Oral Microbiome Profiles: 16S rRNA Pyrosequencing and Microarray Assay Comparison
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{"title"=>"Oral microbiome profiles: 16s rRNA pyrosequencing and microarray assay comparison", "type"=>"journal", "authors"=>[{"first_name"=>"Jiyoung", "last_name"=>"Ahn", "scopus_author_id"=>"7403019290"}, {"first_name"=>"Liying", "last_name"=>"Yang", "scopus_author_id"=>"55732940500"}, {"first_name"=>"Bruce J.", "last_name"=>"Paster", "scopus_author_id"=>"7005348621"}, {"first_name"=>"Ian", "last_name"=>"Ganly", "scopus_author_id"=>"6701500102"}, {"first_name"=>"Luc", "last_name"=>"Morris", "scopus_author_id"=>"7201727299"}, {"first_name"=>"Zhiheng", "last_name"=>"Pei", "scopus_author_id"=>"7101715223"}, {"first_name"=>"Richard B.", "last_name"=>"Hayes", "scopus_author_id"=>"7402082381"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"79960895899", "doi"=>"10.1371/journal.pone.0022788", "pui"=>"362239020", "pmid"=>"21829515", "scopus"=>"2-s2.0-79960895899", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)"}, "id"=>"d4d5b189-ea99-3e64-a5e2-5b03786a995a", "abstract"=>"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.", "link"=>"http://www.mendeley.com/research/oral-microbiome-profiles-16s-rrna-pyrosequencing-microarray-assay-comparison", "reader_count"=>191, "reader_count_by_academic_status"=>{"Unspecified"=>7, "Professor > Associate Professor"=>12, "Researcher"=>44, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>51, "Student > Postgraduate"=>9, "Student > Master"=>25, "Other"=>13, "Student > Bachelor"=>11, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>7, "Professor > Associate Professor"=>12, "Researcher"=>44, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>51, "Student > Postgraduate"=>9, "Student > Master"=>25, "Other"=>13, "Student > Bachelor"=>11, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Agricultural and Biological Sciences"=>107, "Arts and Humanities"=>2, "Chemistry"=>2, "Computer Science"=>1, "Engineering"=>2, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>14, "Nursing and Health Professions"=>1, "Materials Science"=>1, "Medicine and Dentistry"=>35, "Psychology"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>9}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>35}, "Social Sciences"=>{"Social Sciences"=>1}, "Psychology"=>{"Psychology"=>2}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>5}, "Arts and Humanities"=>{"Arts and Humanities"=>2}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>9}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>107}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}}, "reader_count_by_country"=>{"Austria"=>1, "Sweden"=>1, "United States"=>3, "South Africa"=>1, "Malaysia"=>1, "Switzerland"=>1, "Germany"=>2, "Spain"=>2}, "group_count"=>8}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/749973"], "description"=>"a<p>calculated by numbers of concordant counts/discordant counts.</p>b<p>Pearson correlation based on relative intensity of HOMIM and rations of RDP classified sequence read for each genus.</p>", "links"=>[], "tags"=>["37", "genera", "16s", "rrna", "pyrosequencing", "microbe", "microarray"], "article_id"=>420328, "categories"=>["Microbiology", "Cell Biology", "Genetics", "Biotechnology"], "users"=>["Jiyoung Ahn", "Liying Yang", "Bruce J. Paster", "Ian Ganly", "Luc Morris", "Zhiheng Pei", "Richard B. Hayes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022788.t003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concordance_and_correlation_of_37_genera_detected_from_16S_rRNA_gene_pyrosequencing_and_Human_Oral_Microbe_Identification_Microarray_HOMIM_assay_/420328", "title"=>"Concordance and correlation of 37 genera detected from 16S rRNA gene pyrosequencing and Human Oral Microbe Identification Microarray (HOMIM) assay.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-29 00:05:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/749844"], "description"=>"<p>P indicates 16S rRNA gene pyrosequencing results and H indicates Human Oral Microbe Identification Microarray (HOMIM) assay results. Unclassified bacteria in 16S rRNA gene pyrosequencing are excluded.