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 is two sited hierarchal clustered by 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.