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  1. NTU Theses and Dissertations Repository
  2. 醫學院
  3. 牙醫專業學院
  4. 臨床牙醫學研究所
請用此 Handle URI 來引用此文件: http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/80818
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dc.contributor.advisor陳漪紋(Yi-Wen Chen)
dc.contributor.authorPei-Shiuan Yuen
dc.contributor.author余珮璇zh_TW
dc.date.accessioned2022-11-24T03:17:42Z-
dc.date.available2021-11-05
dc.date.available2022-11-24T03:17:42Z-
dc.date.copyright2021-11-05
dc.date.issued2021
dc.date.submitted2021-10-05
dc.identifier.citation1. Jin, L.J., et al., Global oral health inequalities: task group-periodontal disease. Adv Dent Res, 2011. 23(2): p. 221-6. 2. Liu, Y., et al., Infection of microglia with Porphyromonas gingivalis promotes cell migration and an inflammatory response through the gingipain-mediated activation of protease-activated receptor-2 in mice. . Scientific Reports, 2017. 7(1): p. 11759. 3. Lai, H., et al., A prediction model for periodontal disease: modelling and validation from a National Survey of 4061 Taiwanese adults. . J Clin Periodontol, 2015. 42(5): p. 413-21. 4. Grossi, S.G., et al., Assessment of risk for periodontal disease. I. Risk indicators for attachment loss. J Periodontol, 1994. 65(3): p. 260-7. 5. Cekici, A., et al., Inflammatory and immune pathways in the pathogenesis of periodontal disease. Periodontology 2000, 2014. 64(1): p. 57-80. 6. Meyle, J.a.I.C., Molecular aspects of the pathogenesis of periodontitis. . Periodontology 2000, 2015. 69(1): p. 7-17. 7. Socransky, S.S., et al., Microbial complexes in subgingival plaque. Journal of Clinical Periodontology, 1998. 25(2): p. 134-144. 8. Von Troil-Lindén, B., et al., Periodontal findings in spouses. . Journal of Clinical Periodontology, 1995. 22(2): p. 93-99. 9. Caton, J.G., et al., A new classification scheme for periodontal and peri-implant diseases and conditions – Introduction and key changes from the 1999 classification. Journal of Clinical Periodontology, 2018. 45(S20): p. S1-S8. 10. Van Dyke, T.E.a.D.S., Risk factors for periodontitis. Journal of the International Academy of Periodontology, 2005. 7(1): p. 3-7. 11. Bui, F.Q., et al., Association between periodontal pathogens and systemic disease. Biomedical Journal, 2019. 42(1): p. 27-35. 12. Kellesarian, S.V., et al., Association Between Periodontal Disease and Erectile Dysfunction: A Systematic Review. American journal of men's health, 2018. 12(2): p. 338-346. 13. Winning, L.a.G.J.L., Periodontitis and systemic disease. . BDJ Team, 2015. 2(10): p. 15163. 14. Negrato, C.A., et al., Periodontal disease and diabetes mellitus. Journal of applied oral science : revista FOB, 2013. 21(1): p. 1-12. 15. Simpson, T.C., et al., Treatment of periodontal disease for glycaemic control in people with diabetes. . Cochrane Database Syst Rev, 2010. 5: p. Cd004714. 16. Borojevic, T., Smoking and periodontal disease. . Materia socio-medica, 2012. 24(4): p. 274-276. 17. Sarmiento, H.L., M.R. Norton, and J.P. Fiorellini, A Classification System for Peri-implant Diseases and Conditions. Int J Periodontics Restorative Dent, 2016. 36(5): p. 699-705. 18. Leonhardt, A., Renvert, S. Dahlen, G., Microbial findings at failing implants. Clinical Oral Implants Research, 1999. 10: p. 339–345. 19. Lindhe, J., Berglundh, T., Ericsson, I., Liljenberg, B. Marinello, C. , Experimental breakdown of peri-implant and periodontal tissues. A study in the beagle dog. . Clin. Oral Implants Res., 1992. 3: p. 9-16. 20. Juodzbalys, A.R.G., Diagnostic Principles of Peri-Implantitis: a Systematic Review and Guidelines for Peri-Implantitis Diagnosis Proposal. JOURNAL OF ORAL MAXILLOFACIAL RESEARCH, 2016. 7: p. 3. 21. Cionca, D.H.N., A Comprehensive Review of Peri-implantitis Risk Factors. Current Oral Health Reports, 2020. 7: p. 262–273. 22. Paul Rosen, e.a., Academy Report: Peri-Implant Mucositis and Peri-Implantitis: A Current Understanding of Their Diagnoses and Clinical Implications. Journal of Periodontology, 2013. 84(4): p. 436-443. 23. Keijser BJ, Z.E., Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W., Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res, 2008. 87: p. 1016-20. 24. Lazarevic V, W.K., Huse S, Hernandez D, Fari- nelli L, Osteras M, Schrenzel J, Franc ̧ois P., Metage- nomic study of the oral microbiota by Illumina high- throughput sequencing. J Microbiol Methods, 2009. 79: p. 266-71. 25. Zaura E, K.B., Huse SM, Crielaard W. , Defining the healthy 'core microbiome' of oral microbial communities. BMC Microbiol, 2009. 