{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T01:00:20Z","timestamp":1785546020642,"version":"3.56.0"},"reference-count":53,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2015,2,1]],"date-time":"2015-02-01T00:00:00Z","timestamp":1422748800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Appl Environ Microbiol"],"published-print":{"date-parts":[[2015,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The oral microbiome plays a key role for caries, periodontitis, and systemic diseases. A method for rapid, high-resolution, robust taxonomic profiling of subgingival bacterial communities for early detection of periodontitis biomarkers would therefore be a useful tool for individualized medicine. Here, we used Illumina sequencing of the V1-V2 and V5-V6 hypervariable regions of the 16S rRNA gene. A sample stratification pipeline was developed in a pilot study of 19 individuals, 9 of whom had been diagnosed with chronic periodontitis. Five hundred twenty-three operational taxonomic units (OTUs) were obtained from the V1-V2 region and 432 from the V5-V6 region. Key periodontal pathogens like\n            <jats:named-content content-type=\"genus-species\">Porphyromonas gingivalis<\/jats:named-content>\n            ,\n            <jats:named-content content-type=\"genus-species\">Treponema denticola<\/jats:named-content>\n            , and\n            <jats:named-content content-type=\"genus-species\">Tannerella forsythia<\/jats:named-content>\n            could be identified at the species level with both primer sets. Principal coordinate analysis identified two outliers that were consistently independent of the hypervariable region and method of DNA extraction used. The linear discriminant analysis (LDA) effect size algorithm (LEfSe) identified 80 OTU-level biomarkers of periodontitis and 17 of health. Health- and periodontitis-related clusters of OTUs were identified using a connectivity analysis, and the results confirmed previous studies with several thousands of samples. A machine learning algorithm was developed which was trained on all but one sample and then predicted the diagnosis of the left-out sample (jackknife method). Using a combination of the 10 best biomarkers, 15 of 17 samples were correctly diagnosed. Training the algorithm on time-resolved community profiles might provide a highly sensitive tool to detect the onset of periodontitis.\n          <\/jats:p>","DOI":"10.1128\/aem.03534-14","type":"journal-article","created":{"date-parts":[[2014,12,2]],"date-time":"2014-12-02T04:19:53Z","timestamp":1417493993000},"page":"1047-1058","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":97,"title":["High-Resolution Taxonomic Profiling of the Subgingival Microbiome for Biomarker Discovery and Periodontitis Diagnosis"],"prefix":"10.1128","volume":"81","author":[{"given":"Szymon P.","family":"Szafranski","sequence":"first","affiliation":[{"name":"Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa L.","family":"Wos-Oxley","sequence":"additional","affiliation":[{"name":"Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramiro","family":"Vilchez-Vargas","sequence":"additional","affiliation":[{"name":"Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruy","family":"J\u00e1uregui","sequence":"additional","affiliation":[{"name":"Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iris","family":"Plumeier","sequence":"additional","affiliation":[{"name":"Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank","family":"Klawonn","sequence":"additional","affiliation":[{"name":"Bioinformatics and Statistics Research Group, Department of Cellular Proteomics, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"},{"name":"Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenb\u00fcttel, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00fcrgen","family":"Tomasch","sequence":"additional","affiliation":[{"name":"Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christa","family":"Meisinger","sequence":"additional","affiliation":[{"name":"National Cohort Study Center Augsburg, Helmholtz Centre Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"K\u00fchnisch","sequence":"additional","affiliation":[{"name":"Department of Conservative Dentistry, Ludwig-Maximilians-University, Munich, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helena","family":"Sztajer","sequence":"additional","affiliation":[{"name":"Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dietmar H.","family":"Pieper","sequence":"additional","affiliation":[{"name":"Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene","family":"Wagner-D\u00f6bler","sequence":"additional","affiliation":[{"name":"Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, 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Oral health surveys: basic methods, 4th ed. World Health Organization, Geneva, Switzerland. http:\/\/apps.who.int\/iris\/handle\/10665\/41905.","edition":"4"},{"key":"e_1_3_3_16_2","first-page":"281","article-title":"Development of the World Health Organization (WHO) community periodontal index of treatment needs (CPITN)","volume":"32","author":"Ainamo J","year":"1982","unstructured":"Ainamo J, Barmes D, Beagrie G, Cutress T, Martin J, Sardo-Infirri J. 1982. Development of the World Health Organization (WHO) community periodontal index of treatment needs (CPITN). 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