Molecular Diagnostics in Dentistry: From Pathogen Detection to Precision Medicine

Molecular Diagnostics in Dentistry: From Pathogen Detection to Precision Medicine Published in November 2025 Authors: Antonio Sarnataro (Biomolecular Diagnostic Laboratory and Academy, Florence (IT); IMI-EDN Excellence Dental Network, Florence (IT) Jessica Bassignani (EIMS H.E.I.) ORCID iD: https://orcid.org/0009-0009-2506-6595 Prof. Andrea Mascolo (EIMS H.E.I.) ORCID iD: https://orcid.org/0000-0003-2474-0946 1 Molecular Diagnostics in Dentistry: From Pathogen Detection to Precision Medicine © 2025 by Antonio Sarnataro, Jessica Bassignani, Andrea Mascolo is licensed under CC BY 4.0. To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ 2 Summary Introduction ............................................................................................................................. 3 Materials and Methods ............................................................................................................. 3 Results...................................................................................................................................... 3 Discussion ................................................................................................................................ 5 Conclusions .............................................................................................................................. 6 References ................................................................................................................................ 6 3 Introduction Dentistry is undergoing a shift from damage-repair paradigms to biologically informed precision care, where inflammation, genetics, and host–microbe interactions govern disease trajectories (1–4). Contemporary frameworks emphasize molecular determinants of periodontal diseases and systemic interplays, fostering integrated diagnostics and targeted therapies (1–6). Within this context, molecular tools—PCR, NGS, and host-response biomarkers such as aMMP-8—enable early detection, risk stratification, and dynamic monitoring. This review outlines core principles, comparative advantages, and clinical applications of these methods in periodontal and peri-implant care. Beyond microbiological and biochemical methodologies, the scope of molecular diagnostics in dentistry has recently expanded to include genetic and hormonal profiling. The integration of Genetic Periodontal Screening (GPS) and Genetic Multi Screening (GMS) allows clinicians to assess individual susceptibility to inflammation, bone metabolism imbalance, and regenerative potential through the analysis of specific single nucleotide polymorphisms (SNPs). These panels explore variations in cytokine-related genes (IL1, IL-6, TNF-α, IL-10, IL-8) and metabolic regulators (VDR, MTHFR, ESR1, COL1A1), providing a personalized molecular risk map that refines both diagnosis and prevention. In parallel, the Hormonal Profile Plus (HP⁺) complements genetic testing by quantifying endocrine markers (progesterone, estrogen, testosterone, DHEA, cortisol) alongside inflammatory mediators such as interleukin-6 (IL-6), thereby linking endocrine and immune dynamics within periodontal pathophysiology. Together, these assays constitute the next frontier of integrated molecular dentistry, merging genetic, biochemical, and hormonal data to enable truly predictive and personalized care. This expanded molecular framework— encompassing microbial, genetic, and endocrine diagnostics—lays the foundation for the present review, which explores the analytical principles, clinical applications, and future perspectives of integrated molecular dentistry. Materials and Methods This narrative review followed a focused, question-driven approach. We searched PubMed and Scopus for English-language articles (January 2015–October 2025) using: periodontitis, periimplantitis, molecular diagnostics, PCR, qPCR, NGS, metagenomics, aMMP-8, salivary biomarkers, point-of-care. Priority was given to high-level sources (systematic reviews, consensus statements, guideline-oriented papers) and recent clinical or diagnostic studies. Reference lists of retrieved items were screened to identify additional pertinent works. Due to heterogeneity in study designs and