Discriminating Microbial Community Structure Between Peri-Implantitis and Periodontitis With Integrated Metagenomic, Metatranscriptomic, and Network Analysis

Abstract

Peri-implantitis and periodontitis are both polymicrobial diseases induced by subgingival plaque accumulation, with some differing clinical features. Studies on the microbial and gene transcription activity of peri-implantitis microbiota are limited. This study aimed to verify the hypothesis that disease-specific microbial and gene transcription activity lead to disease-specific clinical features, using an integrated metagenomic, metatranscriptomic, and network analysis. Metagenomic data in peri-implantitis and periodontitis were obtained from the same 21 subjects and metatranscriptomic data from 12 subjects were obtained from a database. The microbial co-occurrence network based on metagenomic analysis had more diverse species taxa and correlations than the network based on the metatranscriptomic analysis. Solobacterium moorei and Prevotella denticola had high activity and were core species taxa specific to peri-implantitis in the co-occurrence network. Moreover, the activity of plasmin receptor/glyceraldehyde-3-phosphate dehydrogenase genes was higher in peri-implantitis. These activity differences may increase complexity in the peri-implantitis microbiome and distinguish clinical symptoms of the two diseases. These findings should help in exploring a novel biomarker that assist in the diagnosis and preventive treatment design of peri-implantitis.

Keywords: dysbiosis; metagenome; metatranscriptome; oral microbiome; peri-implantitis; periodontitis.

Figure 1

Taxonomic profile derived from genes comparing the metagenome and metatranscriptome. Principal coordinate analysis (PCoA) was carried out for the dissimilarity matrix value of 1—Spearman’s coefficient. The CDS and mRNA abundances from only species detected in both 16S and mRNA region analyses in the same subject were used in this analysis. (A) PCoA plots among peri-implantitis samples compared between DNA (blue circles) and RNA (light blue circles), (B) among periodontitis samples compared between DNA (red circles) and RNA (light red circles).

Figure 2

Comparison of co-occurrence networks of taxonomic profiles between metagenome and metatranscriptome. Species which were present in more than 50% of individuals in each group were used for co-occurrence network analysis. All networks are shown with each species and co-occurrence relationship indicated by a node and an edge, respectively. (A) Co-occurrence network profile-based taxonomic profile derived from functional genes among peri-implantitis samples comparing metagenome (blue circles) and metatranscriptome (light blue circles) results and (B) among periodontitis samples comparing metagenome (red circles) and metatranscriptome results (light red circles).

Figure 3

Microbial activity. (A) RNA/DNA ratio of species taxa identified in peri-implantitis. (B) RNA/DNA ratio of species taxa identified in periodontitis. Species taxa common to both peri-implantitis and periodontitis are indicated by red text.

Figure 4

Co-occurrence networks based on species taxa common to metagenomic and metatranscriptomic analyses in (A) peri-implantitis and (B) periodontitis. All metagenomic interactions are shown by a gray line and metatranscriptomic interactions common to the metagenome are indicated by a black line. Active taxa (RNA/DNA ratio >3) are indicated by bold circles, and interactions with significant co-occurrence are indicated by bold black lines.

Figure 5

LEfSe analysis comparing peri-implantitis and periodontitis samples based on mRNA indicating enriched genes associated either with the metatranscriptome (green) or metagenome (red). Genes with significant differences common to both diseases are indicated in red. LEfSe analysis based on (A) KEGG, (B) MvirDB, and (C) VFDB mRNA profile assignment.