title: Decade-long bacterial community dynamics in cystic fibrosis airways.
abstract: The structure and dynamics of bacterial communities in the airways of persons with cystic fibrosis (CF) remain largely unknown. We characterized the bacterial communities in 126 sputum samples representing serial collections spanning 8-9 y from six age-matched male CF patients. Sputum DNA was analyzed by bar-coded pyrosequencing of the V3-V5 hypervariable region of the 16S rRNA gene, defining 662 operational taxonomic units (OTUs) from >633,000 sequences. Bacterial community diversity decreased significantly over time in patients with typically progressive lung disease but remained relatively stable in patients with a mild lung disease phenotype. Antibiotic use, rather than patient age or lung function, was the primary driver of decreasing diversity. Interpatient variability in community structure exceeded intrapatient variability in serial samples. Antibiotic treatment was associated with pronounced shifts in community structure, but communities showed both short- and long-term resilience after antibiotic perturbation. There was a positive correlation between OTU occurrence and relative abundance, with a small number of persistent OTUs accounting for the greatest abundance. Significant changes in community structure, diversity, or total bacterial density at the time of pulmonary exacerbation were not observed. Despite decreasing community diversity in patients with progressive disease, total bacterial density remained relatively stable over time. These findings show the critical relationship between airway bacterial community structure, disease stage, and clinical state at the time of sample collection. These features are the key parameters with which to assess the complex ecology of the CF airway.
authors.affiliation: Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
authors.forename: Jiangchao
authors.initials: J
authors.lastname: Zhao
authors.forename: Patrick D
authors.initials: PD
authors.lastname: Schloss
authors.forename: Linda M
authors.initials: LM
authors.lastname: Kalikin
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Carmody
authors.forename: Bridget K
authors.initials: BK
authors.lastname: Foster
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Petrosino
authors.forename: James D
authors.initials: JD
authors.lastname: Cavalcoli
authors.forename: Donald R
authors.initials: DR
authors.lastname: VanDevanter
authors.forename: Susan
authors.initials: S
authors.lastname: Murray
authors.forename: Jun Z
authors.initials: JZ
authors.lastname: Li
authors.forename: Vincent B
authors.initials: VB
authors.lastname: Young
authors.forename: John J
authors.initials: JJ
authors.lastname: LiPuma
mesh_terms: D000293:Adolescent; D000328:Adult; D000375:Aging / Q000187:drug effects; D000900:Anti-Bacterial Agents / Q000494:pharmacology / Q000627:therapeutic use; D001419:Bacteria / Q000145:classification / Q000187:drug effects / Q000254:growth & development*; D058491:Bacterial Load / Q000187:drug effects; D044822:Biodiversity; D003550:Cystic Fibrosis / Q000188:drug therapy / Q000382:microbiology* / Q000503:physiopathology; D018450:Disease Progression; D006801:Humans; D008168:Lung / Q000187:drug effects / Q000382:microbiology* / Q000473:pathology* / Q000503:physiopathology; D008297:Male; D054892:Metagenome / Q000187:drug effects; D025341:Principal Component Analysis; D012129:Respiratory Function Tests; D013183:Sputum / Q000187:drug effects / Q000382:microbiology; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents