1. Albandar JM. Epidemiology and risk factors of periodontal diseases. Dent Clin North Am. 2005;49(3):517-32, v-vi.
2. Kajiya M, Giro G, Taubman MA, Han X, Mayer MP, Kawai T. Role of periodontal pathogenic bacteria in RANKL-mediated bone destruction in periodontal disease. J Oral Microbiol. 2010;2.
3. Bueno AC, Ferreira RC, Cota LO, Silva GC, Magalhaes CS, Moreira AN. Comparison of different criteria for periodontitis case definition in head and neck cancer individuals. Support Care Cancer. 2015;23(9):2599-604.
4. Kinane DF, Stathopoulou PG, Papapanou PN. Periodontal diseases. Nat Rev Dis Primers. 2017;3:17038.
5. Jiao J, Jing W, Si Y, Feng X, Tai B, Hu D, et al. The prevalence and severity of periodontal disease in Mainland China: Data from the Fourth National Oral Health Survey (2015-2016). J Clin Periodontol. 2021;48(2):168-79.
6. Kassebaum NJ, Bernabe E, Dahiya M, Bhandari B, Murray CJ, Marcenes W. Global burden of severe periodontitis in 1990-2010: a systematic review and meta-regression. J Dent Res. 2014;93(11):1045-53.
7. Marcenes W, Kassebaum NJ, Bernabe E, Flaxman A, Naghavi M, Lopez A, et al. Global burden of oral conditions in 1990-2010: a systematic analysis. J Dent Res. 2013;92(7):592-7.
8. Schwarz F, Derks J, Monje A, Wang HL. Peri-implantitis. J Clin Periodontol. 2018;45 Suppl 20:S246-S66.
9. Wang HL, Garaicoa-Pazmino C, Collins A, Ong HS, Chudri R, Giannobile WV. Protein biomarkers and microbial profiles in peri-implantitis. Clin Oral Implants Res. 2016;27(9):1129-36.
10. Alcoforado GA, Rams TE, Feik D, Slots J. Microbial aspects of failing osseointegrated dental implants in humans. J Parodontol. 1991;10(1):11-8.
11. Leonhardt A, Renvert S, Dahlen G. Microbial findings at failing implants. Clin Oral Implants Res. 1999;10(5):339-45.
12. Lee CT, Huang YW, Zhu L, Weltman R. Prevalences of peri-implantitis and peri-implant mucositis: systematic review and meta-analysis. J Dent. 2017;62:1-12.
13. Buser D, Sennerby L, De Bruyn H. Modern implant dentistry based on osseointegration: 50 years of progress, current trends and open questions. Periodontol 2000. 2017;73(1):7-21.
14. Berglundh T, Zitzmann NU, Donati M. Are peri-implantitis lesions different from periodontitis lesions? J Clin Periodontol. 2011;38 Suppl 11:188-202.
15. Carcuac O, Berglundh T. Composition of human peri-implantitis and periodontitis lesions. J Dent Res. 2014;93(11):1083-8.
16. Liu Y, Liu Q, Li Z, Acharya A, Chen D, Chen Z, et al. Long non-coding RNA and mRNA expression profiles in peri-implantitis vs periodontitis. J Periodontal Res. 2020;55(3):342-53.
17. Ng E, Tay JRH, Balan P, Ong MMA, Bostanci N, Belibasakis GN, et al. Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis. J Periodontal Res. 2021.
18. Relman DA. The human microbiome: ecosystem resilience and health. Nutr Rev. 2012;70 Suppl 1:S2-9.
19. Belstrom D, Constancias F, Liu Y, Yang L, Drautz-Moses DI, Schuster SC, et al. Metagenomic and metatranscriptomic analysis of saliva reveals disease-associated microbiota in patients with periodontitis and dental caries. NPJ Biofilms Microbiomes. 2017;3:23.
20. Dabdoub SM, Ganesan SM, Kumar PS. Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis. Sci Rep. 2016;6:38993.
21. Ghensi P, Manghi P, Zolfo M, Armanini F, Pasolli E, Bolzan M, et al. Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics. NPJ Biofilms Microbiomes. 2020;6(1):47.
22. Komatsu K, Shiba T, Takeuchi Y, Watanabe T, Koyanagi T, Nemoto T, et al. Discriminating Microbial Community Structure Between Peri-Implantitis and Periodontitis With Integrated Metagenomic, Metatranscriptomic, and Network Analysis. Front Cell Infect Microbiol. 2020;10:596490.
