Microbial community profiling of human saliva using shotgun metagenomic sequencing.
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...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4028220?pdf=render |
| _version_ | 1818032057142476800 |
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| author | Nur A Hasan Brian A Young Angela T Minard-Smith Kelly Saeed Huai Li Esley M Heizer Nancy J McMillan Richard Isom Abdul Shakur Abdullah Daniel M Bornman Seth A Faith Seon Young Choi Michael L Dickens Thomas A Cebula Rita R Colwell |
| author_facet | Nur A Hasan Brian A Young Angela T Minard-Smith Kelly Saeed Huai Li Esley M Heizer Nancy J McMillan Richard Isom Abdul Shakur Abdullah Daniel M Bornman Seth A Faith Seon Young Choi Michael L Dickens Thomas A Cebula Rita R Colwell |
| author_sort | Nur A Hasan |
| collection | DOAJ |
| description | 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 Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and 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. |
| first_indexed | 2024-12-10T06:01:19Z |
| format | Article |
| id | doaj.art-12eb8722f1bd406289c01654b8e29c19 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-10T06:01:19Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-12eb8722f1bd406289c01654b8e29c192022-12-22T01:59:48ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0195e9769910.1371/journal.pone.0097699Microbial community profiling of human saliva using shotgun metagenomic sequencing.Nur A HasanBrian A YoungAngela T Minard-SmithKelly SaeedHuai LiEsley M HeizerNancy J McMillanRichard IsomAbdul Shakur AbdullahDaniel M BornmanSeth A FaithSeon Young ChoiMichael L DickensThomas A CebulaRita R ColwellHuman 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 Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and 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.http://europepmc.org/articles/PMC4028220?pdf=render |
| spellingShingle | Nur A Hasan Brian A Young Angela T Minard-Smith Kelly Saeed Huai Li Esley M Heizer Nancy J McMillan Richard Isom Abdul Shakur Abdullah Daniel M Bornman Seth A Faith Seon Young Choi Michael L Dickens Thomas A Cebula Rita R Colwell Microbial community profiling of human saliva using shotgun metagenomic sequencing. PLoS ONE |
| title | Microbial community profiling of human saliva using shotgun metagenomic sequencing. |
| title_full | Microbial community profiling of human saliva using shotgun metagenomic sequencing. |
| title_fullStr | Microbial community profiling of human saliva using shotgun metagenomic sequencing. |
| title_full_unstemmed | Microbial community profiling of human saliva using shotgun metagenomic sequencing. |
| title_short | Microbial community profiling of human saliva using shotgun metagenomic sequencing. |
| title_sort | microbial community profiling of human saliva using shotgun metagenomic sequencing |
| url | http://europepmc.org/articles/PMC4028220?pdf=render |
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