The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.

TitleThe Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.
Publication TypeJournal Article
Year of Publication2015
AuthorsLluch, J, Servant, F, Païssé, S, Valle, C, Valière, S, Kuchly, C, Vilchez, G, Donnadieu, C, Courtney, M, Burcelin, R, Amar, J, Bouchez, O, Lelouvier, B
JournalPLoS One
Volume10
Issue11
Paginatione0142334
Date Published2015
ISSN1932-6203
Abstract

BACKGROUND: Substantial progress in high-throughput metagenomic sequencing methodologies has enabled the characterisation of bacteria from various origins (for example gut and skin). However, the recently-discovered bacterial microbiota present within animal internal tissues has remained unexplored due to technical difficulties associated with these challenging samples.RESULTS: We have optimized a specific 16S rDNA-targeted metagenomics sequencing (16S metabarcoding) pipeline based on the Illumina MiSeq technology for the analysis of bacterial DNA in human and animal tissues. This was successfully achieved in various mouse tissues despite the high abundance of eukaryotic DNA and PCR inhibitors in these samples. We extensively tested this pipeline on mock communities, negative controls, positive controls and tissues and demonstrated the presence of novel tissue specific bacterial DNA profiles in a variety of organs (including brain, muscle, adipose tissue, liver and heart).CONCLUSION: The high throughput and excellent reproducibility of the method ensured exhaustive and precise coverage of the 16S rDNA bacterial variants present in mouse tissues. This optimized 16S metagenomic sequencing pipeline will allow the scientific community to catalogue the bacterial DNA profiles of different tissues and will provide a database to analyse host/bacterial interactions in relation to homeostasis and disease.

DOI10.1371/journal.pone.0142334
Alternate JournalPLoS ONE
PubMed ID26544955
PubMed Central IDPMC4636327