Association of exacerbation phenotype with the sputum microbiome in chronic obstructive pulmonary disease patients during the clinically stable state

Abstract

Background Chronic obstructive pulmonary disease (COPD) is a progressive, life-threatening lung disease with increasing prevalence and incidence worldwide. Increasing evidence suggests that lung microbiomes might play a physiological role in acute exacerbations of COPD. The objective of this study was to characterize the association of the microbiota and exacerbation risk or airflow limitation in stable COPD patients. Methods The sputum microbiota from 78 COPD outpatients during periods of clinical stability was investigated using 16S rRNA V3-V4 amplicon sequencing. The microbiome profiles were compared between patients with different risks of exacerbation, i.e., the low risk exacerbator (LRE) or high risk exacerbator (HRE) groups, and with different airflow limitation severity, i.e., mild to moderate (FEV1 ≥ 50; PFT I) or severe to very severe (FEV1 < 50; PFT II). Results The bacterial diversity (Chao1 and observed OTUs) was significantly decreased in the HRE group compared to that in the LRE group. The top 3 dominant phyla in sputum were Firmicutes, Actinobacteria, and Proteobacteria, which were similar in the HRE and LRE groups. At the genus level, compared to that in the LRE group (41.24%), the proportion of Streptococcus was slightly decreased in the HRE group (28.68%) (p = 0.007). However, the bacterial diversity and the proportion of dominant bacteria at the phylum and genus levels were similar between the PFT I and PFT II groups. Furthermore, the relative abundances of Gemella morbillorum, Prevotella histicola, and Streptococcus gordonii were decreased in the HRE group compared to those in the LRE group according to linear discriminant analysis effect size (LEfSe). Microbiome network analysis suggested altered bacterial cooperative regulation in different exacerbation phenotypes. The proportions of Proteobacteria and Neisseria were negatively correlated with the FEV1/FVC value. According to functional prediction of sputum bacterial communities through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis, genes involved in lipopolysaccharide biosynthesis and energy metabolism were enriched in the HRE group. Conclusion The present study revealed that the sputum microbiome changed in COPD patients with different risks of exacerbation. Additionally, the bacterial cooperative networks were altered in the HRE patients and may contribute to disease exacerbation. Our results provide evidence that sputum microbiome community dysbiosis is associated with different COPD phenotypes, and we hope that by understanding the lung microbiome, a potentially modifiable clinical factor, further targets for improved COPD therapies during the clinically stable state may be elucidated.

Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease

“…Analysis of the airway microbiota by PCoA found three distinct clusters in our cohort of stable COPD patients. They showed no differences in proportion of the phylum, all dominated by Firmicutes, Proteobacteria, and Actinobacteria, as previously described in other reports analyzing the microbiota of stable COPD patients ( Garcia-Nuñez et al, 2014 ; Einarsson et al, 2016 ; Wang et al, 2018 ; Tangedal et al, 2019 ; Yang et al, 2021 ). Similar to other microbiome studies in stable COPD patients ( Wilkinson et al, 2003 ; Garcia-Nuñez et al, 2014 ; Aguirre et al, 2015 ; Einarsson et al, 2016 ; Wang et al, 2018 ; Tangedal et al, 2019 ; Dicker et al, 2021 ; Yang et al, 2021 ), the vast majority of bacteria belonged to the genera Streptococcus , Rothia , Veillonella , and Actinomyces , in the same proportion as in the three clusters.…”

“…They showed no differences in proportion of the phylum, all dominated by Firmicutes, Proteobacteria, and Actinobacteria, as previously described in other reports analyzing the microbiota of stable COPD patients ( Garcia-Nuñez et al, 2014 ; Einarsson et al, 2016 ; Wang et al, 2018 ; Tangedal et al, 2019 ; Yang et al, 2021 ). Similar to other microbiome studies in stable COPD patients ( Wilkinson et al, 2003 ; Garcia-Nuñez et al, 2014 ; Aguirre et al, 2015 ; Einarsson et al, 2016 ; Wang et al, 2018 ; Tangedal et al, 2019 ; Dicker et al, 2021 ; Yang et al, 2021 ), the vast majority of bacteria belonged to the genera Streptococcus , Rothia , Veillonella , and Actinomyces , in the same proportion as in the three clusters. We also found some PPM, such as S. aureus , H. influenzae , M. catarrhalis , and P. aeruginosa , in proportions quite similar to those previously described in stable patients ( Marin et al, 2009 ; Garcia-Nuñez et al, 2014 ; Aguirre et al, 2015 ; Einarsson et al, 2016 ; Leung et al, 2017 ), and the prevalence was identical in the three clusters.…”

“…Airway microbiota analyses in stable COPD also showed inconsistent results ( Garcia-Nuñez et al, 2014 ; Diao et al, 2018 ; Wang et al, 2018 ; Tangedal et al, 2019 ; Dicker et al, 2021 ; Yang et al, 2021 ), highlighting a predominance of Streptococcus spp. ( Tangedal et al, 2019 ; Yang et al, 2021 ) or Neisseria spp. ( Diao et al, 2018 ).…”

“…Most of the studies aiming at describing the airway microbiota used culture-independent techniques, such as PCR amplification and sequencing of the bacterial 16S ribosomal RNA gene ( Pragman et al, 2012 ; Garcia-Nuñez et al, 2014 ; Wang et al, 2016 ; Diao et al, 2018 ; Jubinville et al, 2018 ; Mayhew et al, 2018 ; Tangedal et al, 2019 ; Dicker et al, 2021 ; Yang et al, 2021 ). Conversely to the 16S rRNA sequencing, conventional culture-based approaches have the great advantage to be applicable in any clinical microbiology laboratory using MALDI-TOF technologies, which are now very commonly used for identification ( Dingle and Butler-Wu, 2013 ).…”

Oral Prevotella Species and Their Connection to Events of Clinical Relevance in Gastrointestinal and Respiratory Tracts

“…pneumonia e were the most abundant species, the bacterial compositions did not differ from those found in non-asthmatic individuals. As regards COPD, a recent study characterizing a potential association between the microbiota and risk for exacerbation or airflow limitation revealed significantly reduced proportions of P. histicola , Gemella morbillorum , and Streptococcus gordonii in sputum of patients with high risk of COPD exacerbation ( Yang et al, 2021 ). The authors assumed that this kind of alteration in the resident microbiota to a dysbiotic direction could enhance inflammation in respiratory mucosae.…”