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

Research output: Contribution to journalArticle


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

Colleges, School and Institutes

External organisations

  • Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, California 94143-0538, USA.


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