The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.
<h4>Background</h4>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 r...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0142334 |
| _version_ | 1818589790579195904 |
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| author | Jérôme Lluch Florence Servant Sandrine Païssé Carine Valle Sophie Valière Claire Kuchly Gaëlle Vilchez Cécile Donnadieu Michael Courtney Rémy Burcelin Jacques Amar Olivier Bouchez Benjamin Lelouvier |
| author_facet | Jérôme Lluch Florence Servant Sandrine Païssé Carine Valle Sophie Valière Claire Kuchly Gaëlle Vilchez Cécile Donnadieu Michael Courtney Rémy Burcelin Jacques Amar Olivier Bouchez Benjamin Lelouvier |
| author_sort | Jérôme Lluch |
| collection | DOAJ |
| description | <h4>Background</h4>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.<h4>Results</h4>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).<h4>Conclusion</h4>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. |
| first_indexed | 2024-12-16T09:46:15Z |
| format | Article |
| id | doaj.art-3711211887bd4729b1d03fcf5255e919 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-16T09:46:15Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-3711211887bd4729b1d03fcf5255e9192022-12-21T22:36:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-011011e014233410.1371/journal.pone.0142334The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.Jérôme LluchFlorence ServantSandrine PaïsséCarine ValleSophie ValièreClaire KuchlyGaëlle VilchezCécile DonnadieuMichael CourtneyRémy BurcelinJacques AmarOlivier BouchezBenjamin Lelouvier<h4>Background</h4>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.<h4>Results</h4>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).<h4>Conclusion</h4>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.https://doi.org/10.1371/journal.pone.0142334 |
| spellingShingle | Jérôme Lluch Florence Servant Sandrine Païssé Carine Valle Sophie Valière Claire Kuchly Gaëlle Vilchez Cécile Donnadieu Michael Courtney Rémy Burcelin Jacques Amar Olivier Bouchez Benjamin Lelouvier The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline. PLoS ONE |
| title | The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline. |
| title_full | The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline. |
| title_fullStr | The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline. |
| title_full_unstemmed | The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline. |
| title_short | The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline. |
| title_sort | characterization of novel tissue microbiota using an optimized 16s metagenomic sequencing pipeline |
| url | https://doi.org/10.1371/journal.pone.0142334 |
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