A persistent and diverse airway microbiota present during chronic obstructive pulmonary disease exacerbations

Yvonne J Huang, Eugenia Kim, Michael J Cox, Eoin L Brodie, Ron Brown, Jeanine P Wiener-Kronish, Susan V Lynch

Research output: Contribution to journalArticlepeer-review

160 Citations (Scopus)


Acute exacerbations of chronic obstructive pulmonary disease (COPD) are a major source of morbidity and contribute significantly to healthcare costs. Although bacterial infections are implicated in nearly 50% of exacerbations, only a handful of pathogens have been consistently identified in COPD airways, primarily by culture-based methods, and the bacterial microbiota in acute exacerbations remains largely uncharacterized. The aim of this study was to comprehensively profile airway bacterial communities using a culture-independent microarray, the 16S rRNA PhyloChip, of a cohort of COPD patients requiring ventilatory support and antibiotic therapy for exacerbation-related respiratory failure. PhyloChip analysis revealed the presence of over 1,200 bacterial taxa representing 140 distinct families, many previously undetected in airway diseases; bacterial community composition was strongly influenced by the duration of intubation. A core community of 75 taxa was detected in all patients, many of which are known pathogens. Bacterial community diversity in COPD airways is substantially greater than previously recognized and includes a number of potential pathogens detected in the setting of antibiotic exposure. Comprehensive assessment of the COPD airway microbiota using high-throughput, culture-independent methods may prove key to understanding the relationships between airway bacterial colonization, acute exacerbation, and clinical outcomes in this and other chronic inflammatory airway diseases.

Original languageEnglish
Pages (from-to)9-59
Number of pages51
JournalOMICS: A Journal of Integrative Biology
Issue number1
Publication statusPublished - Feb 2010


  • Aged
  • Aged, 80 and over
  • Bacteria/classification
  • Base Sequence
  • Bronchi/microbiology
  • Bronchoalveolar Lavage Fluid
  • Cohort Studies
  • DNA Primers
  • Female
  • Humans
  • Male
  • Middle Aged
  • Phylogeny
  • Polymerase Chain Reaction
  • Pulmonary Disease, Chronic Obstructive/microbiology
  • RNA, Ribosomal, 16S/genetics


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