA Primers; D006801:Humans; D007223:Infant; D008875:Middle Aged; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction
chemical_list: D017931:DNA Primers; D019005:Cystic Fibrosis Transmembrane Conductance Regulator