Characterization of subgingival plaque microbiota in patients with severe periodontitis using full-length 16S rRNA gene sequencing

Sep 30, 2026

Upload by Miles

Periodontitis is a prevalent inflammatory disease with major systemic implications, making precise microbiota profiling essential. Using PacBio long-read full-length 16S rRNA sequencing and amplicon sequence variant (ASV) analysis, the study examined subgingival plaque, supragingival plaque, and tongue microbiota in 34 individuals with severe periodontitis. Alpha and beta diversities of subgingival and supragingival communities differed from tongue microbiota. Although shared on average 20 ASVs per participant, subgingival plaque contained 17 species specifically enriched, dominated by Porphyromonas gingivalis, Parvimonas micra, and Mogibacterium timidum.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages10

Reading Time25 min

AccessFree to download

Introduction

Methods

Participants and sampling

Sequencing and analysis

Results

Participants’ characteristics and full-length 16S rRNA gene sequences

Microbial differences and the link between tongue and plaque microbiota

Discussion

[www. nature.com/scientificreports](www. nature.com/scientificreports) OPEN Characterization of subgingival plaque microbiota in patients with severe periodontitis using fulllength 16S rRNA gene sequencing Jiale Ma, Shinya Kageyama􀀍, Mikari Asakawa, Michiko Furuta, Yoshihisa Yamashita & Toru Takeshita Periodontitis is a widespread global health issue with significant systemic health implications. Subgingival plaque microbiota is considered its driving factor. Thus, accurate profiling of the microbiota is essential for understanding the etiology of periodontitis. We investigated the subgingival plaque, supragingival plaque, and tongue microbiota in 34 patients with severe periodontitis using PacBio long-read sequencing of the full-length 16S ribosomal RNA gene and amplicon sequence variant (ASV) analysis. The alpha and beta diversities of subgingival and supragingival plaque microbiota were distinct from those of tongue microbiota. Despite their distinct bacterial compositions, the tongue and plaque microbiota shared an average of 20 ASVs per participant, accounting for approximately 13% and 38% of the tongue and plaque microbiota, respectively. Comparative microbiota analysis across these oral niches identified 17 species that were specifically enriched in the subgingival plaque. They accounted for 18.9 ± 20.2%(mean ± SD) of the subgingival plaque microbiota and predominantly consisted of Porphyromonas gingivalis, Parvimonas micra, and Mogibacterium timidum. Altogether, we demonstrate a high-resolution profile of the subgingival microbiota, thereby providing information to improve our understanding of the complex etiology of periodontitis. Keywords Periodontitis, Amplicon sequence variant, Tongue microbiota, Plaque microbiota, 16S rRNA gene, PacBio long-read sequencing Periodontal disease is a global health issue affecting a substantial proportion of the population1. Periodontitis is a chronic inflammatory disease that primarily damages the supporting tissues surrounding the teeth, includingthe gingiva, periodontal ligament, and alveolar bone, and can cause tooth mobility and eventual tooth loss2. Furthermore, periodontitis is associated with systemic diseases, such as cardiovascular diseases, aspiration pneumonia, and cancer, emphasizing its potential impact on overall health3. Subgingival microbiota, a community of microorganisms residing in the gingival sulcus or periodontal pockets, has been implicated in the onset and progression of periodontitis by inducing harmful inflammatory responses in the host4,5. Therefore, numerous previous studies have attempted to profile the subgingival microbiota to elucidate the etiology of periodontal disease6–10. The advent of the PacBio sequencing system and full-length 16S ribosomal RNA (rRNA) sequencing offer new opportunities for studying microbial communities with high accuracy and resolution11, 12. Although full-length PacBio sequencing has been applied to periodontal and peri-implant samples in a few studies, its potential in oral microbiome research, particularly for analyzing subgingival plaque microbiota, remains underexplored13–17. Accurate identification of subgingival bacterial species could provide key information about the pathogens associated with periodontitis and deepen our understanding of the etiology of periodontal disease. The difficulty in profiling the subgingival microbiota is partly due to the proximal presence of supragingival plaque and the difficulty in discriminating bacterial species from the subgingival specimen. We collected supragingival plaque (SUPP), subgingival plaque (SUBP), and tongue coating (TC) samples from 34 Japanese adults diagnosed with severe periodontitis who visited dental clinics. A comparison of the subgingival microbiota with other niche microbiota, particularly those of supragingival microbiota, enabled the identification of bacterial species specific to subgingival plaque. The relationship between microbiota in differe

FAQs

What samples were analyzed to characterize oral microbiota in severe periodontitis?

Subgingival plaque, supragingival plaque, and tongue coating samples were collected from 34 adults with severe periodontitis for microbiota profiling.

How was bacterial composition determined?

Bacterial composition was identified using PacBio long-read sequencing of full-length 16S rRNA genes followed by an amplicon sequence variant (ASV) analysis approach.

Which oral niche showed distinct microbial patterns compared with the tongue?

The alpha and beta diversities of subgingival and supragingival plaque microbiota were distinct from those of tongue microbiota.

Sep 30, 2026

Upload by Miles