05). At phylum level, the composition of the lung tissue samples appeared to be very similar to the vaginal samples except for a larger abundance of Cyanobacteria in vaginal
samples (KW, p < 0.05). Bacterial sequences of the caecum Looking at the caecum samples, they contained more Firmicutes and Bacteroidetes KW, p < 0.0001) find protocol than the lung samples and Acidobacteria and Cyanobacteria were absent. The phylum Bacteroidetes (29%) appeared to be the second most abundant after the Firmicutes (59%). The vaginal and the caecal communities only had Ruminococcus in common, a genus that was not observed in the lung microbiota. Three genera were found in caecal samples alone; Robinsoniella, Parasutterella and Ramlibacter. The low numbers of genera detected in the caecal samples is due to the depth of taxonomic information obtained for these particular OTU sequences Fludarabine purchase towards the consensus lineage of the database.
Overlapping genera For an overview comparison between the different sample types, we have merged the results found in the different lung communities and displayed the overlapping generawit hcaecum and vagina in a venn diagram. This diagram reflects 255 identified genera (summarized in Additional file 3: Table S4), that covers 76% of the sequences from BAL-plus, 68% from BAL-minus, 66% of vaginal and lung tissue community and 27% of sequences assigned to the caecum community (Figure 1B). Lung samples, vaginal and caecum samples shared the 12 core genera Bacteroides, Barnesiella, Odoribacter, Alistipes, Mucispirillum, these Lactobacillus, Streptococcus, Peptoniphilus, Roseburia, Anaerotruncus, Oscillibacter,
Pseudomonas. We observed Parabacteroides, Eubacterium, Marvinbryantia, Butyricicoccus, Papillibacter, Bosea, Anaeroplasma, lung and caecum. The pulmonic and vaginal community shared 103 genera (Additional file 3: Table S4). Additionally Akkermansia was also found in the lung but only in one caecum sample in the raw data set. Variability in community composition between samples obtained from the same sampling site (Beta_diversity) To make a sample to sample comparison and illustrate the variation between our mice we have performed a principle coordinate Thiazovivin mw analysis (PCoA) based on the Bray-Curtis dissimilarity between OTU count metric PCoA plot (Figure 1C), which explains the largest variance between all samples (Additional PCoA 2 and 3 are found in Additional file 4: Figure S4). The caecal samples cluster together at a significant distance from lung and vaginal communities, confirmed by the analysis of similarity, anosim (R = 0.673, p = 0.001) The dissimilarity between the three lung communities was found to be little due to strong cluster overlap (anosim, R = 0.09, p = 0.05) when comparing only the lung distances.