The sputum microbiome is distinct between COPD and health, independent of smoking history

Abstract

Background: Airway bacterial dysbiosis is a feature of chronic obstructive pulmonary disease (COPD). However, there is limited comparative data of the lung microbiome between healthy smokers, non-smokers and COPD.

Methods: We compared the 16S rRNA gene-based sputum microbiome generated from pair-ended Illumina sequencing of 124 healthy subjects (28 smokers and 96 non-smokers with normal lung function), with single stable samples from 218 COPD subjects collected from three UK clinical centres as part of the COPDMAP consortium.

Results: In healthy subjects Firmicutes, Bacteroidetes and Actinobacteria were the major phyla constituting 88% of the total reads, and Streptococcus, Veillonella, Prevotella, Actinomyces and Rothia were the dominant genera. Haemophilus formed only 3% of the healthy microbiome. In contrast, Proteobacteria was the most dominant phylum accounting for 50% of the microbiome in COPD subjects, with Haemophilus and Moraxella at genus level contributing 25 and 3% respectively. There were no differences in the microbiome profile within healthy and COPD subgroups when stratified based on smoking history. Principal coordinate analysis on operational taxonomic units showed two distinct clusters, representative of healthy and COPD subjects (PERMANOVA, p = 0·001).

Conclusion: The healthy and COPD sputum microbiomes are distinct and independent of smoking history. Our results underline the important role for Gammaproteobacteria in COPD.

Keywords: COPD; Haemophilus; Healthy airway; Microbiome; Proteobacteria.

Conflict of interest statement

KH, LG, ZW, VM, MYR, RCF, NFR, AJW, AJB, MRB have nothing to declare. JRB, BEM and RTS are employees and shareholders of GSK; GCD reports grants and personal fees from Astrazeneca and grants from Micom ltd and American Thoracic Society; MDT reports grants from GSK and other from Orion; JAW reports grants from GSK, grants from Johnson and Johnson, other from Novartis, other from Boehringer Ingelheim, other from Astra Zeneca, other from GSK, grants from GSK, grants from Astra Zeneca, grants from Boehringer Ingelheim, grants from Novartis; DS reports grants and personal fees from GlaxoSmithKline, grants and personal fees from AstraZeneca, grants and personal fees from Boehringer Ingleheim, grants and personal fees from Chiesi, personal fees from Cipla, personal fees from Genentech, grants and personal fees from Glenmark, grants and personal fees from Menarini, grants and personal fees from Mundipharma, grants and personal fees from Novartis, personal fees from Peptinnovate, grants and personal fees from Pfizer, grants and personal fees from Pulmatrix, grants and personal fees from Therevance, grants and personal fees from Verona; CEB reports grants and personal fees from GSK, grants and personal fees from Novartis, grants and personal fees from Genentech, grants and personal fees from Chiesi, personal fees from Sanofi/Regeneron, grants and personal fees from 4DPharma, grants and personal fees from BI, grants and personal fees from Mologics, grants and personal fees from Gossamer, grants and personal fees from AZ/MedImmune, grants and personal fees from TEVA, outside the submitted work. CEB reports grants from MRC COPDMAP, grants from AirPROM (FP7–270194), during the conduct of the study.

Figures

Fig. 1

Microbiome profile of Healthy volunteers based on smoking pack year history. a Relative abundance of major phyla between all healthy (n = 124) represented in the outer ring followed by healthy < 10 PY smoking history subgroup (n = 96) in the middle ring and innermost ring representing healthy ≥10 PY history subgroup (n = 28). b Relative abundance of major genera between all healthy (n = 124) represented in the outer ring followed by healthy < 10 PY (n = 96) in the middle ring and innermost ring representing healthy ≥10 PY history (n = 28). c Principal coordinate analysis (PCoA) analysis of weighted unifrac distance measures relative to pack year history. d Alpha diversity indices comparison between. < 10 PY and ≥ 10 PY smoking sub-groups. Chao1 and observed_otus are represented as bar chart as mean and standard deviation; Shannon index is represented by box whisker plot showing median, interquartile range and minimum and maximum. **. P < 0.01

Fig. 2

Microbiome profile of COPD subjects based on smoking pack year history. a Relative abundance of major phyla between all COPD (n = 218) represented in the outer ring followed by ex-smokers (n = 148) in the middle ring and innermost ring representing current smokers history (n = 70). b Relative abundance of major genera between all COPD (n = 218) represented in the outer ring followed by ex- smokers (n = 148) in the middle ring and innermost ring representing current smoker (n = 70). c PCoA analysis of weighted unifrac distance measures relative to pack year history. d Alpha diversity indices comparison between the two smoking groups

Fig. 3

Comparison of Microbiome profile between Healthy and COPD. a Relative abundance of major phyla between COPD (n = 218) represented in the outer and inner ring representing healthy (n = 124). b Relative abundance of major genera between COPD (n = 218) represented in the outer ring and inner ring representing healthy volunteers (n = 28). c PCoA analysis of weighted unifrac distance measures between healthy and COPD subjects. d Alpha diversity indices comparison between Healthy and COPD subjects. ****, P < 0.00001

Fig. 4

Bacterial groups distinguishing health and COPD microbiome. Each of the circles in the cladogram represent a bacterial taxa and each ring a taxonomy level starting with Kingdom (Archaea and Bacteria) in the innermost circle. Green coloured circles and zones represent bacterial taxa dominant in health and red in COPD. Circle sizes are correlated to bacterial abundance. Taxa level phylum (p_) and class (c_) are mentioned in the figure. Order (o_), Family (f_) and genus (g_) are abbreviated in the figure

Fig. 5

Predictive functional profiling shows distinct clustering of COPD and Healthy sputum microbiome. a PCA analysis of functional groups inferred from 16S rDNA microbial community. b lists the top 19 functional groups which were significantly different (p < 0.05, multiple comparison corrected) and had > 0.2% difference between COPD and healthy subjects