Lung Microbiota and Bacterial Abundance in Patients with Bronchiectasis when Clinically Stable and during Exacerbation

Michael M. Tunney, Gisli G. Einarsson, Lan Wei, Maire Drain, Erich R Klem, Chris Cardwell, Madeleine Ennis, Richard C. Boucher, Matthew C. Wolfgang, J. Stuart Elborn

Research output: Contribution to journalArticlepeer-review

197 Citations (Scopus)


RATIONALE: Characterization of bacterial populations in infectious respiratory diseases will provide improved understanding of the relationship between the lung microbiota, disease pathogenesis and treatment outcomes.

OBJECTIVES: To comprehensively define lung microbiota composition during stable disease and exacerbation in bronchiectasis patients.

METHODS: Sputum was collected from patients when clinically stable and before and after completion of antibiotic treatment of exacerbations. Bacterial abundance and community composition were analyzed using anaerobic culture and 16S rDNA pyrosequencing.

MEASUREMENTS AND MAIN RESULTS: In clinically stable patients, aerobic and anaerobic bacteria were detected in 40/40 (100%) and 33/40 (83%) sputum samples, respectively. The dominant organisms cultured were P. aeruginosa (n=10 patients), H. influenzae (n=12), Prevotella (n=18) and Veillonella (n=13). Pyrosequencing generated over 150,000 sequences, representing 113 distinct microbial taxa; the majority of observed community richness resulted from taxa present in low abundance with similar patterns of phyla distribution in clinically stable patients and patients at the onset of exacerbation. Following treatment of exacerbation, there was no change in total (p=0.925), aerobic (p=0.917) or anaerobic (p=0.683) load and only a limited shift in community composition. Agreement for detection of bacteria by culture and pyrosequencing was good for aerobic bacteria such as P. aeruginosa (kappa=0.84) but poorer for other genera including anaerobes. Lack of agreement was largely due to bacteria been detected by pyrosequencing but not by culture.

CONCLUSIONS: A complex microbiota is present in the lungs of bronchiectasis patients which remains stable through treatment of exacerbations suggesting that changes in microbiota composition do not account for exacerbations.

Original languageEnglish
Pages (from-to)1118-1126
Number of pages9
JournalAmerican Journal of Respiratory Critical Care Medicine
Issue number10
Early online date24 Jan 2013
Publication statusPublished - 15 May 2013


  • Aged
  • Anti-Bacterial Agents/therapeutic use
  • Bronchiectasis/drug therapy
  • Cohort Studies
  • Cross-Sectional Studies
  • Female
  • Humans
  • Longitudinal Studies
  • Lung/microbiology
  • Male
  • Metagenome
  • Sputum/microbiology


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