The OTU table was randomly subsampled to avoid differences based on sequencing effort leaving 3318 OTUs for further analysis (Rarefaction curve are shown in Additional file 1: Figure S5). We found a total

of 19 bacterial phyla in the samples analysed. The most dominant (>0.5% abundance) phyla observed were Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria Roscovitine and TM7. The difference in bacterial composition at the phylum level between sampling sites is shown in Figure 1A. Figure 1 Community composition. (A) Distribution of Phyla between sample types. LF-plus bronchoalveolar lavage (BAL) fluids and LF-minus is BAL where the mouse cells have been removed. LT is lung tissue and VF is vaginal flushing, (B) Venn diagram of identified shared and unique genera from each sampling site. All the lung type samples are considered here as one. (complete list shown in Additional file 3: Table S4), (C) The PcoA plot is generated of the Bray-Curtis dissimilarity metric based on OTU counts and explains the largest variance between all samples (PCoA plot 1vs 3 and PCoA plot

2 vs. 3 are attached in Additional file 4: Figure S4), (D) Heat map of even subsampled OTU table. The dendrogram GS-9973 is two sited hierarchal clustered by MK0683 abundance dissimilarity and the data are log transformed. Shown are only taxa, which counted for at least 0.5% of the generated sequences. The x-axis clusters the animal samples and the y-axis the taxonomical information. * marks Vaginal subcluster S1 and ** subcluster S2. In Additional

file 2: Table S2 we have listed all the bacteria that were found, which were unique for the cAMP lung samples and which were shared between sampling sites. The bacterial sequences of the lung samples If we only look at the lung samples, the most dominant lung phyla found were Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria. Additionally we observed Fusobacteria and Cyanobacteria in the lung and vaginal samples. In order to highlight phyla variations in the lung community compared to vaginal and caecal communities, we first we took the three lung sample types: bronchoalveolar lavage fluids (BAL-plus), and BAL-minus, where the mouse cells have been removed by a spin protocol and finally lung tissue from the distal tip of the lung and considered them as one ecological community. In this lung community profile, Actinobacteria, and Proteobacteria were clearly more abundant than in the caecum community (KW, p < 0.0001). Then, looking at the differences between the three lung sample types, Firmicutes appeared (KW, p < 0.05) more abundant in lung tissue (57%) than in BAL samples (20%). The SR1 bacteria were found only in BAL-minus and Lung tissue samples, but Tenericutes was observed in all samples, except in the vaginal samples. Other phyla observed below 0.5% abundance were Chloroflexi, Deinococcus-Thermus, Fibrobacteres, Gemmatimonadetes, OD1, OP10, Planctomycetes, Verrucomicrobia, and WS3.