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Analysis of the salivary microbiome using culture-independent techniques
BACKGROUND: The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated. METHODS: We explored the bacterial community composition in the saliv...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296672/ https://www.ncbi.nlm.nih.gov/pubmed/22300522 http://dx.doi.org/10.1186/2043-9113-2-4 |
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author | Lazarevic, Vladimir Whiteson, Katrine Gaïa, Nadia Gizard, Yann Hernandez, David Farinelli, Laurent Østerås, Magne François, Patrice Schrenzel, Jacques |
author_facet | Lazarevic, Vladimir Whiteson, Katrine Gaïa, Nadia Gizard, Yann Hernandez, David Farinelli, Laurent Østerås, Magne François, Patrice Schrenzel, Jacques |
author_sort | Lazarevic, Vladimir |
collection | PubMed |
description | BACKGROUND: The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated. METHODS: We explored the bacterial community composition in the saliva sample using metagenomic whole genome shotgun (WGS) sequencing, the extraction of 16S rRNA gene fragments from metagenomic sequences (16S-WGS) and high-throughput sequencing of PCR-amplified bacterial 16S rDNA gene (16S-HTS) regions V1 and V3. RESULTS: The hierarchical clustering of data based on the relative abundance of bacterial genera revealed that distances between 16S-HTS datasets for V1 and V3 regions were greater than those obtained for the same V region with different numbers of PCR cycles. Datasets generated by 16S-HTS and 16S-WGS were even more distant. Finally, comparison of WGS and 16S-based datasets revealed the highest dissimilarity. The analysis of the 16S-HTS, WGS and 16S-WGS datasets revealed 206, 56 and 39 bacterial genera, respectively, 124 of which have not been previously identified in salivary microbiomes. A large fraction of DNA extracted from saliva corresponded to human DNA. Based on sequence similarity search against completely sequenced genomes, bacterial and viral sequences represented 0.73% and 0.0036% of the salivary metagenome, respectively. Several sequence reads were identified as parts of the human herpesvirus 7. CONCLUSIONS: Analysis of the salivary metagenome may have implications in diagnostics e.g. in detection of microorganisms and viruses without designing specific tests for each pathogen. |
format | Online Article Text |
id | pubmed-3296672 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-32966722012-03-08 Analysis of the salivary microbiome using culture-independent techniques Lazarevic, Vladimir Whiteson, Katrine Gaïa, Nadia Gizard, Yann Hernandez, David Farinelli, Laurent Østerås, Magne François, Patrice Schrenzel, Jacques J Clin Bioinforma Research BACKGROUND: The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated. METHODS: We explored the bacterial community composition in the saliva sample using metagenomic whole genome shotgun (WGS) sequencing, the extraction of 16S rRNA gene fragments from metagenomic sequences (16S-WGS) and high-throughput sequencing of PCR-amplified bacterial 16S rDNA gene (16S-HTS) regions V1 and V3. RESULTS: The hierarchical clustering of data based on the relative abundance of bacterial genera revealed that distances between 16S-HTS datasets for V1 and V3 regions were greater than those obtained for the same V region with different numbers of PCR cycles. Datasets generated by 16S-HTS and 16S-WGS were even more distant. Finally, comparison of WGS and 16S-based datasets revealed the highest dissimilarity. The analysis of the 16S-HTS, WGS and 16S-WGS datasets revealed 206, 56 and 39 bacterial genera, respectively, 124 of which have not been previously identified in salivary microbiomes. A large fraction of DNA extracted from saliva corresponded to human DNA. Based on sequence similarity search against completely sequenced genomes, bacterial and viral sequences represented 0.73% and 0.0036% of the salivary metagenome, respectively. Several sequence reads were identified as parts of the human herpesvirus 7. CONCLUSIONS: Analysis of the salivary metagenome may have implications in diagnostics e.g. in detection of microorganisms and viruses without designing specific tests for each pathogen. BioMed Central 2012-02-02 /pmc/articles/PMC3296672/ /pubmed/22300522 http://dx.doi.org/10.1186/2043-9113-2-4 Text en Copyright ©2012 Lazarevic et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Lazarevic, Vladimir Whiteson, Katrine Gaïa, Nadia Gizard, Yann Hernandez, David Farinelli, Laurent Østerås, Magne François, Patrice Schrenzel, Jacques Analysis of the salivary microbiome using culture-independent techniques |
title | Analysis of the salivary microbiome using culture-independent techniques |
title_full | Analysis of the salivary microbiome using culture-independent techniques |
title_fullStr | Analysis of the salivary microbiome using culture-independent techniques |
title_full_unstemmed | Analysis of the salivary microbiome using culture-independent techniques |
title_short | Analysis of the salivary microbiome using culture-independent techniques |
title_sort | analysis of the salivary microbiome using culture-independent techniques |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296672/ https://www.ncbi.nlm.nih.gov/pubmed/22300522 http://dx.doi.org/10.1186/2043-9113-2-4 |
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