title: The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation.
abstract: BACKGROUND
  Recent work indicates that the airways of persons with cystic fibrosis (CF) typically harbor complex bacterial communities. However, the day-to-day stability of these communities is unknown. Further, airway community dynamics during the days corresponding to the onset of symptoms of respiratory exacerbation have not been studied.
  
  
  RESULTS
  Using 16S rRNA amplicon sequencing of 95 daily sputum specimens collected from four adults with CF, we observed varying degrees of day-to-day stability in airway bacterial community structures during periods of clinical stability. Differences were observed between study subjects with respect to the degree of community changes at the onset of exacerbation. Decreases in the relative abundance of dominant taxa were observed in three subjects at exacerbation. We observed no relationship between total bacterial load and clinical status and detected no viruses by multiplex PCR.
  
  
  CONCLUSIONS
  CF airway microbial communities are relatively stable during periods of clinical stability. Changes in microbial community structure are associated with some, but not all, pulmonary exacerbations, supporting previous observations suggesting that distinct types of exacerbations occur in CF. Decreased abundance of species that are dominant at baseline suggests a role for less abundant taxa in some exacerbations. Daily sampling revealed patterns of change in microbial community structures that may prove useful in the prediction and management of CF pulmonary exacerbations.
authors.affiliation: Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA.
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Carmody
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.affiliation: Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA.
authors.forename: Linda M
authors.initials: LM
authors.lastname: Kalikin
authors.affiliation: Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 USA.
authors.forename: William
authors.initials: W
authors.lastname: LeBar
authors.affiliation: Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 USA.
authors.forename: Richard H
authors.initials: RH
authors.lastname: Simon
authors.affiliation: Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA.
authors.forename: Arvind
authors.initials: A
authors.lastname: Venkataraman
authors.affiliation: Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA.
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Schmidt
authors.affiliation: USDA-ARS, South Atlantic Area, Athens, GA USA.
authors.forename: Zaid
authors.initials: Z
authors.lastname: Abdo
authors.affiliation: Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA.
authors.forename: Patrick D
authors.initials: PD
authors.lastname: Schloss
authors.affiliation: Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA.
authors.forename: John J
authors.initials: JJ
authors.lastname: LiPuma
keywords: Airway microbiome; Cystic fibrosis; Lung microbiome; Respiratory exacerbation
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