Open Access Highly Accessed Research article

The murine lung microbiome in relation to the intestinal and vaginal bacterial communities

Kenneth Klingenberg Barfod12*, Michael Roggenbuck3, Lars Hestbjerg Hansen3, Susanne Schjørring1, Søren Thor Larsen2, Søren Johannes Sørensen3 and Karen Angeliki Krogfelt1

  • * Corresponding author: Kenneth K Barfod

  • † Equal contributors

Author Affiliations

1 Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark

2 National Research Centre for the Working Environment, Lersø Parkallé 105, 2100 Copenhagen O, Denmark

3 Department of Biology, Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen O, Denmark

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BMC Microbiology 2013, 13:303  doi:10.1186/1471-2180-13-303

Published: 28 December 2013



This 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.


Using 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.


We 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.