9: p. 259. 26. Chen, C., et al., Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy. . The ISME Journal, 2018. 12(5): p. 1210-1224. 27. Patini, R., et al., Relationship between oral microbiota and periodontal disease: a systematic review. Eur Rev Med Pharmacol Sci, 2018. 22(18): p. 5775-5788. 28. Charalampakis, G. and G.N. Belibasakis, Microbiome of peri-implant infections: lessons from conventional, molecular and metagenomic analyses. Virulence, 2015. 6(3): p. 183-7. 29. Devides SL, F.A., Evaluation of peri-implant microbiota using the polymerase chain reaction in completely edentulous patients before and after place- ment of implant-supported prostheses submitted to immediate load. Int J Oral Maxillofac Implants, 2006. 21: p. 262-9. 30. Galassi F, K.W., Anssari Moin D, van der Horst J, Wismeijer D, Crielaard W, Laine ML, Veerman EC, Bikker FJ, Loos BG., Comparing culture, real-time PCR and fluorescence resonance energy transfer tech- nology for detection of Porphyromonas gingivalis in patients with or without peri-implant infections. J Peri- odontal Res, 2012. 47: p. 616-25. 31. Al-Radha AS, P.A., Pettemerides AP, Jenkinson HF., Molecular analysis of microbiota associated with peri- implant diseases. J Dent, 2012. 40: p. 989-98. 32. Socransky SS, S.C., Martin L, Paster BJ, Dewhirst FE, Levin AE., 'Checkerboard' DNA-DNA hybridization. . Biotechniques, 1994. 17: p. 788-92. 33. Chen K, P.L., Bioinformatics for whole-genome shotgun sequencing of microbial communities. . PLoS Comput Biol, 2005. 1: p. 106-12. 34. Papapanou, P.N., et al., Periodontitis: Consensus report of workgroup 2 of the 2017 World Workshop on the Classification of Periodontal and Peri‐Implant Diseases and Conditions. Journal of periodontology, 2018. 89: p. S173-S182. 35. Caton, J.G., et al., A new classification scheme for periodontal and peri-implant diseases and conditions – Introduction and key changes from the 1999 classification. Journal of Clinical Periodontology, 2018. 45(S20): p. S1-S8. 36. Lloyd-Price, J., Abu-Ali, G., Huttenhower, C. , The healthy human microbiome. Genome Medicine, 2016. 8(1): p. 51. 37. Maruyama, N., Maruyama, F., Takeuchi, Y., Aikawa, C., Izumi, Y., Nakagawa, I., Intraindividual variation in core microbiota in peri-implantitis and periodontitis. Scientific Reports, 2014. 4: p. 6602. 38. Payne, J.B., Johnson, P. G., Kok, C. R., Gomes-Neto, J. C., Ramer-Tait, A. E., Schmid, M. J., Hutkins, R. W. , Subgingival Microbiome Colonization and Cytokine Production during Early Dental Implant Healing. . mSphere, 2017. 2(6): p. e00527-17. 39. Schincaglia, G., Hong, B., Rosania, A., Barasz, J., Thompson, A., Sobue, T., Panagakos, F., and J.A. Burleson, Dongari-Bagtzoglou, A. Diaz, P., Clinical, Immune, and Microbiome Traits of Gingivitis and Peri-implant Mucositis. Journal of Dental Research, 2017. 96(1): p. 47-55. 40. Belibasakis, G.N.M.-M., J.; Sahrmann, P.; Sanz-Martin, I.; Schmidlin, P.R., Clinical association of Spirochaetes and Synergistetes with peri-implantitis. Clin. Oral Implants Res., 2016. 27: p. 656–661. 41. Sanz-Martin, I., Exploring the microbiome of healthy and diseased peri-implant sites using Illumina sequencing. J Clin Periodontol., 2017. 44: p. 1274–1284. 42. Belstrøm, D., Paster, B. J., Fiehn, N. E., Bardow, A., Holmstrup, P. , Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMI NGS) technique. . Journal of Oral Microbiology, 2016. 8(1): p. 30-170. 43. Socransky, S.S., et al., Microbial complexes in subgingival plaque. J Clin Periodontol, 1998. 25(2): p. 134-44. 44. Philipp Sahrmann, F.G., Daniel B. Wiedemeier, Thomas Attin, Patrick R. Schmidlin and Lamprini Karygianni, The Microbiome of Peri-Implantitis: A Systematic Review and Meta-Analysis. Microorganisms, 2020. 8(5): p. 661. 45. Kumar PS, M.M., Brooker MR, O’Brien K., Pyrosequencing reveals unique microbial signatures associated with healthy and failing dental implants. . J Clin Periodontol. , 2012. 39(5): p. 425–433. 46. Olmedo, G.A.K.a.D.G., Peri-implantitis is not periodontitis: Scientific discoveries shed light on microbiome-biomaterial interactions that may determine disease phenotype. Periodontology 2000, 2021. 86: p. 231–240. 47. Daubert, D., Titanium as a modifier of the peri-implant microbiome structure. Clin Implant Dent Relat Res., 2018. 20(6): p. 945-953. 48. Esposito M, G.M., Worthington HV., Interventions for replacing missing teeth: treatment of peri-implantitis. Cochrane Database Syst Rev, 2012. 1:CD: p. 004970.
