Metagenomic Analysis of Subgingival Microbiota Following Non-Surgical Periodontal Therapy: a Pilot Study

Theresia Laksmana 1, Weerayuth Kittichotirat 2, 3, Yanyan Huang 1, Weizhen Chen 1, Michael Jorgensen 1, Roger Bumgarner 2, Casey Chen 1, *
1 Ostrow School of Dentistry of USC, Los Angeles, CA, USA
2 Department of Microbiology, University of Washington, Seattle, WA, USA
3 Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkhuntien, Bangkok, Thailand

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© Laksmana et al.; Licensee Bentham Open.

open-access license: This is an open access article licensed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted, non-commercial use, distribution and reproduction in any medium, provided the work is properly cited.

* Address correspondence to this author at the Area Division of Periodontology, Diagnostic Sciences and Dental Hygiene, Herman Ostrow School of Dentistry of USC, 925 W 34th Street, Room 4107, Los Angeles, CA 90089-0641; Tel: (213) 740-1075; Fax: (213) 740-6778; E-mail:


This study tested the feasibility of a high throughput metagenomic approach to analyze the pre- and posttreatment of subgingival plaque in two subjects with aggressive periodontitis. DNA was extracted from subgingival samples and subjected to PCR amplification of the c2-c4 regions of the 16S rDNA using primers with bar codes to identify individual samples. The PCR products were pooled and sequenced for the v4 region of the 16S rDNA using the 454 FLX standard platform. The results were analyzed for species/phylotypes in the Human Oral Microbiome Database (HOMD) and Ribosomal Database Project (RDP) database. The sequencing of the amplicons resulted in 24,673 reads and identified 208 species/phylotypes. Of those, 129 species/phylotypes were identified in both patients but their proportions varied. While >120 species/phylotypes were identified in all samples, 28-42 species/phylotypes cumulatively represent 90% of all subgingival bacteria in each sample. The remaining species/phylotypes each constituted ≤0.2% of the total subgingival bacteria. In conclusion, the subgingival microbiota are characterized by high species richness dominated by a few species/ phylotypes. The microbiota changed after periodontal therapy. High throughput metagenomic analysis is applicable to assess the complexity and changes of the subgingival microbiota.

Keywords: Aggressive periodontitis, metagenomics, subgingival plaque, nonsurgical treatment.