Metagenome and Metatranscriptome Profiling of Moderate and Severe COPD Sputum in Taiwanese Han Males

• Published in: PloS one Vol. 11; no. 7; p. e0159066
• Main Authors: Lee, Shih-Wei, Kuan, Chin-Sheng, Wu, Lawrence Shih-Hsin, Weng, Julia Tzu-Ya
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 18.07.2016; Public Library of Science (PLoS)
• Subjects: Aged; Aged, 80 and over; Air flow; Airflow; Analysis; Antibiotics; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacterial infections; Bacterial Infections - complications; Bacterial Infections - microbiology; Biology and life sciences; Care and treatment; Chronic obstructive lung disease; Chronic obstructive pulmonary disease; Computer science; Deoxyribonucleic acid; DNA; DNA sequencing; DNA, Bacterial - genetics; DNA, Bacterial - isolation & purification; Fusobacterium; Gene expression; Gene sequencing; Genetic aspects; Genome, Bacterial; Humans; Inflammation; Inflammatory diseases; Lung - microbiology; Lung diseases; Lungs; Male; Males; Medicine and Health Sciences; Metagenome; Microbiomes; Microbiota; Microorganisms; Middle Aged; Mortality; Neisseria; Obstructive lung disease; Pathogenesis; Patients; Porphyromonas; Prevotella; Pulmonary Disease, Chronic Obstructive - epidemiology; Pulmonary Disease, Chronic Obstructive - microbiology; Relative abundance; Research and analysis methods; Respiratory diseases; Ribonucleic acid; Risk factors; RNA; RNA, Bacterial - genetics; RNA, Bacterial - isolation & purification; RNA, Ribosomal, 16S - genetics; RNA, Ribosomal, 16S - isolation & purification; rRNA 16S; Smoking; Sputum; Sputum - microbiology; Streptococcus; Streptococcus infections; Studies; Taiwan - epidemiology; Technology; Transcription (Genetics); Transcriptome; Veillonella; Viral infections; Taiwan
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0159066

Chronic obstructive pulmonary disease (COPD) is an inflammatory lung disorder characterized by the progressive obstruction of airflow and is currently the fourth leading cause of death in the world. The pathogenesis of COPD is thought to involve bacterial infections and inflammations. Owing to advancement in sequencing technology, evidence is emerging that supports an association between the lung microbiome and COPD. However, few studies have looked into the expression profile of the bacterial communities in the COPD lungs. In this study, we analyzed the sputum microbiome of four moderate and four severe COPD male patients both at the DNA and RNA level, using next generation sequencing technology. We found that bacterial composition determined by 16S rRNA gene sequencing may not directly translate to the set of actively expressing bacteria as defined by transcriptome sequencing. The two sequencing data agreed on Prevotella, Rothia, Neisseria, Porphyromonas, Veillonella, Fusobacterium and Streptococcus being among the most differentially abundant genera between the moderate and severe COPD samples, supporting their association with COPD severity. However, the two sequencing analyses disagreed on the relative abundance of these bacteria in the two COPD groups, implicating the importance of studying the actively expressing bacteria for enriching our understanding of COPD. Though we have described the metatranscriptome profiles of the lung microbiome in moderate and severe COPD, further investigations are required to determine the functional basis underlying the relationship between the microbial species in the lungs and pathogenesis of COPD.