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Journal of Clinical Bioinformatics

, 2:4

First Online: 02 February 2012Received: 29 August 2011Accepted: 02 February 2012DOI: 10.1186-2043-9113-2-4

Cite this article as: Lazarevic, V., Whiteson, K., Gaïa, N. et al. J Clin Bioinform 2012 2: 4. doi:10.1186-2043-9113-2-4


BackgroundThe 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.

MethodsWe 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.

ResultsThe 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.

ConclusionsAnalysis of the salivary metagenome may have implications in diagnostics e.g. in detection of microorganisms and viruses without designing specific tests for each pathogen.

List of abbreviationsHHVhuman herpes virus

HTShigh throughput sequencing

OTUoperational taxonomic unit

WGSwhole genome shotgun.

Electronic supplementary materialThe online version of this article doi:10.1186-2043-9113-2-4 contains supplementary material, which is available to authorized users.

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Autor: Vladimir Lazarevic - Katrine Whiteson - Nadia Gaïa - Yann Gizard - David Hernandez - Laurent Farinelli - Magne Østerås -


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