Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease

Abstract

Specific bacterial species are implicated in the pathogenesis of exacerbations of chronic obstructive pulmonary disease (COPD). However, recent studies of clinically stable COPD patients have demonstrated a greater diversity of airway microbiota, whose role in acute exacerbations is unclear. In this study, temporal changes in the airway microbiome before, at the onset of, and after an acute exacerbation were examined in 60 sputum samples collected from subjects enrolled in a longitudinal study of bacterial infection in COPD. Microbiome composition and predicted functions were examined using 16S rRNA-based culture-independent profiling methods. Shifts in the abundance (≥ 2-fold, P < 0.05) of many taxa at exacerbation and after treatment were observed. Microbiota members that were increased at exacerbation were primarily of the Proteobacteria phylum, including nontypical COPD pathogens. Changes in the bacterial composition after treatment for an exacerbation differed significantly among the therapy regimens clinically prescribed (antibiotics only, oral corticosteroids only, or both). Treatment with antibiotics alone primarily decreased the abundance of Proteobacteria, with the prolonged suppression of some microbiota members being observed. In contrast, treatment with corticosteroids alone led to enrichment for Proteobacteria and members of other phyla. Predicted metagenomes of particular microbiota members involved in these compositional shifts indicated exacerbation-associated loss of functions involved in the synthesis of antimicrobial and anti-inflammatory products, alongside enrichment in functions related to pathogen-elicited inflammation. These trends reversed upon clinical recovery. Further larger studies will be necessary to determine whether specific compositional or functional changes detected in the airway microbiome could be useful indicators of exacerbation development or outcome.

FIG 1

Time points of sample collection before, at the onset of, and after an acute COPD exacerbation. The line coloring indicates the type of treatment for the exacerbation that the subject received.

FIG 2

(A) Nonmetric multidimensional scaling (NMDS) ordination demonstrates that samples from all subjects in the study segregate into distinct clusters (indicated by ellipses) on the basis of the type of treatment prescribed for exacerbation (antibiotics [Abx] only, oral steroids only, or both; n = 4 subjects per treatment group; Bray-Curtis distance-based PERMANOVA, P < 0.05). Ellipses represent the 95% confidence interval for the standard error of the distances of samples in each treatment group. (B) An NMDS plot of only postexacerbation treatment samples from all subjects demonstrates that the relationship between sample community composition and treatment type remains strong, though not statistically significant (P = 0.08), when the analysis is limited to only these samples. (C) An NMDS plot of only preexacerbation samples from all subjects shows that chronic use of inhaled corticosteroids may be associated with differences in bacterial community composition (Bray-Curtis distance-based PERMANOVA, P = 0.08).

FIG 2

(A) Nonmetric multidimensional scaling (NMDS) ordination demonstrates that samples from all subjects in the study segregate into distinct clusters (indicated by ellipses) on the basis of the type of treatment prescribed for exacerbation (antibiotics [Abx] only, oral steroids only, or both; n = 4 subjects per treatment group; Bray-Curtis distance-based PERMANOVA, P < 0.05). Ellipses represent the 95% confidence interval for the standard error of the distances of samples in each treatment group. (B) An NMDS plot of only postexacerbation treatment samples from all subjects demonstrates that the relationship between sample community composition and treatment type remains strong, though not statistically significant (P = 0.08), when the analysis is limited to only these samples. (C) An NMDS plot of only preexacerbation samples from all subjects shows that chronic use of inhaled corticosteroids may be associated with differences in bacterial community composition (Bray-Curtis distance-based PERMANOVA, P = 0.08).

FIG 3

(A) Volcano plots indicating taxa that are significantly increased (upper right quadrant) or decreased (upper left quadrant) in the pairwise comparisons indicated, using moderated t-test models (R package limma). Results shown are from analyses of all subjects. Dashed lines, significant false discovery rate-adjusted P values and changes in relative abundance of at least 2-fold, or log₂ equal to 1. Taxa exhibiting significant changes are colored by phylum-level classification, as shown. Note that in addition to the highlighted taxa, many other microbiota members exhibited smaller-scale changes in abundance, which cumulatively may contribute importantly to microbiome community function, (B) Changes in the relative abundance of taxa from Exac to Post1 and Post1 to Post2, segregated by type of exacerbation treatment (antibiotics only, systemic corticosteroids only, or both; n = 4 subjects in each treatment group).

FIG 4

Correlations between the relative abundance of H. influenzae (a member of the Pasteurellaceae/Gammaproteobacteria) and that of all other identified taxa. The analysis was performed using data from all 60 samples in this study. Significant positive and negative correlations are shown (Pearson R ≥ 0.5, Benjamini-Hochberg-adjusted P < 0.05). Positive correlations (red) occur predominantly with members of Pasteurellaceae or closely related bacterial families and classes of Proteobacteria. Negative correlations (blue) occur with bacterial families and classes that phylogenetically are more distant to H. influenzae/Pasteurellaceae. Tree branches are color coded by bacterial class in the key on the right.

FIG 5

KEGG pathways associated with predicted gene functions (KOs) encoded by metagenomes of bacterial taxa that either were increased (red) or decreased (blue) in relative abundance by ≥2-fold at the time of and after exacerbations. Among the microbiome-related functions identified were those involved in the promotion of inflammation by pathogens (*) and the production of antimicrobial and anti-inflammatory compounds (**), functions that were differentially represented at exacerbation compared to postexacerbation.