Deep Sequencing Identifies Ethnicity-Specific Bacterial Signatures in the Oral Microbiome
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{"title"=>"Deep Sequencing Identifies Ethnicity-Specific Bacterial Signatures in the Oral Microbiome", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew R.", "last_name"=>"Mason", "scopus_author_id"=>"55091674300"}, {"first_name"=>"Haikady N.", "last_name"=>"Nagaraja", "scopus_author_id"=>"7003457638"}, {"first_name"=>"Terry", "last_name"=>"Camerlengo", "scopus_author_id"=>"13807418100"}, {"first_name"=>"Vinayak", "last_name"=>"Joshi", "scopus_author_id"=>"16047774800"}, {"first_name"=>"Purnima S.", "last_name"=>"Kumar", "scopus_author_id"=>"9745930400"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24194878", "sgr"=>"84886019355", "doi"=>"10.1371/journal.pone.0077287", "scopus"=>"2-s2.0-84886019355", "pui"=>"370091228", "isbn"=>"1932-6203 %/ Public Library of Science", "issn"=>"19326203"}, "id"=>"a84f0321-bab7-3d60-966e-0e03b2d44284", "abstract"=>"Oral infections have a strong ethnic predilection; suggesting that ethnicity is a critical determinant of oral microbial colonization. Dental plaque and saliva samples from 192 subjects belonging to four major ethnicities in the United States were analyzed using terminal restriction fragment length polymorphism (t-RFLP) and 16S pyrosequencing. Ethnicity-specific clustering of microbial communities was apparent in saliva and subgingival biofilms, and a machine-learning classifier was capable of identifying an individual's ethnicity from subgingival microbial signatures. The classifier identified African Americans with a 100% sensitivity and 74% specificity and Caucasians with a 50% sensitivity and 91% specificity. The data demonstrates a significant association between ethnic affiliation and the composition of the oral microbiome; to the extent that these microbial signatures appear to be capable of discriminating between ethnicities.", "link"=>"http://www.mendeley.com/research/deep-sequencing-identifies-ethnicityspecific-bacterial-signatures-oral-microbiome", "reader_count"=>133, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>5, "Researcher"=>25, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>4, "Student > Master"=>21, "Other"=>9, "Student > Bachelor"=>19, "Lecturer > Senior Lecturer"=>2, "Professor"=>7}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>5, "Researcher"=>25, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>4, "Student > Master"=>21, "Other"=>9, "Student > Bachelor"=>19, "Lecturer > Senior Lecturer"=>2, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Agricultural and Biological Sciences"=>62, "Arts and Humanities"=>1, "Chemistry"=>1, "Computer Science"=>3, "Decision Sciences"=>1, "Engineering"=>3, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>23, "Mathematics"=>1, "Medicine and Dentistry"=>18, "Physics and Astronomy"=>2, "Psychology"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>8}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>18}, "Social Sciences"=>{"Social Sciences"=>1}, "Decision Sciences"=>{"Decision Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>3}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>8}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>62}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>23}}, "reader_count_by_country"=>{"Colombia"=>1, "Netherlands"=>1, "Belgium"=>1, "United States"=>6, "Ireland"=>1, "Japan"=>1, "France"=>2, "Germany"=>3, "Russia"=>1, "India"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1255561"], "description"=>"<p>Non-Hispanic Blacks (AA) demonstrated the greatest accuracy, with 100% sensitivity and 74% specificity, followed by Latinos(LA) and Caucasians (CA).</p>", "links"=>[], "tags"=>["discriminating", "ethnicity", "subgingival", "microbial"], "article_id"=>830598, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Matthew R. Mason", "Haikady N. Nagaraja", "Terry Camerlengo", "Vinayak Joshi", "Purnima S. Kumar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077287.g005", "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accuracy_of_discriminating_between_ethnicity_using_the_subgingival_microbial_signature_/830598", "title"=>"Accuracy of discriminating between ethnicity using the subgingival microbial signature.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255556"], "description"=>"<p>2% of s-OTUs were shared by all individuals, 8% of s-OTUs were shared by 90% of individuals and over a third of the s-OTUs were shared by 50% of the subjects, supporting the existence of a core microbiome at both levels. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077287#pone-0077287-g003\" target=\"_blank\">Figure 3C</a> shows relative abundances of species shared by all individuals. Abundances of 4 shared species were different between ethnicities (p<0.001, ANOVA on transformed variable).</p>", "links"=>[], "tags"=>["subject-level", "ethnicity-level"], "article_id"=>830595, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Matthew R. Mason", "Haikady N. Nagaraja", "Terry Camerlengo", "Vinayak Joshi", "Purnima S. Kumar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077287.g003", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Shared_species_at_subject_level_Figure_3A_and_ethnicity_level_Figure_3B_/830595", "title"=>"Shared species at subject-level (Figure 3A) and ethnicity-level (Figure 3B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255555"], "description"=>"<p>Diversity is shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077287#pone-0077287-g002\" target=\"_blank\">Figure 2A</a> and equitability in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077287#pone-0077287-g002\" target=\"_blank\">Figure 2B</a>. Non-Hispanic blacks demonstrated significantly lower bacterial diversity (***p<0.001, ANOVA) and equitability (***p<0.001, ANOVA) compared to the other ethnicities.</p>", "links"=>[], "tags"=>["equitability", "indices"], "article_id"=>830594, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Matthew R. Mason", "Haikady N. Nagaraja", "Terry Camerlengo", "Vinayak Joshi", "Purnima S. Kumar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077287.g002", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Shannon_diversity_and_equitability_indices_by_ethnicity_/830594", "title"=>"Shannon diversity and equitability indices by ethnicity.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255565"], "description"=>"<p>These OTUs were identified based on presence/absence in each individual. The likelihood of discriminating between ethnicities using presence/absence of these s-OTUs is shown in parenthesis. The mere presence of these ethnicity-specific consortia was capable of identifying an individual’s ethnicity better than chance.</p>", "links"=>[], "tags"=>["diagram", "ethnicity"], "article_id"=>830602, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Matthew R. Mason", "Haikady N. Nagaraja", "Terry Camerlengo", "Vinayak Joshi", "Purnima S. Kumar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077287.g006", "stats"=>{"downloads"=>4, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagram_of_ethnicity_specific_s_OTUs_/830602", "title"=>"Venn diagram of ethnicity specific s-OTUs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255557"], "description"=>"<p>Figure was generated using ITOL. Non-Hispanic blacks are indicated by red, non-Hispanic whites are indicated by green, Chinese are indicated by blue, and Latinos are indicated by orange. The abundances of four s-OTUs and several g-OTUs were significantly different between ethnicities (*p<0.05, **p<0.01, ***p<0.001, ****p<0.0001, ANOVA on transformed variable).</p>", "links"=>[], "tags"=>["abundances", "77", "genus-level"], "article_id"=>830596, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Matthew R. Mason", "Haikady N. Nagaraja", "Terry Camerlengo", "Vinayak Joshi", "Purnima S. Kumar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077287.g004", "stats"=>{"downloads"=>3, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_abundances_of_77_genus_level_OTUs_g_OTUs_/830596", "title"=>"Relative abundances of 77 genus-level OTUs(g-OTUs).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/1255554"], "description"=>"<p>Subgingival plaque is shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077287#pone-0077287-g001\" target=\"_blank\">Figure 1A</a>, saliva in 1B, and supragingival plaque in 1C. Non-Hispanic blacks are indicated by red, non-Hispanic whites are in green, Chinese are in blue, and Latinos are indicated by orange. Significant ethnicity-based clustering was seen in subgingival and saliva samples (Subgingival stress value = 0.09, Saliva stress value = 0.11, Supragingival stress value = 0.12).</p>", "links"=>[], "tags"=>["multidimensional", "scaling", "t-rflp"], "article_id"=>830593, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Matthew R. Mason", "Haikady N. Nagaraja", "Terry Camerlengo", "Vinayak Joshi", "Purnima S. Kumar"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0077287.g001", "stats"=>{"downloads"=>3, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Non_metric_multidimensional_scaling_NMDS_of_t_RFLP_peak_areas_/830593", "title"=>"Non-metric multidimensional scaling (NMDS) of t-RFLP peak areas.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-10-23 02:48:54"}

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