Investigation of the Effect of Type 2 Diabetes Mellitus on Subgingival Plaque Microbiota by High-Throughput 16S rDNA Pyrosequencing
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{"title"=>"Investigation of the Effect of Type 2 Diabetes Mellitus on Subgingival Plaque Microbiota by High-Throughput 16S rDNA Pyrosequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Mi", "last_name"=>"Zhou", "scopus_author_id"=>"57198736328"}, {"first_name"=>"Ruichen", "last_name"=>"Rong", "scopus_author_id"=>"55109538800"}, {"first_name"=>"Daniel", "last_name"=>"Munro", "scopus_author_id"=>"9134089600"}, {"first_name"=>"Chunxia", "last_name"=>"Zhu", "scopus_author_id"=>"55656894700"}, {"first_name"=>"Xiang", "last_name"=>"Gao", "scopus_author_id"=>"56949404900"}, {"first_name"=>"Qi", "last_name"=>"Zhang", "scopus_author_id"=>"56308826400"}, {"first_name"=>"Qunfeng", "last_name"=>"Dong", "scopus_author_id"=>"8148229300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84876427116", "pui"=>"368766938", "doi"=>"10.1371/journal.pone.0061516", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"84876427116", "pmid"=>"23613868"}, "id"=>"4e61e9c2-2b64-3711-9d5e-b148c8d32582", "abstract"=>"Diabetes mellitus is a major risk factor for chronic periodontitis. We investigated the effects of type 2 diabetes on the subgingival plaque bacterial composition by applying culture-independent 16S rDNA sequencing to periodontal bacteria isolated from four groups of volunteers: non-diabetic subjects without periodontitis, non-diabetic subjects with periodontitis, type 2 diabetic patients without periodontitis, and type 2 diabetic patients with periodontitis. A total of 71,373 high-quality sequences were produced from the V1-V3 region of 16S rDNA genes by 454 pyrosequencing. Those 16S rDNA sequences were classified into 16 phyla, 27 classes, 48 orders, 85 families, 126 genera, and 1141 species-level OTUs. Comparing periodontally healthy samples with periodontitis samples identified 20 health-associated and 15 periodontitis-associated OTUs. In the subjects with healthy periodontium, the abundances of three genera (Prevotella, Pseudomonas, and Tannerella) and nine OTUs were significantly different between diabetic patients and their non-diabetic counterparts. In the subjects carrying periodontitis, the abundances of three phyla (Actinobacteria, Proteobacteria, and Bacteriodetes), two genera (Actinomyces and Aggregatibacter), and six OTUs were also significantly different between diabetics and non-diabetics. Our results show that type 2 diabetes mellitus could alter the bacterial composition in the subgingival plaque.", "link"=>"http://www.mendeley.com/research/investigation-effect-type-2-diabetes-mellitus-subgingival-plaque-microbiota-highthroughput-16s-rdna-2", "reader_count"=>54, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>13, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>4, "Student > Master"=>11, "Other"=>2, "Student > Bachelor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>13, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>4, "Student > Master"=>11, "Other"=>2, "Student > Bachelor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>20, "Medicine and Dentistry"=>19, "Arts and Humanities"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>19}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>20}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>1, "Portugal"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1030720"], "description"=>"<p>The figure shows the results of non-metric multidimensional scaling (NMDS) applied to the unweighted UniFrac distances between different subsets of samples. The X- and Y-axes represent the first and second NMDS dimensions, respectively. The label next to each data point indicates the sample name. (A) Among diabetes-negative samples, a PERMANOVA test indicates significant (p<0.01) differences in the UniFrac distances according to the presence or absence of periodontitis. (B) A similar comparison among diabetes-positive samples is also significant (p<0.01). (C) Among periodontitis-negative samples, there is no clear separation based on diabetes status (p = 0.06). (D) In periodontitis-positive samples, however, significant differences do exist based on diabetes status (p<0.01).</p>", "links"=>[], "tags"=>["genomics", "metagenomics", "microbiology", "Host-pathogen interaction", "Medical microbiology", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Oral medicine", "Oral diseases", "plaque", "bacterial"], "article_id"=>687320, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mi Zhou", "Ruichen Rong", "Daniel Munro", "Chunxia Zhu", "Xiang Gao", "Qi Zhang", "Qunfeng Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061516.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Subgingival_plaque_bacterial_community_composition_comparison_/687320", "title"=>"Subgingival plaque bacterial community composition comparison.