outcomes, a meta-analysis was not attempted. Results PCR (including qPCR): sensitivity, specificity, and speed PCR remains foundational for detecting bacterial and viral nucleic acids at very low copy numbers, enabling species-level identification of key periodontal pathogens and quantification of microbial burden via qPCR (7–9). Its strengths include high analytical sensitivity/specificity, reproducibility, and 24–48hour turnaround suitable for clinical monitoring. Limitations include inability to discriminate viable from non-viable DNA, requiring clinical contextualization (7–9). NGS: ecological and functional insight NGS provides broad, unbiased profiling of the oral microbiome, capturing both cultivable and uncultivable taxa and allowing diversity analyses, co-occurrence patterns, and longitudinal tracking (10– 12). Its depth is invaluable for precision screening and research, albeit with higher cost and bioinformatic requirements (10–12). 4 aMMP-8 and related ELISA assays: host-response activity Protein assays (notably aMMP-8) quantify inflammatory activity and collagenolytic burden in saliva or gingival crevicular fluid, correlating with disease status and response to therapy (13–18). aMMP-8 testing is rapid, clinic-friendly, and cost-effective, making it well-suited for routine monitoring and staging support (13–18). Comparative synthesis Across modalities, PCR excels in targeted pathogen detection; NGS in ecosystem-level mapping; and aMMP-8 in functional host-response readouts. Integrating these levels of information enhances diagnosis, risk assessment, and therapeutic monitoring, complementing emerging point-of-care solutions (19,20). Table 1. Comparative overview of main molecular diagnostic techniques in dentistry Technique Analytical principle Diagnostic focus Key advantages Main limitations Clinical applications Representative references PCR (qPCR) Amplification of specific microbial DNA targets Detection and quantification of periodontal pathogens High sensitivity and specificity; rapid turnaround (24–48 h); reproducibility Cannot distinguish viable vs. nonviable DNA; requires clinical interpretation Periodontitis, peri-implantitis, monitoring after therapy (7–9) NGS Massive parallel sequencing (16S rRNA or wholegenome) Comprehensive oral microbiome profiling Identifies cultivable + uncultivable taxa; reveals ecological structure and diversity; enables longitudinal studies Expensive; bioinformatic expertise required; longer processing time Research, precision screening, refractory or complex cases (10–12) aMMP-8 (ELISA/POCT) Enzymatic quantification of collagenolytic biomarker in saliva or GCF Host inflammatory and tissue breakdown activity Rapid (<1 h); low cost; chairside applicability; reflects functional disease activity Non-specific to microbial species; requires contextual correlation Diagnosis, staging, and monitoring of periodontal inflammation (13–18) Legend: Summary of key analytical and clinical features of PCR, NGS, and aMMP-8-based ELISA assays in periodontal and peri-implant diagnostics. Abbreviations: PCR, polymerase chain reaction; NGS, next-generation sequencing; ELISA, enzyme-linked immunosorbent assay; aMMP-8, active-matrix metalloproteinase-8; POCT, point-of-care testing. 5 Figure 1 . Comparative performance profile of molecular diagnostic modalities in dentistry. Figure 1 - Legenda Relative evaluation (1–5 scale) of analytical sensitivity, specificity, cost, turnaround speed, and clinical practicality for PCR (qPCR), NGS, and aMMP-8 (ELISA/POCT). Discussion This review highlights the emergence of a comprehensive molecular framework that unites microbial, genetic, and biochemical dimensions in periodontal diagnostics. Microbial detection through polymerase chain reaction (PCR), ecological profiling via next-generation sequencing (NGS), and host-response measurement with aMMP-8 collectively provide a triangulated model of periodontal disease biology (1– 20). In clinical settings, qPCR enables targeted antimicrobial strategies based on pathogen identification; NGS reveals dysbiotic microbial communities and their ecological shifts; and aMMP8 assays reflect real-time tissue activity, inflammation, and healing dynamics (13–18, 21). Beyond these classical molecular pillars, the integration of genetic (GPS, GMS) and endocrine (HP⁺) assessments represents the next step toward biologically individualized care (23–30). The Genetic Periodontal Screening (GPS) identifies polymorphisms in inflammatory cytokine genes such as IL-1, IL-6, IL-10, and TNF-α, elucidating inter-individual immune reactivity and guiding host-modulation strategies (23, 24, 29). Meanwhile, the Genetic Multi Screening (GMS) expands this analysis to metabolic and osteogenic pathways—particularly VDR, MTHFR, and ESR1 polymorphisms—thereby linking genetic background to bone turnover and regenerative potential (25–28). Complementarily, the Hormonal Profile Plus (HP⁺) bridges endocrine and inflammatory domains by quantifying sex steroids, adrenal markers, and interleukin-6, offering insight into how hormonal imbalances influence tissue healing and disease recurrence (30). Together, these multidimensional diagnostics converge into a multi-omics paradigm where microbial, genetic, biochemical, and hormonal data are integrated through AI-enabled analytics to enhance precision, prediction, and prevention (5, 6, 20, 21). This evolution marks a shift from static disease classification to dynamic biological monitoring, enabling clinicians to stratify patients according to their molecular risk profile and to align therapeutic protocols with real-time biological responses. Ultimately, this framework establishes the foundations of integrated molecular dentistry—a discipline in which microbial ecology, genetic predisposition, and endocrine regulation coalesce to guide personalized periodontal and peri-implant management. 6 Conclusions 1. qPCR remains the most accessible and sensitive method for detecting and quantifying periodontal pathogens, providing clinicians with actionable microbial data for targeted therapy and post-treatment monitoring. 2. NGS adds ecological and functional insight, mapping the oral microbiome to identify dysbiotic networks and refine precision treatment strategies. 3. aMMP-8 assays enable rapid chairside evaluation of inflammatory activity and healing dynamics, translating molecular findings into real-time clinical decisions. 4. The integration of genetic panels (GPS, GMS) and hormonal profiling (HP⁺) expands this framework, linking host susceptibility, metabolic resilience, and endocrine modulation to periodontal outcomes. 5. Collectively, these multi-axis diagnostics establish a biologically driven model of periodontal medicine that moves beyond observation toward prediction, prevention, and personalization. 6. As digital and AI-assisted analytics mature, integrated molecular dentistry will increasingly connect microbial, genetic, and biochemical data to optimize patient-specific prevention, therapy, and long-term oral–systemic health. Table 2. aMMP-8 thresholds and clinical interpretation Parameter Clinical interpretation Diagnostic value Key references aMMP-8 > 20 ng/mL Active collagen degradation; tissue breakdown Indicates active inflammation / higher risk of progression (15–17) aMMP-8 < 20 ng/mL Stable or resolved condition Suggests remission or effective therapy (15–17) Post-therapy reduction > 40% Healing response Correlates with clinical improvement (15–17) Legend: aMMP-8 levels reflect collagenolytic activity and periodontal disease dynamics; thresholds and response criteria support staging and monitoring. Abbreviations: aMMP-8, active matrix metalloproteinase-8; POCT, point-of-care testing. References 1. Loos BG, Van Dyke TE. The role of inflammation and genetics in periodontal disease. Periodontol 2000.2020;83(1):26-39. doi:10.1111/prd.12294 2. Bartold PM, Van Dyke TE. Periodontitis: A host-mediated disruption of microbial homeostasis. Periodontol 2000. 2020;62(1):203-217. doi:10.1111/prd.12325 3. Kinane DF, Stathopoulou PG, Papapanou PN. Periodontal diseases. Nat Rev Dis Primers. 2017;3:17038. doi:10.1038/nrdp.2017.38 4. Tonetti MS, Greenwell H, Kornman KS. Staging and grading of periodontitis. J Periodontol. 