Sequencing of the human lung microbiome – Methodical challenges, controls and first metagenome assembled genomes from a nearly sterile habitat

Question: Microbial populations are usually present within many sites of the human body and in the past, it became increasingly clear that they play key roles in maintaining health, as well as causing diseases, when its natural composition is disrupted. While the healthy lung was considered traditionally sterile, an increasing number of studies, culture dependent and independent, indicate otherwise. A better understanding of the lung microbiome is therefore needed to assess its potential role in disease development and prevention. However, due to the low bacterial biomass nature of the lung, molecular research has remained challenging and to date was mostly restricted on 16S rRNA-gene amplicon analysis. In our study, we aimed to overcome these limitations and conduct a first metagenomic analysis of bacterial communities of the human lung.

Methods: By performing bronchoscopy on healthy individuals of smokers and non-smokers, bronchoalveolar lavage was collected and subjected to metagenomic analysis. To enable bacterial metagenomic analyses, samples had to be subjected to extensive clean up procedures, depleting human background DNA, while preserving the original microbial community.

Results & Conclusions: In the end, a robust method could be developed to create the first metagenome assembled genomes from this habitat characterized by very low microbial abundances. This represents a key step forward in understanding of the human lung microbiome and provides the baseline for future microbiome analyses.