dc.identifier.urihttp://tdr.lib.ntu.edu.tw/jspui/handle/123456789/80818-
dc.description.abstract研究背景:植體赴周圍炎與慢性牙周炎的致病因子相似,由相似的致病菌組成,然而,植體周圍炎的致病因子及治療方法卻沒有更確切的結論。牙根整平術通常在慢性牙周炎的治療上,有益於減少炎症和牙周探測深度,被公認是牙周治療的黃金標準。文獻報導,藉由次世代分析,可以找到更多不同於以往的植體周圍炎致病微生物組成,藉由確認植體周圍炎的病因,進而找到更有效的治療方式。這項研究的目的是利用次世代分析,探討慢性牙周炎及植體周圍炎的致病菌微生物組成差異,並評估牙根整平術對已確診的慢性牙周炎及植體周圍炎患者的治療抗菌效果。 材料與方法:從台灣大學附屬醫院的牙科部招募了22名同時患有慢性牙周炎及植體周圍炎的患者,進行牙周病及植體周圍炎的常規治療及全口牙周檢查(殘留齒數、牙周囊袋深度、臨床附連喪失、牙菌斑指數、牙齦發炎指數、放射線骨高度),此研究收集患者治療前的牙周病患齒及見健康牙、植體周圍炎植牙及健康植牙等四個齒位以及治療後植體周圍炎植牙的牙齦下牙菌斑,做次世代分析微生物組成,並觀察比較非手術治療後的臨床牙周參數變化。 結果:微生物組成分析出512個菌種,且精細到菌種分枝的階層有377個菌種。在整體微生物組成中定義出47個核心菌種(每組百分之八十以上的樣本中都有,且相對豐度為百分之一以上),針對47個核心菌種做5組的數據分析比對,發現植體周圍炎組別及健康牙齒組別擁有較多種類的核心菌種;植體周圍炎與牙周病患齒之間相異的核心菌種彼此間的相關性為負相關,顯現植體周圍炎的細菌並非與牙周炎完全一致,與以往的研究不同;植體周圍炎在非手術治療後的微生物組成並無太大改變。 結論:透過次世代分析16S rDNA的全長序列,植體周圍炎的微生物組成能精細到菌種分枝,有助於比較疾病之間的相關性和交互作用、致病菌的探索及治療的的成效。未來透過更進一步的DNA分析方式(第三代分析或是全基因霰彈槍定序法),可以分析細菌的功能性基因,建立疾病診斷及預後預測模型。zh_TW
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dc.description.tableofcontents口試委員會審定書 i 誌謝 ii 中文摘要 iv ABSTRACT v CONTENTS vii LIST OF FIGURES xi LIST OF TABLES xiii Chapter 1 Literature Review 1 1.1 Periodontitis 1 1.1.1 Epidemiology 1 1.1.2 Etiology of periodontitis 2 1.1.3 Clinical manifestations and diagnosis of periodontal disease 4 1.1.3.1 Common symptoms and clinical examination methods of periodontal disease 4 1.1.3.2 clinical examination 4 1.1.3.3 Radiographic imaging examination: 4 1.1.3.4 Diagnosis of periodontal disease 4 1.1.4 Risk factors for periodontal disease 7 1.1.5 Treatment of periodontal disease 8 1.2 Peri-implant disease 9 1.2.1 Clinical definition and epidemiology of peri-implant disease 9 1.2.2 Diagnosis of peri-implantitis 9 1.2.3 Risk factors of peri-implantitis 10 1.2.4 Treatment of peri-implantitis 10 1.3 Metagenomics DNA sequencing 11 1.3.1 Next generation sequencing (NGS) 11 1.3.2 16S rDNA in microbiome 14 1.3.2.1 16S rDNA structure 14 1.3.2.2 16S rDNA variable regions 14 1.3.3 Microbiome of periodontitis 15 1.3.4 Microbiome of peri-implantitis 16 Chapter 2 Research Purposes and Hypothesis 18 2.1 Research purposes 18 2.2 Hypothesis 18 Chapter 3 Materials and Methods 19 3.1 Study design and subjects 19 3.1.1 Inclusion criteria and exclusion criteria 19 3.2 Clinical periodontal and radiographic examination 19 3.3 Periodontal treatment 20 3.4 Sample collections 20 3.4.1 Tris-EDTA (TE) buffer 20 3.4.2 Sample collection procedure 20 3.5 DNA extraction 22 3.5.1 Qiagen® DNeasy® PowerBiofilm® kit 22 3.5.2 DNA extraction procedure 22 3.5.3 DNA quantification 24 3.6 NGS with LoopSeqTM 16S Long Read Kit 24 3.6.1 LoopSeqTM 16S Long Read Kit 24 3.6.2 NGS 24 3.7 Data Analysis 25 Chapter 4 Result 26 4.1 Demographic and clinical