Advances in the microbiological characteristics of peri‐implant health and peri‐implant diseases. A systematic review

BACKGROUND: Peri-implant diseases represent a major and increasingly prevalent clinical challenge. Peri-implant mucositis and peri-implantitis are inflammatory conditions associated with dysbiotic biofilms, yet the specific microbial features that distinguish peri-implant health from disease have still to be conclusively demonstrated. The present systematic review compared microbiological profiles across peri-implant health, peri-implant mucositis, and peri-implantitis, with particular emphasis on how conventional and next-generation sequencing (NGS)-based detection methods influence reported microbial findings. MATERIALS AND METHODS: This review was registered in the PROSPERO registry (CRD42020182626) and conducted according to PRISMA guidelines. Electronic searches of MEDLINE, Embase, and the Cochrane Library were conducted up to December 31st 2025. Comparative experimental or observational studies reporting microbiological outcomes for at least two peri-implant conditions (health, mucositis, peri-implantitis) were eligible. Study selection, data extraction, and risk-of-bias assessment (adapted Newcastle-Ottawa Scale, evaluated across four domains: selection, comparability, outcome assessment, and statistical analysis) were performed independently by three reviewers. Twenty-eight studies were included, using either conventional methods (culture, checkerboard DNA-DNA hybridization, and PCR-based techniques) or next-generation sequencing (16S rRNA sequencing and shotgun metagenomics). RESULTS: Across studies using conventional detection methods, classical periodontal pathobionts-including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Prevotella intermedia, and Fusobacterium nucleatum-were detected more frequently at diseased than at healthy implant sites, while healthy sites were characterized by higher proportions of commensal taxa such as Streptococcus sp. NGS-based studies similarly reported a higher relative abundance of periodontal pathobionts at diseased sites, but findings on microbial diversity were inconsistent: some studies reported higher alpha diversity at healthy implant sites, whereas others reported the opposite, suggesting that abundance and diversity shifts do not necessarily follow the same pattern across studies. The risk of bias assessment identified comparability and confounder control as the most frequent methodological limitations. Substantial heterogeneity in disease definitions, patient characteristics, sampling strategies, and microbiological methodologies limited direct comparisons across studies and detection methods. CONCLUSION: Across both conventional and NGS-based detection methods, mucositis and peri-implantitis are consistently associated with enrichment of periodontal pathobionts and depletion of health-associated commensals, supporting a dysbiotic shift in peri-implant diseases. However, findings on microbial diversity are inconsistent, and methodological heterogeneity, including variable risk of bias across studies, limits the strength of cross-study conclusions. Standardization of disease definitions and sampling protocols, along with comparison of methodological approaches (including sequencing targets, platforms, and reference databases), is needed before microbiological profiles can inform clinical predictions or treatment implications.