Abstract
BackgroundThis work provides the first description of the bacterial population of the lung microbiota in mice. The aim of this study was to examine the lung microbiome in mice, the most used animal model for inflammatory lung diseases such as COPD, cystic fibrosis and asthma.Bacterial communities from broncho-alveolar lavage fluids and lung tissue were compared to samples taken from fecal matter (caecum) and vaginal lavage fluid from female BALB/cJ mice.ResultsUsing a customized 16S rRNA sequencing protocol amplifying the V3-V4 region our study shows that the mice have a lung microbiome that cluster separately from mouse intestinal microbiome (caecum). The mouse lung microbiome is dominated by Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria overlapping the vaginal microbiome. We also show that removal of host tissue or cells from lung fluid during the DNA extraction step has an impact on the resulting bacterial community profile. Sample preparation needs to be considered when choosing an extraction method and interpreting data.ConclusionsWe have consistently amplified bacterial DNA from mouse lungs that is distinct from the intestinal microbiome in these mice. The gut microbiome has been extensively studied for its links to development of disease. Here we suggest that also the lung microbiome could be important in relation to inflammatory lung diseases. Further research is needed to understand the contribution of the lung microbiome and the gut-lung axis to the development of lung diseases such as COPD and asthma.
Highlights
This work provides the first description of the bacterial population of the lung microbiota in mice
To determine the airway bacterial microbiota of the BALB/cJ mouse model based on 16S rDNA gene sequencing, we have compared sequences found in the lungs with three different approaches, to sequences found in corresponding vaginal and caecal samples
After quality filtering and chimera check, 27% of sequences were removed and 660319 sequences were further processed for Operational Taxonomic Units (OTU) picking
Summary
This work provides the first description of the bacterial population of the lung microbiota in mice. Bacterial communities from broncho-alveolar lavage fluids and lung tissue were compared to samples taken from fecal matter (caecum) and vaginal lavage fluid from female BALB/cJ mice. Studies of the lung microbiome by culture independent techniques and its impact on lung immunity is a relatively new field and may contribute to new advances in understanding respiratory diseases [1]. The bacterial communities in BAL samples were compared using DNA extractions from washed lung tissue, caecum samples and vaginal flushing. The vaginal microbiome of BALB/c has not previously been described and could have influence on microbial “priming” and transfer from mother to pup. In this study, it serves a reference sample from a different mucoid epithelium than lung. An OTU is an approximation to taxonomy derived from classical cultivation techniques
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