Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.

<h4>Objectives</h4>The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome i...

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Autores principales:	Jiyoung Ahn, Liying Yang, Bruce J Paster, Ian Ganly, Luc Morris, Zhiheng Pei, Richard B Hayes
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/360a7452f0c345118dfe7ea7edd195fb
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spelling	oai:doaj.org-article:360a7452f0c345118dfe7ea7edd195fb2021-11-18T06:49:02ZOral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.1932-620310.1371/journal.pone.0022788https://doaj.org/article/360a7452f0c345118dfe7ea7edd195fb2011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21829515/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Objectives</h4>The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray.<h4>Methods</h4>Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3-V5 region (450 bp). Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM). Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity.<h4>Results</h4>The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70∼0.86). 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence) and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70-0.84).<h4>Conclusion</h4>Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.Jiyoung AhnLiying YangBruce J PasterIan GanlyLuc MorrisZhiheng PeiRichard B HayesPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e22788 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jiyoung Ahn Liying Yang Bruce J Paster Ian Ganly Luc Morris Zhiheng Pei Richard B Hayes Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
description	<h4>Objectives</h4>The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray.<h4>Methods</h4>Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3-V5 region (450 bp). Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM). Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity.<h4>Results</h4>The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70∼0.86). 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence) and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70-0.84).<h4>Conclusion</h4>Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.
format	article
author	Jiyoung Ahn Liying Yang Bruce J Paster Ian Ganly Luc Morris Zhiheng Pei Richard B Hayes
author_facet	Jiyoung Ahn Liying Yang Bruce J Paster Ian Ganly Luc Morris Zhiheng Pei Richard B Hayes
author_sort	Jiyoung Ahn
title	Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
title_short	Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
title_full	Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
title_fullStr	Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
title_full_unstemmed	Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.
title_sort	oral microbiome profiles: 16s rrna pyrosequencing and microarray assay comparison.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/360a7452f0c345118dfe7ea7edd195fb
work_keys_str_mv	AT jiyoungahn oralmicrobiomeprofiles16srrnapyrosequencingandmicroarrayassaycomparison AT liyingyang oralmicrobiomeprofiles16srrnapyrosequencingandmicroarrayassaycomparison AT brucejpaster oralmicrobiomeprofiles16srrnapyrosequencingandmicroarrayassaycomparison AT ianganly oralmicrobiomeprofiles16srrnapyrosequencingandmicroarrayassaycomparison AT lucmorris oralmicrobiomeprofiles16srrnapyrosequencingandmicroarrayassaycomparison AT zhihengpei oralmicrobiomeprofiles16srrnapyrosequencingandmicroarrayassaycomparison AT richardbhayes oralmicrobiomeprofiles16srrnapyrosequencingandmicroarrayassaycomparison
_version_	1718424343774494720

Oral microbiome profiles: 16S rRNA pyrosequencing and microarray assay comparison.

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