</p>", "links"=>[], "tags"=>["abundance", "phyla"], "article_id"=>420209, "categories"=>["Microbiology", "Cell Biology", "Genetics", "Biotechnology"], "users"=>["Jiyoung Ahn", "Liying Yang", "Bruce J. Paster", "Ian Ganly", "Luc Morris", "Zhiheng Pei", "Richard B. Hayes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022788.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relative_abundance_of_phyla_for_each_subject_n_8202_8202_20_/420209", "title"=>"The relative abundance of phyla for each subject (n = 20).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-29 00:03:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/377966", "https://ndownloader.figshare.com/files/377999"], "description"=>"<div><h3>Objectives</h3><p>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.</p> <h3>Methods</h3><p>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.</p> <h3>Results</h3><p>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 (<em>Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus</em>; Correlation = 0.70–0.84).</p> <h3>Conclusion</h3><p>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.</p> </div>", "links"=>[], "tags"=>["microbiome", "16s", "rrna", "pyrosequencing", "microarray", "assay"], "article_id"=>134684, "categories"=>["Microbiology", "Cell Biology", "Genetics", "Biotechnology"], "users"=>["Jiyoung Ahn", "Liying Yang", "Bruce J. Paster", "Ian Ganly", "Luc Morris", "Zhiheng Pei", "Richard B. Hayes"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0022788.s001", "https://dx.doi.org/10.1371/journal.pone.0022788.s002"], "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Oral_Microbiome_Profiles_16S_rRNA_Pyrosequencing_and_Microarray_Assay_Comparison/134684", "title"=>"Oral Microbiome Profiles: 16S rRNA Pyrosequencing and Microarray Assay Comparison", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-07-29 01:18:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/750047"], "description"=>"<p>Strengths and limitations of 16S rRNA gene pyrosequencing and Human Oral Microbe Identification Microarray (HOMIM) assay.</p>", "links"=>[], "tags"=>["limitations", "16s", "rrna", "pyrosequencing", "microbe", "microarray"], "article_id"=>420408, "categories"=>["Microbiology", "Cell Biology", "Genetics", "Biotechnology"], "users"=>["Jiyoung Ahn", "Liying Yang", "Bruce J. Paster", "Ian Ganly", "Luc Morris", "Zhiheng Pei", "Richard B. Hayes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022788.t004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Strengths_and_limitations_of_16S_rRNA_gene_pyrosequencing_and_Human_Oral_Microbe_Identification_Microarray_HOMIM_assay_/420408", "title"=>"Strengths and limitations of 16S rRNA gene pyrosequencing and Human Oral Microbe Identification Microarray (HOMIM) assay.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-29 00:06:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/749922"], "description"=>"<p>*Relative Distribution was calculated after exclusion of 3.2% unclassified bacteria.</p><p>**ND: non determined.</p><p>Note: P value for chi-square test of the relative abundance distribution = 0.65.</p>", "links"=>[], "tags"=>["abundance", "16s", "rrna", "pyrosequencing", "microbe", "microarray"], "article_id"=>420289, "categories"=>["Microbiology", "Cell Biology", "Genetics", "Biotechnology"], "users"=>["Jiyoung Ahn", "Liying Yang", "Bruce J. Paster", "Ian Ganly", "Luc Morris", "Zhiheng Pei", "Richard B. Hayes"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0022788.t001", "stats"=>{"downloads"=>1, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relative_abundance_correlation_of_phyla_data_from_16S_rRNA_gene_pyrosequencing_and_Human_Oral_Microbe_Identification_Microarray_HOMIM_assay_/420289", "title"=>"The relative abundance correlation of phyla: data from 16S rRNA gene pyrosequencing and Human Oral Microbe Identification Microarray (HOMIM) assay.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-07-29 00:04:49"}

PMC Usage Stats | Further Information

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Relative Metric

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