characteristics of the subjects 26 4.2 Taxonomic Profile on 16S rDNA Sequencing 29 4.3 Microbiome diversity 32 4.3.1 -diversity 32 4.3.1 -diversity 37 4.4 Core microbiome 39 4.4.1 Linear discriminant analysis (LDA) Effect Size (LEFSe) 48 4.5 Difference between peri-implantitis sites (DI) and periodontitis sites (DT) 59 4.6 Difference between before and after non-surgical treatment of peri-implantitis (DI vs DIRE) 64 4.7 Difference between peri-implantitis sites (DI) and healthy implant sites (HI) 69 4.8 Difference between peri-implantitis sites (DI) and healthy tooth sites (HT) 72 4.9 Difference between periodontitis sites (DT) and healthy tooth sites (HT) 75 4.10 Difference between healthy implant sites (HI) and healthy tooth sites (HT) 78 4.11 Difference between different probing depth sites 81 4.12 Co-occurrence analysis among the core species 87 4.13 Correlations between core microbiome and clinical parameters 90 Chapter 5 Discussion 92 5.1 The novelty of this study is using full length of 16S rDNA in NGS microbiome investigation 92 5.2 Samples collection to correct inter-individual variations and reflect intra-individual interaction 92 5.3 and -diversity showed that peri-implantitis sites didn’t have lower diversity than others. 93 5.4 Comparing the core microbiome with Socransky complex and the result implied the disease shifting 93 5.5 The same and the difference compared with the previous research 94 5.6 The peri-implantitis-related species (DI-related) 95 5.7 The comparison of peri-implantitis (DI) and periodontitis (DT) 97 5.8 The impact of Non-surgical treatment of peri-implantitis to the microbiome of peri-implantitis 98 5.9 Difficulties in research 99 Chapter 6 Conclusion 100 Reference 101
dc.language.isoen
dc.subject植體周圍炎zh_TW
dc.subject次世代分析zh_TW
dc.subject宏基因組學分析zh_TW
dc.subject慢性牙周炎zh_TW
dc.subjectmetagenomics analysisen
dc.subjectNext-generation sequencing (NGS)en
dc.subjectchronic periodontitisen
dc.subjectperi-implantitisen
dc.title利用次世代分析比對慢性牙周炎患者之牙周炎及植體周圍炎致病菌微生物組成之臨床研究zh_TW
dc.titleMetagenomic Analysis of the Microbiome Diversity of Peri-implantitis and Periodontitis in Chronic Periodontitis Patientsen
dc.date.schoolyear109-2
dc.description.degree碩士
dc.contributor.oralexamcommittee王振穎(Hsin-Tsai Liu),侯欣翰(Chih-Yang Tseng),廖玉潔
dc.subject.keyword植體周圍炎,慢性牙周炎,次世代分析,宏基因組學分析,zh_TW
dc.subject.keywordperi-implantitis,chronic periodontitis,Next-generation sequencing (NGS),metagenomics analysis,en
dc.relation.page104
dc.identifier.doi10.6342/NTU202103521
dc.rights.note同意授權(限校園內公開)
dc.date.accepted2021-10-05
dc.contributor.author-college醫學院zh_TW
dc.contributor.author-dept臨床牙醫學研究所zh_TW
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