Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing
Identifieur interne : 000D23 ( Ncbi/Curation ); précédent : 000D22; suivant : 000D24Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing
Auteurs : Nur A. Hasan [États-Unis] ; Brian A. Young [États-Unis] ; Angela T. Minard-Smith [États-Unis] ; Kelly Saeed [États-Unis] ; Huai Li [États-Unis] ; Esley M. Heizer [États-Unis] ; Nancy J. Mcmillan [États-Unis] ; Richard Isom [États-Unis] ; Abdul Shakur Abdullah [États-Unis] ; Daniel M. Bornman [États-Unis] ; Seth A. Faith [États-Unis] ; Seon Young Choi [États-Unis] ; Michael L. Dickens [États-Unis] ; Thomas A. Cebula [États-Unis] ; Rita R. Colwell [États-Unis]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also
Url:
DOI: 10.1371/journal.pone.0097699
PubMed: 24846174
PubMed Central: 4028220
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PMC:4028220Le document en format XML
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<affiliation wicri:level="2"><nlm:aff id="aff6"><addr-line>Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America</addr-line>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland</wicri:regionArea>
<placeName><region type="state">Maryland</region>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">PLoS ONE</title>
<idno type="eISSN">1932-6203</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><p>Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also <italic>Haemophilus influenzae</italic>
, <italic>Neisseria meningitidis</italic>
, <italic>Streptococcus pneumoniae</italic>
, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported <italic>ca</italic>
. five times more species than those actually comprising the <italic>in silico</italic>
sample. Both GENIUSand BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.</p>
</div>
</front>
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