Severity-Related Changes of Bronchial Microbiome in Chronic Obstructive Pulmonary Disease

Marian Garcia-Nuñez, Laura Millares, Xavier Pomares, Rafaela Ferrari, Vicente Pérez-Brocal, Miguel Gallego, Mateu Espasa, Andrés Moya, Eduard Monsó

Bronchial colonization by potentially pathogenic microorganisms (PPMs) is often demonstrated in chronic obstructive pulmonary disease (COPD), but culture-based techniques only identify a part of the bacteria in mucosal surfaces. The aim of the study was to determine changes in the bronchial microbiome of COPD associated with the severity of the disease. Bronchial microbiome of COPD patients was analyzed by 16S rRNA gene amplification and pyrosequencing in sputum samples obtained during stability. Seventeen COPD patients were studied (forced expiratory volume in the first second [FEV1%] median 35.0% [interquartile range (IQR) 31.5-52.0]), providing a mean of 4493 (SD 2598) sequences corresponding to 47 Operational Taxonomic Units (OTUs) (SD 17) at a 97% identity level. Patients were dichotomized according to their lung function as moderate-severe, when their FEV1% was over the median, and as advanced, when FEV1% values were lower. Most prevalent phyla in sputum were Proteobacteria (44%) and Firmicutes (16%), followed by Actinobacteria (13%). A greater microbial diversity was found in patients with moderate-severe disease, and alpha-diversity showed a statistically significant decrease in patients with advanced disease when assessed by Shannon (ρ=0.528, p=0.029, Spearman correlation coeficient) and Chao1 alpha diversity indexes (ρ=0.53, p=0.028, Spearman correlation coeficient). The higher severity that characterizes advanced COPD is paralleled by a decrease in the diversity of bronchial microbiome, with a loss of part of the resident flora, that is replaced by a more restricted microbiota that includes PPMs.