2018;89(S1):S159-S172. doi:10.1002/JPER.18-0006 5. Dolińska E, et al. Periodontal molecular diagnostics: state of knowledge and future directions. Int J Mol Sci.2024;25(23):12624. doi:10.3390/ijms252312624 6. Gürsoy UK. Advances in periodontal biomarkers. In: Biomarkers in Oral Health and Disease. Academic Press; 2024. doi:10.1016/B978-0-12-824487-1.00005-X 7. A view on polymerase chain reaction as an outstanding molecular diagnostic tool in periodontology. Biomed Res Int. 2021;2021:9979948. doi:10.1155/2021/9979948 8. Kuret S, Kalajzic N, Ruzdjak M, et al. Real-time PCR as a diagnostic tool for periodontal pathogens in periodontitis. Int J Mol Sci. 2024;25(10):5097. doi:10.3390/ijms25105097 9. D’Urso F, Paladini F, Pollini M, Broccolo F. Salivary molecular testing for periodontal pathogen monitoring. Diagnostics (Basel). 2025;15(19):2548. doi:10.3390/diagnostics15192548 10. Next-generation sequencing technologies and applications in oral microbiome research. Front Cell Infect Microbiol. 2024;14:1409238. doi:10.3389/fcimb.2024.1409238 11. Belstrøm D, Holmstrup P, Bardow A, Kokaras A, Paster BJ. Comparative analysis of the salivary microbiome. J Clin Periodontol. 2021;48(2):230-242. doi:10.1111/jcpe.13388 7 12. Meyle J, Chapple I; European Federation of Periodontology (EFP). Molecular aspects of the pathogenesis of periodontitis. Periodontol 2000. 2015;69(1):7-17. doi:10.1111/prd.12102 13. Boynes SG, et al. Assessment of salivary MMP-8 (MMP-8/aMMP-8). Front Oral Health. 2025;6:1444399. doi:10.3389/froh.2025.1444399 14. Aji NRAS, et al. aMMP-8 POCT vs other biomarkers. Int J Mol Sci. 2024;25(17):9421. doi:10.3390/ijms25179421 15. Thomas JT, et al. Diagnostic accuracy of aMMP-8 levels in oral biofluids. Clin Oral Investig. 2025. doi:10.1007/s00784-025-06584-y 16. Penttala M, et al. Determination of periodontitis stage with aMMP-8 test. Diagnostics (Basel). 2025;15(11):1411. doi:10.3390/diagnostics15111411 17. Host Markers of Periodontal Diseases: Meta-Analysis. J Clin Periodontol. 2025. doi:10.1111/jcpe.14167 18. Balogun AO, Taiwo JO, Opeodu OI, Adeyemi BF, Kolude BM. Diagnostic utility of salivary MMP-8 in chronic periodontitis. Open J Stomatol. 2020;10:41-49. doi:10.4236/ojst.2020.104004 19. Evaluating salivary MMP-8 as a biomarker for periodontal diseases: A systematic review. J Dent Sci.2024;19(2):120-134. 20. Korgaonkar J, et al. Periodontal disease and emerging point-of-care technologies: a review. Lab Chip.2024;24:lcd4lc00295d. doi:10.1039/d4lc00295d 21. Consensus Report of the 20th European Federation of Periodontology Workshop on Periodontology. J Clin Periodontol. 2025. doi:10.1111/jcpe.14152 22. Importance of metalloproteinase-8 (MMP-8) in the diagnosis of periodontitis. Int J Mol Sci. 2023;25(5):2721. doi:10.3390/ijms25052721 23. Brodzikowska A, Górski B. Polymorphisms in genes involved in inflammation and periodontitis: a narrative review. Biomolecules. 2022;12(4):552. doi:10.3390/biom12040552 24. Mashhadiabbas F, Neamatzadeh H, Nasiri R, et al. Association of vitamin D receptor gene polymorphisms (BsmI, TaqI, FokI, ApaI) with susceptibility to chronic periodontitis: a systematic review and metaanalysis. Dent Res J (Isfahan). 2018;15(3):155-165. doi:10.15171/drj.2018.28 25. Cafiero C, Grippaudo C, Dell’Aquila M, et al. Association between vitamin D receptor gene polymorphisms and periodontal bacteria: a clinical pilot study. Biomolecules. 2022;12(6):833. doi:10.3390/biom12060833 26. Nibali L, Donos N, Henderson B. The role of interleukin-6 in periodontitis and its complications. Int J Mol Sci. 2024;25(4):2146. doi:10.3390/ijms25042146 27. Chen L, Xia M, Zhu H, et al. VDR polymorphism and its correlation with chronic periodontitis: an updated systematic review and meta-analysis of the Chinese population. Arch Oral Biol. 2024;150:105094. doi:10.1016/j.archoralbio.2023.105094 28. Zhang X, Wang J, Wang S, et al. The interleukin gene landscape: understanding its influence on apical and periodontal bone resorption. Mol Genet Genomics. 2025;300(3):151-165. doi:10.1007/s11033-02510477-4 29. Chapple ILC, Van Dyke TE, Bartold PM, et al. Host modulation in periodontitis: the role of genetic susceptibility and inflammatory networks. Periodontol 2000. 2023;92(1):173-196. doi:10.1111/prd.12480 30. Hirschfeld J, Chapple ILC. Endocrine–immune crosstalk in periodontal diseases. Periodontol 2000. 2025;97(1):114-139. To cite this report, please use the following format: Sarnataro, A., Bassignani, J., & Mascolo, A. (2025). Molecular diagnostics in dentistry: From pathogen detection to precision medicine (EIMS Review). Zenodo. https://doi.org/10.5281/zenodo.17604805