23. Ai D, Huang R, Wen J, Li C, Zhu J, Xia LC. Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis. BMC Genomics. 2017;18(Suppl 1):1041.
24. Babaev EA, Balmasova IP, Mkrtumyan AM, Kostryukova SN, Vakhitova ES, Il'ina EN, et al. Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus. Bull Exp Biol Med. 2017;163(6):718-21.
25. Papapanou PN, Sanz M, Buduneli N, Dietrich T, Feres M, Fine DH, et al. Periodontitis: Consensus report of workgroup 2 of the 2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions. J Periodontol. 2018;89 Suppl 1:S173-S82.
26. Lindhe J, Meyle J, Group DoEWoP. Peri-implant diseases: Consensus Report of the Sixth European Workshop on Periodontology. J Clin Periodontol. 2008;35(8 Suppl):282-5.
27. Jervoe-Storm PM, Alahdab H, Koltzscher M, Fimmers R, Jepsen S. Comparison of curet and paper point sampling of subgingival bacteria as analyzed by real-time polymerase chain reaction. J Periodontol. 2007;78(5):909-17.
28. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-60.
29. Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015;12(10):902-3.
30. Bastian M, Heymann S, Jacomy M, editors. Gephi: an open source software for exploring and manipulating networks. Third international AAAI conference on weblogs and social media; 2009.
31. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498-504.
32. Otasek D, Morris JH, Boucas J, Pico AR, Demchak B. Cytoscape Automation: empowering workflow-based network analysis. Genome Biol. 2019;20(1):185.
33. May RM. Will a large complex system be stable? Nature. 1972;238(5364):413-4.
34. May RM. Stability and complexity in model ecosystems. Monogr Popul Biol. 1973;6:1-235.
35. Allesina S, Tang S. Stability criteria for complex ecosystems. Nature. 2012;483(7388):205-8.
36. Diaz PI, Valm AM. Microbial Interactions in Oral Communities Mediate Emergent Biofilm Properties. J Dent Res. 2020;99(1):18-25.
37. Stacy A, Everett J, Jorth P, Trivedi U, Rumbaugh KP, Whiteley M. Bacterial fight-and-flight responses enhance virulence in a polymicrobial infection. Proc Natl Acad Sci U S A. 2014;111(21):7819-24.
38. Stein RR, Bucci V, Toussaint NC, Buffie CG, Ratsch G, Pamer EG, et al. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. PLoS Comput Biol. 2013;9(12):e1003388.
39. Oh J, Byrd AL, Park M, Program NCS, Kong HH, Segre JA. Temporal Stability of the Human Skin Microbiome. Cell. 2016;165(4):854-66.
40. Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, et al. Genomic variation landscape of the human gut microbiome. Nature. 2013;493(7430):45-50.
41. Marsh PD, Zaura E. Dental biofilm: ecological interactions in health and disease. J Clin Periodontol. 2017;44 Suppl 18:S12-S22.
42. Girvan M, Newman ME. Community structure in social and biological networks. Proc Natl Acad Sci U S A. 2002;99(12):7821-6.
43. Gravel D, Canard E, Guichard F, Mouquet N. Persistence increases with diversity and connectance in trophic metacommunities. PLoS One. 2011;6(5):e19374.
44. Kulkarni D, De Laender F. The combined effects of biotic and abiotic stress on species richness and connectance. PLoS One. 2017;12(3):e0172828.
45. Gardner MR, Ashby WR. Connectance of large dynamic (cybernetic) systems: critical values for stability. Nature. 1970;228(5273):784.
46. Coyte KZ, Schluter J, Foster KR. The ecology of the microbiome: Networks, competition, and stability. Science. 2015;350(6261):663-6.
47. Ohishi K, Yamamoto T, Tomofuji T, Tamaki N, Watanabe T. Isolation and characterization of aminopeptidase from Capnocytophaga granulosa ATCC 51502. Oral Microbiol Immunol. 2005;20(2):67-72.
48. Morita M, Yamamoto T, Watanabe T. Identification by biotinylated DNA probes of Capnocytophaga species isolated from supragingival calculus. J Dent Res. 1991;70(7):1048-51.
49. Ellen RP, Galimanas VB. Spirochetes at the forefront of periodontal infections. Periodontology 2000. 2005;38:13-32.
50. Takeuchi Y, Umeda M, Sakamoto M, Benno Y, Huang Y, Ishikawa I. Treponema socranskii, Treponema denticola, and Porphyromonas gingivalis are associated with severity of periodontal tissue destruction. J Periodontol. 2001;72(10):1354-63.