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-22 02:02:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/1030721"], "description"=>"<p>Within the periodontitis-negative and periodontitis-positive sample groups, the listed OTUs were significantly either more or less abundant in diabetes-positive samples than in diabetes-negative samples, as indicated by the rows. The three columns indicate whether each OTU was significantly enriched in periodontitis-negative samples, periodontitis-positive samples, or neither, as found in the comparisons shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061516#pone-0061516-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["genomics", "metagenomics", "microbiology", "Host-pathogen interaction", "Medical microbiology", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Oral medicine", "Oral diseases", "otus", "diabetic", "non-diabetic"], "article_id"=>687321, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mi Zhou", "Ruichen Rong", "Daniel Munro", "Chunxia Zhu", "Xiang Gao", "Qi Zhang", "Qunfeng Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061516.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Signature_OTUs_associated_with_diabetic_and_non_diabetic_samples_/687321", "title"=>"Signature OTUs associated with diabetic and non-diabetic samples.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-22 02:02:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1030722"], "description"=>"<p>All OTUs listed had significantly different abundances or prevalence between the healthy and periodontitis samples within the diabetes-negative group, diabetes-positive group, or in both groups, as indicated by the three rows. The two columns indicate whether each OTU was more abundant or prevalent in periodontitis-negative or periodontitis-positive samples.</p>", "links"=>[], "tags"=>["genomics", "metagenomics", "microbiology", "Host-pathogen interaction", "Medical microbiology", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Oral medicine", "Oral diseases", "periodontitis-associated"], "article_id"=>687322, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mi Zhou", "Ruichen Rong", "Daniel Munro", "Chunxia Zhu", "Xiang Gao", "Qi Zhang", "Qunfeng Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061516.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Health_associated_and_periodontitis_associated_OTUs_/687322", "title"=>"Health-associated and periodontitis-associated OTUs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-22 02:02:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/1030724", "https://ndownloader.figshare.com/files/1030725", "https://ndownloader.figshare.com/files/1030726", "https://ndownloader.figshare.com/files/1030727"], "description"=>"<div><p>Diabetes mellitus is a major risk factor for chronic periodontitis. We investigated the effects of type 2 diabetes on the subgingival plaque bacterial composition by applying culture-independent 16S rDNA sequencing to periodontal bacteria isolated from four groups of volunteers: non-diabetic subjects without periodontitis, non-diabetic subjects with periodontitis, type 2 diabetic patients without periodontitis, and type 2 diabetic patients with periodontitis. A total of 71,373 high-quality sequences were produced from the V1-V3 region of 16S rDNA genes by 454 pyrosequencing. Those 16S rDNA sequences were classified into 16 phyla, 27 classes, 48 orders, 85 families, 126 genera, and 1141 species-level OTUs. Comparing periodontally healthy samples with periodontitis samples identified 20 health-associated and 15 periodontitis-associated OTUs. In the subjects with healthy periodontium, the abundances of three genera (<i>Prevotella</i>, <i>Pseudomonas</i>, and <i>Tannerella</i>) and nine OTUs were significantly different between diabetic patients and their non-diabetic counterparts. In the subjects carrying periodontitis, the abundances of three phyla (<i>Actinobacteria</i>, <i>Proteobacteria</i>, and <i>Bacteriodetes</i>), two genera (<i>Actinomyces</i> and <i>Aggregatibacter</i>), and six OTUs were also significantly different between diabetics and non-diabetics. Our results show that type 2 diabetes mellitus could alter the bacterial composition in the subgingival plaque.</p></div>", "links"=>[], "tags"=>["genomics", "metagenomics", "microbiology", "Host-pathogen interaction", "Medical microbiology", "Diagnostic medicine", "pathology", "Clinical pathology", "Clinical microbiology", "Oral medicine", "Oral diseases", "mellitus", "subgingival", "plaque", "microbiota", "high-throughput", "16s", "rdna"], "article_id"=>687323, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Mi Zhou", "Ruichen Rong", "Daniel Munro", "Chunxia Zhu", "Xiang Gao", "Qi Zhang", "Qunfeng Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061516.s001", "https://dx.doi.org/10.1371/journal.pone.0061516.s002", "https://dx.doi.org/10.1371/journal.pone.0061516.s003", "https://dx.doi.org/10.1371/journal.pone.0061516.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Investigation_of_the_Effect_of_Type_2_Diabetes_Mellitus_on_Subgingival_Plaque_Microbiota_by_High_Throughput_16S_rDNA_Pyrosequencing_/687323", "title"=>"Investigation of the Effect of Type 2 Diabetes Mellitus on Subgingival Plaque Microbiota by High-Throughput 16S rDNA Pyrosequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-04-22 02:02:03"}

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Relative Metric

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