title: High-resolution taxonomic profiling of the subgingival microbiome for biomarker discovery and periodontitis diagnosis.
abstract: 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 Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia 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.
authors.affiliation: Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors.forename: Szymon P
authors.initials: SP
authors.lastname: Szafranski
authors.affiliation: Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors.forename: Melissa L
authors.initials: ML
authors.lastname: Wos-Oxley
authors.affiliation: Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors.forename: Ramiro
authors.initials: R
authors.lastname: Vilchez-Vargas
authors.affiliation: Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors.forename: Ruy
authors.initials: R
authors.lastname: Jáuregui
authors.affiliation: Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors.forename: Iris
authors.initials: I
authors.lastname: Plumeier
authors.affiliation: Bioinformatics and Statistics Research Group, Department of Cellular Proteomics, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany Department of Computer Science, Ostfalia University of Applied Sciences, Wolfenbüttel, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Klawonn
authors.affiliation: Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Tomasch
authors.affiliation: National Cohort Study Center Augsburg, Helmholtz Centre Munich, Germany.
authors.forename: Christa
authors.initials: C
authors.lastname: Meisinger
authors.affiliation: Department of Conservative Dentistry, Ludwig-Maximilians-University, Munich, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Kühnisch
authors.affiliation: Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors.forename: Helena
authors.initials: H
authors.lastname: Sztajer
authors.affiliation: Microbial Interactions and Processes Research Group, Department of Medical Microbiology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany.
authors.forename: Dietmar H
authors.initials: DH
authors.lastname: Pieper
authors.affiliation: Microbial Communication Research Group, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany Irene.Wagner-Doebler@helmholtz-hzi.de.
authors.forename: Irene
authors.initials: I
authors.lastname: Wagner-Döbler
mesh_terms: D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D015415:Biomarkers; D058448:Biota; D002908:Chronic Disease; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D005881:Gingiva / Q000382:microbiology*; D006801:Humans; D010518:Periodontitis / Q000175:diagnosis* / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D015415:Biomarkers; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S