title: Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity.
abstract: Chronic Obstructive Pulmonary Disease (COPD) is a major source of mortality and morbidity worldwide. The microbiome associated with this disease may be an important component of the disease, though studies to date have been based on sequencing of the 16S rRNA gene, and have revealed unequivocal results. Here, we employed metagenomic sequencing of the upper bronchial tract (UBT) microbiome to allow for greater elucidation of its taxonomic composition, and revealing functional changes associated with the disease. The bacterial metagenomes within sputum samples from eight COPD patients and ten 'healthy' smokers (Controls) were sequenced, and suggested significant changes in the abundance of bacterial species, particularly within the Streptococcus genus. The functional capacity of the COPD UBT microbiome indicated an increased capacity for bacterial growth, which could be an important feature in bacterial-associated acute exacerbations. Regression analyses correlated COPD severity (FEV1% of predicted) with differences in the abundance of Streptococcus pneumoniae and functional classifications related to a reduced capacity for bacterial sialic acid metabolism. This study suggests that the COPD UBT microbiome could be used in patient risk stratification and in identifying novel monitoring and treatment methods, but study of a longitudinal cohort will be required to unequivocally relate these features of the microbiome with COPD severity.
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom.
authors.forename: Simon J S
authors.initials: SJ
authors.lastname: Cameron
authors.affiliation: Department of Respiratory Medicine, Prince Phillip Hospital, Hywel Dda University Health Board, Llanelli, SA14 8QF, United Kingdom.|College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom.
authors.forename: Keir E
authors.initials: KE
authors.lastname: Lewis
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom.
authors.forename: Sharon A
authors.initials: SA
authors.lastname: Huws
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom.
authors.forename: Wanchang
authors.initials: W
authors.lastname: Lin
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Hegarty
authors.affiliation: College of Medicine, Swansea University, Swansea, SA2 8PP, United Kingdom.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Lewis
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom.
authors.forename: Luis A J
authors.initials: LA
authors.lastname: Mur
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Edward Llywd Building, Penglais Campus, Aberystwyth, Ceredigion, SY23 3FG, United Kingdom.
authors.forename: Justin A
authors.initials: JA
authors.lastname: Pachebat
mesh_terms: D000368:Aged; D001980:Bronchi / Q000382:microbiology*; D005260:Female; D006801:Humans; D008297:Male; D054892:Metagenome; D064307:Microbiota; D029424:Pulmonary Disease, Chronic Obstructive / Q000382:microbiology* / Q000473:pathology; D017422:Sequence Analysis, DNA; D012720:Severity of Illness Index