title: The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.
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).
  
  
  CONCLUSIONS
  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.
authors.affiliation: Vaiomer SAS, Labège, France.|INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Lluch
authors.affiliation: Vaiomer SAS, Labège, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Servant
authors.affiliation: Vaiomer SAS, Labège, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Païssé
authors.affiliation: Vaiomer SAS, Labège, France.
authors.forename: Carine
authors.initials: C
authors.lastname: Valle
authors.affiliation: INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.|INRA, UAR1209, Castanet-Tolosan, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Valière
authors.affiliation: INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.|INRA, UAR1209, Castanet-Tolosan, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Kuchly
authors.affiliation: INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.|INRA, UAR1209, Castanet-Tolosan, France.
authors.forename: Gaëlle
authors.initials: G
authors.lastname: Vilchez
authors.affiliation: INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.|INRA, UMR1388, GenPhySE, Castanet-Tolosan, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Donnadieu
authors.affiliation: Vaiomer SAS, Labège, France.
authors.forename: Michael
authors.initials: M
authors.lastname: Courtney
authors.affiliation: INSERM U1048, I2MC, Toulouse, France.
authors.forename: Rémy
authors.initials: R
authors.lastname: Burcelin
authors.affiliation: INSERM U1048, I2MC, Toulouse, France.|Rangueil Hospital, Department of Therapeutics, Toulouse, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Amar
authors.affiliation: INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.|INRA, UMR1388, GenPhySE, Castanet-Tolosan, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Bouchez
authors.affiliation: Vaiomer SAS, Labège, France.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Lelouvier
mesh_terms: D000825:Animal Structures / Q000382:microbiology*; D000818:Animals; D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056186:Metagenomics; D051379:Mice; D008810:Mice, Inbred C57BL; D064307:Microbiota / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S