Comparative analysis of the microbial profiles in supragingival and subgingival plaques obtained from different dental prostheses

Statement of problem: The oral microbial ecosystem significantly influences periodontal and peri-implant health. Although various studies have investigated the microbial influence of specific dental restorative materials, studies that directly compared the microbial diversity across different restoration types within the same oral cavity are sparse, limiting the identification of consistent, material-specific microbial profiles. Purpose: The purpose of this clinical study was to analyze and compare the supragingival and subgingival microbial diversity and composition associated with an unrestored natural tooth, a gold crown–restored tooth, a zirconia crown–restored tooth, and an implant-supported restoration within the same participant. A secondary objective was to evaluate whether specific restorative materials induced reproducible microbial profiles across individuals. Material and methods: Thirty participants possessing all 4 types of restorations (unrestored natural tooth, gold crown, zirconia crown, and implant) in their oral cavity were enrolled. Supra- and subgingival biofilm samples were collected by using sterile swabs. Deoxyribonucleic acid (DNA) was extracted, and microbial identification was conducted via 16S rRNA sequencing targeting the V3-V4 regions. Alpha diversity was quantified by using Shannon, npShannon, and Simpson indices; beta diversity was assessed by using Bray-Curtis and UniFrac distances. Taxonomic classification and biomarker identification were performed by using the EzBioCloud software program (CJ Bioscience) and linear discriminant analysis effect size (LEfSe). Statistical significance was determined with Kruskal–Wallis and permutational multivariate analysis of variance tests (α=.05). Sample collection was standardized and conducted by a single calibrated examiner. DNA extraction, sequencing, and bioinformatics analyses were completed at a single laboratory facility to ensure methodological consistency. Results: Gold crown- and zirconia crown-restored teeth exhibited significantly higher alpha diversity than unrestored natural teeth orimplant-supported restorations (Shannon: Gold, 4.3 ±0.6; Zirconia, 4.1 ±0.5; Natural tooth, 3.5 ±0.4; Implant, 3.0 ±0.6, P<.05). The lowest microbial diversity was noted in implant-supported restorations, predominantly characterized by anaerobic taxa, including Clostridiales. Beta diversity analysis revealed distinct and significant microbial clustering based on restorative types (PERMANOVA, pseudo-F=2.8, R²=.04, P<.01). LEfSe analysis identified Actinomyces spp. predominance in unrestored teeth, Prevotella and Spirochaetes in gold crowns, Porphyromonas and Atopobium in zirconia crowns, and Clostridiales in implants. These microbial signatures remained consistent within individuals and across the study population. Conclusions: Restorative materials significantly influenced the supragingival and subgingival microbiome composition within the same oral environment. Implant-supported restorations displayed lower microbial diversity and a higher prevalence of pathogenic taxa. Thus, restorative material selection may critically impact long-term periodontal and peri-implant health outcomes.