title: Lung microbiota across age and disease stage in cystic fibrosis.
abstract: Understanding the significance of bacterial species that colonize and persist in cystic fibrosis (CF) airways requires a detailed examination of bacterial community structure across a broad range of age and disease stage. We used 16S ribosomal RNA sequencing to characterize the lung microbiota in 269 CF patients spanning a 60 year age range, including 76 pediatric samples from patients of age 4-17, and a broad cross-section of disease status to identify features of bacterial community structure and their relationship to disease stage and age. The CF lung microbiota shows significant inter-individual variability in community structure, composition and diversity. The core microbiota consists of five genera - Streptococcus, Prevotella, Rothia, Veillonella and Actinomyces. CF-associated pathogens such as Pseudomonas, Burkholderia, Stenotrophomonas and Achromobacter are less prevalent than core genera, but have a strong tendency to dominate the bacterial community when present. Community diversity and lung function are greatest in patients less than 10 years of age and lower in older age groups, plateauing at approximately age 25. Lower community diversity correlates with worse lung function in a multivariate regression model. Infection by Pseudomonas correlates with age-associated trends in community diversity and lung function.
authors.affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Bryan
authors.initials: B
authors.lastname: Coburn
authors.affiliation: Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Pauline W
authors.initials: PW
authors.lastname: Wang
authors.affiliation: Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Julio
authors.initials: J
authors.lastname: Diaz Caballero
authors.affiliation: Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Shawn T
authors.initials: ST
authors.lastname: Clark
authors.affiliation: Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Vijaya
authors.initials: V
authors.lastname: Brahma
authors.affiliation: Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Sylva
authors.initials: S
authors.lastname: Donaldson
authors.affiliation: 1] Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada [2] Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Anu
authors.initials: A
authors.lastname: Surendra
authors.affiliation: Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Yunchen
authors.initials: Y
authors.lastname: Gong
authors.affiliation: Adult Cystic Fibrosis Clinic, St. Michael's Hospital, Toronto, Ontario, Canada.
authors.forename: D
authors.initials: D
authors.lastname: Elizabeth Tullis
authors.affiliation: 1] Department of Pediatric Laboratory Medicine, Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada [2] Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada.
authors.forename: Yvonne C W
authors.initials: YC
authors.lastname: Yau
authors.affiliation: Division of Infectious Diseases, Department of Pediatrics, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Valerie J
authors.initials: VJ
authors.lastname: Waters
authors.affiliation: 1] Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada [2] Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada [3] Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada.
authors.forename: David M
authors.initials: DM
authors.lastname: Hwang
authors.affiliation: 1] Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada [2] Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
authors.forename: David S
authors.initials: DS
authors.lastname: Guttman
mesh_terms: D000293:Adolescent; D000328:Adult; D044822:Biodiversity; D002648:Child; D002675:Child, Preschool; D003550:Cystic Fibrosis / Q000382:microbiology*; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D005260:Female; D006801:Humans; D008168:Lung / Q000382:microbiology*; D008297:Male; D064307:Microbiota / Q000235:genetics*; D008875:Middle Aged; D011446:Prospective Studies; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013183:Sputum / Q000382:microbiology*; D055815:Young Adult
chemical_list: C505032:CFTR protein, human; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D019005:Cystic Fibrosis Transmembrane Conductance Regulator