Exploring the microbiota difference of bronchoalveolar lavage fluid between community-acquired pneumonia with or without COPD based on metagenomic sequencing: a retrospective study

Abstract

Background: Community-acquired pneumonia (CAP) patients with chronic obstructive pulmonary disease (COPD) have higher disease severity and mortality compared to those without COPD. However, deep investigation into microbiome distribution of lower respiratory tract of CAP with or without COPD was unknown.

Methods: So we used metagenomic next generation sequencing (mNGS) to explore the microbiome differences between the two groups.

Results: Thirty-six CAP without COPD and 11 CAP with COPD cases were retrieved. Bronchoalveolar lavage fluid (BALF) was collected and analyzed using untargeted mNGS and bioinformatic analysis. mNGS revealed that CAP with COPD group was abundant with Streptococcus, Prevotella, Bordetella at genus level and Cutibacterium acnes, Rothia mucilaginosa, Bordetella genomosp. 6 at species level. While CAP without COPD group was abundant with Ralstonia, Prevotella, Streptococcus at genus level and Ralstonia pickettii, Rothia mucilaginosa, Prevotella melaninogenica at species level. Meanwhile, both alpha and beta microbiome diversity was similar between groups. Linear discriminant analysis found that pa-raburkholderia, corynebacterium tuberculostearicum and staphylococcus hominis were more enriched in CAP without COPD group while the abundance of streptococcus intermedius, streptococcus constellatus, streptococcus milleri, fusarium was higher in CAP with COPD group.

Conclusions: These findings revealed that concomitant COPD have an mild impact on lower airway microbiome of CAP patients.

Keywords: Bronchoalveolar lavage fluid; Chronic obstructive pulmonary disease; Community acquired pneumonia; Metagenomic next-generation sequencing.

Fig. 1

Relative abundance of top 15 microbiome taxa in CAP patients with COPD or without COPD. a Relative abundance of top 15 bacterial genera between CAP patients with COPD or without COPD. b Relative abundance of top 15 bacterial species between CAP patients with COPD or without COPD. c Relative abundance of top 15 fungal and viral genera between CAP patients with COPD or without COPD. d Relative abundance of top 15 fungal and viral species between CAP patients with COPD or without COPD

Fig. 2

Alpha and beta diversity comparison between CAP patients with COPD or without COPD. (a) Shannon index, (b) Simpson index, (c) Richness index, (d) ACE index and (e) Chao 1 index were similar between CAP patients with COPD or without COPD. PCA (f) and PCoA (g) plot were presented as well

Fig. 3

Linear discriminant analysis revealed differentially abundant bacterial taxa of BALF between CAP patients with COPD or without COPD. a Differences in bacterial genera between CAP patients with COPD or without COPD. b Differences in bacterial species between CAP patients with COPD or without COPD. c Difference in fungal and viral genera between CAP patients with COPD or without COPD

Fig. 4

Correlation between BALF microbiome diversity and clinical variables in CAP patients. a Age had a negative correlation with Simpson index(r = -0.308, p = 0.0355). b Number of eosinophils had a positive correlation with ACE index (r = 0.3, p = 0.0403)

Fig. 5

BALF microbiome networks separately in CAP patients with or without COPD. a Heatmap of Spearman correlation of top 30 bacterial genera in CAP patients with COPD. b Heatmap of Spearman correlation of top 30 bacterial species in CAP patients with COPD. c Heatmap of Spearman correlation of top 30 bacterial genera in CAP patients without COPD. d Heatmap of Spearman correlation of top 30 bacterial species in CAP patients without COPD