Association of nine pathobionts with periodontitis in four South American and European countries

References

• Kumar PS, Dabdoub SM, Ganesan SM. Probing periodontal microbial dark matter using metataxonomics and metagenomics. Periodontol 2000. 2021;85(1):12–10.
   PubMed Web of Science ®Google Scholar
• Belibasakis GN, Bostanci N, Marsh PD, et al. Applications of the oral microbiome in personalized dentistry. Arch Oral Biol. 2019;104(March):7–12.
   PubMedGoogle Scholar
• Hajishengallis G. Periodontitis: from microbial immune subversion to systemic inflammation. Nat Rev Immunol. 2015;15(1):30–44.
   PubMed Web of Science ®Google Scholar
• Radaic A, Kapila YL. The oralome and its dysbiosis: new insights into oral microbiome-host interactions. Comput Struct Biotechnol J. 2021;19:1335–1360.
   PubMed Web of Science ®Google Scholar
• Socransky SS, Haffajee AD, Cugini MA, et al. Microbial complexes in subgingival plaque. J Clin Periodontol. 1998;25(2):134–144.
   PubMed Web of Science ®Google Scholar
• Kumar PS, Griffen AL, Barton JA, et al. New bacterial species associated with chronic periodontitis. J Dent Res. 2003;82(5):338–344.
   PubMed Web of Science ®Google Scholar
• Feres M, Retamal‐valdes B, Gonçalves C, et al. Did Omics change periodontal therapy? Periodontol 2000. 2021;85(1):182–209.
   PubMed Web of Science ®Google Scholar
• Griffen AL, Beall CJ, Campbell JH, et al. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. Isme J. 2012;6(6):1176–1185.
   PubMed Web of Science ®Google Scholar
• Teles F, Wang Y, Hajishengallis G, et al. Impact of systemic factors in shaping the periodontal microbiome. Periodontol 2000. 2021;85(1):126–160.
   PubMed Web of Science ®Google Scholar
• Abusleme L, Dupuy AK, Dutzan N, et al. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. Isme J. 2013;7(5):1016–1025.
   PubMed Web of Science ®Google Scholar
• Abu Fanas S, Brigi C, Varma SR, et al. The prevalence of novel periodontal pathogens and bacterial complexes in stage II generalized periodontitis based on 16S rRNA next generation sequencing. J Appl Oral Sci. 2021;29:e20200787.
   PubMed Web of Science ®Google Scholar
• Mason MR, Nagaraja HN, Camerlengo T, et al. Deep sequencing identifies ethnicity-specific bacterial signatures in the oral microbiome. PLoS ONE. 2013;8(10):e77287. Biswas I, ed. doi:10.1371/journal.pone.0077287.
   PubMed Web of Science ®Google Scholar
• Johnson JS, Spakowicz DJ, Hong BY, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10(1):5029.
   PubMed Web of Science ®Google Scholar
• Jeong J, Yun K, Mun S, et al. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Sci Rep. 2021;11(1):1727.
   PubMed Web of Science ®Google Scholar
• Vincent JW, Falkler WA, Suzuki JB. Systemic antibody response of clinically characterized patients with antigens of eubacterium brachy initially and following periodontal therapy. J Periodontol. 1986;57(10):625–631.
   PubMed Web of Science ®Google Scholar
• Papapanou PN, Sanz M, Buduneli 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. J Periodontol. 2018;89(March):S173–182.
   PubMedGoogle Scholar
• Caton JG, Armitage G, Berglundh T, et al. A new classification scheme for periodontal and peri-implant diseases and conditions - Introduction and key changes from the 1999 classification. J Clin Periodontol. 2018;45:S1–8.
   PubMed Web of Science ®Google Scholar
• Tonetti MS, Greenwell H, Kornman KS. Staging and grading of periodontitis: framework and proposal of a new classification and case definition. J Periodontol. 2018;89:S159–172.
   PubMed Web of Science ®Google Scholar
• Cafiero C, Matarasso S. Predictive, preventive, personalised and participatory periodontology: ‘the 5ps age’ has already started. EPMA Journal. 2013;4(1):16.
