Analysis of the Airway Microbiota of Healthy Individuals and Patients with Chronic Obstructive Pulmonary Disease by T-RFLP and Clone Sequencing

Abstract

Chronic obstructive pulmonary disease (COPD) is a progressive, inflammatory lung disease that affects a large number of patients and has significant impact. One hallmark of the disease is the presence of bacteria in the lower airways. Objective: The aim of this study was to analyze the detailed structure of microbial communities found in the lungs of healthy individuals and patients with COPD. Nine COPD patients as compared and 9 healthy individuals underwent flexible bronchoscopy and BAL was performed. Bacterial nucleic acids were subjected to terminal restriction fragment (TRF) length polymorphism and clone library analysis. Overall, we identified 326 T-RFLP band, 159 in patients and 167 in healthy controls. The results of the TRF analysis correlated partly with the data obtained from clone sequencing. Although the results of the sequencing showed high diversity, the genera Prevotella, Sphingomonas, Pseudomonas, Acinetobacter, Fusobacterium, Megasphaera, Veillonella, Staphylococcus, and Streptococcus constituted the major part of the core microbiome found in both groups. A TRF band possibly representing Pseudomonas sp. monoinfection was associated with a reduction of the microbial diversity. Non-cultural methods reveal the complexity of the pulmonary microbiome in healthy individuals and in patients with COPD. Alterations of the microbiome in pulmonary diseases are correlated with disease.

Combined exposure to bacteria and cigarette smoke resembles characteristic phenotypes of human COPD in a murine disease model

“…One hallmark of COPD is the increased susceptibility to colonization and infection by bacterial microorganisms (Sethi, 2010;Sethi and Murphy, 2008). Already in stable COPD, the microbiome of the lung differs from the microbiome of healthy individuals (Zakharkina et al, 2013). Specific bacterial species such as H. influenzae, M.catarrhalis, S. pneumonia, or P. aeruginosa are present in COPD lungs (Sethi et al, 2002).…”

“…Lungs of COPD patients are often colonized or infected with Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pneumonia, and Pseudomonas aeruginosa (Murphy et al, 2004;Sethi et al, 2006). Culture-independent approaches showed that the microbiome of the COPD lung differs significantly from the microbiome of healthy lungs (Erb-Downward et al, 2011;Sze et al, 2012;Zakharkina et al, 2013). The acquisition of a new bacterial strain during an AECOPD correlates with a more severe pulmonary neutrophilic inflammation and systemic inflammation (Sethi et al, 2002).…”

Lung microbiome dynamics in COPD exacerbations

“…Studies using culture-independent techniques such as PCR amplification and sequencing of the 16S ribosomal (r)RNA gene have characterised a distinct bacterial community in the airway of COPD patients compared to healthy subjects and suggest that changes in the lung microbiota could be associated with enhanced airway inflammation and disease progression [8][9][10][11]. However, most lung microbiome studies to date have involved relatively small cohorts of subjects with limited longitudinal sampling and concurrent clinical information.…”

Microbiota Promotes Chronic Pulmonary Inflammation by Enhancing IL-17A and Autoantibodies

“…Previously considered sterile, breakthroughs in non-culture based detection methods have provided evidence that the respiratory tract harbors a microbiota (9)(10)(11)(12)(13)(14)(15)(16)(17)(18). Notably, the microbiota in the respiratory tract of healthy volunteers, smokers without COPD and patients with severe disease are distinct (9,10,(12)(13)(14). Though microbial dysbiosis has been shown to increase susceptibility to chronic diseases such as inflammatory bowel disease (IBD) (19,20), it is currently unknown whether such a phenomenon contributes to COPD.…”