The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach

Area of Science:

• Respiratory medicine
• Microbiome research
• Genomics

Background:

• Current respiratory microbiome studies primarily use 16S rRNA sequencing.
• Metatranscriptomics offers deeper insights into viable microbiome and host interactions but its feasibility in lung biopsies is under-explored.

Purpose of the Study:

• To assess the feasibility of metatranscriptomic analysis in bronchial biopsies from COPD patients.
• To investigate differences in the respiratory microbiome between stable COPD smokers and ex-smokers.
• To explore host-microbiome interactions using transcriptomic data.

Main Methods:

• RNA sequencing was performed on bronchial biopsies from 5 stable COPD smokers and 6 ex-smokers.
• The Trinity assembler was used for unbiased microbial transcriptional analysis.
• Host-microbiome interactions were analyzed by correlating host and microbial transcriptomic data.

Main Results:

• Ultra-low microbial mass (0.009%) was detected in RNA-seq data from bronchial biopsies.
• No significant differences in microbiome diversity or microbial transcriptional profiles were observed between COPD smokers and ex-smokers.
• An upregulated host gene set associated with specific bacteria (Bradyrhizobium, Roseomonas, Brevibacterium spp.) and the PERK-mediated unfolded protein response was identified.

Conclusions:

• Metatranscriptomic profiling of bronchial biopsies from stable COPD patients yields minimal microbial RNA.
• The study demonstrates the potential of transcriptional profiling for understanding host-microbiome interactions in the airways.
• Further research is needed to optimize methods for detecting and analyzing the respiratory microbiome in lung tissue.