As an added layer of complexity
Givinostat chemical structure we should remember that the total mouse microbiota do not only consists of bacteria but also fungi and viruses. In particular bacteriophages could influence gut or lung microbiology and indirectly have adverse effects on health [56]. Future studies into the lung microbiota of mice should include a comparison between nasal lavages and BAL to distinguish between upper and lower respiratory tract microbiota and possibly longitudinal studies with culture independent techniques. Conclusions BALB/cj mice were shown to have a lung microbiome that was distinct from their caecal but overlapping with their vaginal bacterial community. We have consistently amplified bacterial DNA from mouse BAL fluid and have shown that host DNA present in the DNA extraction PFT�� chemical structure step influences the community profiles obtained and that this needs to be taken into account when choosing methods, performing the analyses and prior to biological interpretation. Mouse models provide the means to obtain mechanistic insights into
the lung microbiome. We believe that the lung microbiota should be considered when working with these mouse models of human disease and further research is needed to reveal the contribution of the lung microbiota to the pathogenesis of diseases such as respiratory disease common in infants (i.e. RSV), cystic fibrosis, COPD and asthma. Availability of supporting data All supporting data are included as additional files and all sequences used in this study are available in the NCBI Sequence Read Archive under study accession number SRP033710 (http://www.ncbi.nlm.nih.gov/sra). Suplatast tosilate Acknowledgements The Danish National Advanced Technology Foundation, Lundbæk Foundation, Lars Andrup, Michael Guldbrandsen, Sofia Forssten, Al-Soud Waleed, Shannon Russell and Karin Vestberg. Electronic supplementary material Additional file 1: Figure S5: Rarefaction curves. (A) Observed species – raw data.
(B) Observed species after random even subsampling. The data shown in (A) accounted for all sequences generated. The graphs evened out after approx. 2000 sequences observed and revealed that the random even subsampled OTU table (B) at a sequencing depth of 3530 will be efficient to include also the rare OTUs. The subsampled OTU table (B) was used for the statistical analysis of this study and is the basis of the Figures 1 and 2. (PDF 29 KB) Additional file 2: Table S2: List of interesting taxa. This list shows the distribution of lung associated taxa between sampling methods and sites. Most of the lung-associated bacteria could only be found in the lung and vagina samples but not in the caecum. LF-plus is bronchoalveolar lavage (BAL) fluids and LF-minus is BAL where the mouse cells have been removed. LT is lung tissue,VF is vaginal flushing and caecum from the gut microbiota. (XLSX 11 KB) Additional file 3: Table S4: Distribution of genera between samples.