The lung microbiome in moderate and severe chronic obstructive pulmonary disease

Abstract

Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompletely reversible airflow obstruction. Bacterial infection of the lower respiratory tract contributes to approximately 50% of COPD exacerbations. Even during periods of stable lung function, the lung harbors a community of bacteria, termed the microbiome. The role of the lung microbiome in the pathogenesis of COPD remains unknown. The COPD lung microbiome, like the healthy lung microbiome, appears to reflect microaspiration of oral microflora. Here we describe the COPD lung microbiome of 22 patients with Moderate or Severe COPD compared to 10 healthy control patients. The composition of the lung microbiomes was determined using 454 pyrosequencing of 16S rDNA found in bronchoalveolar lavage fluid. Sequences were analyzed using mothur, Ribosomal Database Project, Fast UniFrac, and Metastats. Our results showed a significant increase in microbial diversity with the development of COPD. The main phyla in all samples were Actinobacteria, Firmicutes, and Proteobacteria. Principal coordinate analyses demonstrated separation of control and COPD samples, but samples did not cluster based on disease severity. However, samples did cluster based on the use of inhaled corticosteroids and inhaled bronchodilators. Metastats analyses demonstrated an increased abundance of several oral bacteria in COPD samples.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1. Taxonomic Identification at the Phylum Level.

All sequences were submitted to RDP Classifier for taxonomic identification with a bootstrap cutoff of 50%. Taxonomic results at the phylum level are displayed for each sample with Control samples at the bottom, Moderate COPD samples in the middle, and Severe COPD samples at the top. The legend is organized from most (top) to least abundant (bottom) phyla.

Figure 2. Principal Coordinate Analysis Demonstrates Clustering of COPD Samples, Inhaled Corticosteroid Users, and Inhaled Bronchodilator Users.

Principal coordinate analysis was performed using mothur and Fast UniFrac, and the results for principal coordinates 1 and 2 are shown. A. Control, Moderate COPD, and Severe COPD. Control samples (red) cluster separately from Moderate COPD (blue) and Severe COPD (yellow) samples. Moderate and Severe COPD samples do not cluster separately. Seven COPD samples that separate the most from the control samples are circled and designated “left lower quadrant” (LLQ) samples for further analysis. B. Smokers and Non-Smokers. Smokers (blue) do not cluster separately from Non-Smokers (red). All of the COPD patients had been non-smokers for at least 6 months prior to bronchoscopy. C. Inhaled Corticosteroid Users and Non-Users. Inhaled corticosteroid users (blue, 14 of 22 COPD patients) are more likely to cluster near the intersection of principal coordinates 1 and 2 than non-users (red). D. Inhaled Bronchodilator Users and Non-Users. Inhaled bronchodilator users (blue, 16 of 22 COPD patients) are more likely to cluster near the intersection of principal coordinates 1 and 2 than non-users (red). All patients who received inhaled corticosteroids also received inhaled bronchodilators.