Patient-specific analysis of periodontal and peri-implant microbiomes

Abstract

Periodontally involved teeth have been implicated as 'microbial reservoirs' in the etiology of peri-implant diseases. Therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the degree of congruence between adjacent peri-implant and periodontal microbiomes in states of health and disease. Subgingival and peri-implant biofilm samples were collected from 81 partially edentulous individuals with periodontal and peri-implant health and disease. Bacterial DNA was isolated, and the 16S rRNA gene was amplified and sequenced by pyrotag sequencing. Chimera-depleted sequences were compared against a locally hosted curated database for bacterial identification. Statistical significance was determined by paired Student's t tests between tooth-implant pairs. The 1.9 million sequences identified represented 523 species. Sixty percent of individuals shared less than 50% of all species between their periodontal and peri-implant biofilms, and 85% of individuals shared less than 8% of abundant species between tooth and implant. Additionally, the periodontal microbiome demonstrated significantly higher diversity than the implant, and distinct bacterial lineages were associated with health and disease in each ecosystem. Analysis of our data suggests that simple geographic proximity is not a sufficient determinant of colonization of topographically distinct niches, and that the peri-implant and periodontal microbiomes represent microbiologically distinct ecosystems.

Keywords: biofilms; computational biology; dental implants; peri-implantitis; periodontitis; phylogenetic biogeography.

Conflict of interest statement

The authors declare no potential conflicts of interest with respect to the authorship and/or publication of this article.

Figures

Figure 1.

Percentage of shared microbial species between each pair of tooth and implant overall and across the health status groups. (A) Shared microbial species at 0.01% site-relative abundance cutoff value. (B) 0.1% cutoff value. (C) 1.0% cutoff value. (D-G) Shared species calculated at 0.01% abundance cutoff value for the 4 groups.

Figure 2.

Shannon Diversity Index. (A) Teeth. (B) Implants. (C) Teeth minus implants. The difference between the 2 distributions was significant (p < .05, Wilcoxon signed-rank test) in favor of the teeth. (D-G) Shannon Diversity indices by health status. Statistically significant difference was found only in the HT/HI group (p < .05, Wilcoxon signed-rank test).

Figure 3.

Relative abundance of the species-level Operational Taxonomic Units (sOTUs) for each of the 4 groups. The center of the Fig. is a circular phylogenetic tree representing the evolutionary relationships of the identified sOTUs. The sOTUs are color-coded by Gram status and oxygen use, represented in the inner ring of each Fig. The outer ring represents the normalized mean relative abundance of the identified sOTUs from the peri-implant and periodontal biofilm samples.