   PubMedGoogle Scholar
• Àlvarez G, González M, Isabal S, et al. Method to quantify live and dead cells in multi-species oral biofilm by real-time PCR with propidium monoazide. AMB Express. 2013;3(1). Published online. DOI:10.1186/2191-0855-3-1.
   PubMedGoogle Scholar
• Sambrook J, Fritsch EF, Maniatis T. Molecular cloning - a laboratory manual. 2nd ed. New York: Cold Spring Harbor Laboratory Press; 1987.
   Google Scholar
• R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing; 2022. Published online. Available from: https://www.R-project.org/
   Google Scholar
• Wickham H, Averick M, Bryan J, et al. Welcome to the Tidyverse. J Open Source Softw. 2019;4(43):1686.
   Google Scholar
• Cheng M. ggpattern. Available from: https://coolbutuseless.github.io/package/ggpattern/index.html
   Google Scholar
• Hope RM. Rmisc. R package version 15; 2013. Published online.
   Google Scholar
• Peña EA, Slate EH. Global validation of linear model assumptions. J Am Stat Assoc. 2006;101(473):341–354.
   PubMed Web of Science ®Google Scholar
• Fox J, Weisberg S. An {R} companion to applied regression. 3rd ed. Sage; 2019. Available from: https://socialsciences.mcmaster.ca/jfox/Books/Companion/
   Google Scholar
• Lenth RV, Buerkner P, Herve M, et al. Emmeans. R package version 155; 2021. Published online.
   Google Scholar
• Kassambara A, Mundt F Factoextra. R package version 107; 2020. Published online.
   Google Scholar
• Richardson DB, Ciampi A. Effects of exposure measurement error when an exposure variable is constrained by a lower limit. Am J Epidemiol. 2003;157(4):355–363.
   PubMed Web of Science ®Google Scholar
• Sattari M, Taheri RA, ArefNezhad R, et al. The expression levels of MicroRNA-146a, RANKL and OPG after non-surgical periodontal treatment. BMC Oral Health. 2021;21(1):523.
   PubMed Web of Science ®Google Scholar
• Chapple ILC, Mealey BL, van Dyke TE, et al. Periodontal health and gingival diseases and conditions on an intact and a reduced periodontium: consensus report of workgroup 1 of the 2017 world workshop on the classification of periodontal and peri-implant diseases and conditions. J Periodontol. 2018;89:S74–84.
   PubMed Web of Science ®Google Scholar
• Zaura E, Pappalardo VY, Buijs MJ, et al. Optimizing the quality of clinical studies on oral microbiome: a practical guide for planning, performing, and reporting. Periodontol 2000. 2021;85(1):210–236.
   PubMed Web of Science ®Google Scholar
• Takeshita T, Matsuo K, Furuta M, et al. Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults. Sci Rep. 2015;4(1):6990.
   Google Scholar
• Camelo-Castillo AJ, Mira A, Pico A, et al. Subgingival microbiota in health compared to periodontitis and the influence of smoking. Front Microbiol. 2015;6. DOI:10.3389/fmicb.2015.00119.
   PubMed Web of Science ®Google Scholar
• Billings M, Holtfreter B, Papapanou PN, et al. Age-dependent distribution of periodontitis in two countries: findings from NHANES 2009 to 2014 and SHIP-TREND 2008 to 2012. J Periodontol. 2018;89:S140–158.
   PubMed Web of Science ®Google Scholar
• Xu X, He J, Xue J, et al. Oral cavity contains distinct niches with dynamic microbial communities. Environ Microbiol. 2015;17(3):699–710.
   PubMed Web of Science ®Google Scholar
• Schwartz JL, Peña N, Kawar N, et al. Old age and other factors associated with salivary microbiome variation. BMC Oral Health. 2021;21(1):490. DOI:10.1186/s12903-021-01828-1
   PubMed Web of Science ®Google Scholar
• Faraway JJ. Linear models with R. 2nd ed. Boca Ratón: CRC Press, Taylor & Francis Group; 2015. (Dominici F, Faraway J, Tanner M, and Zidek J, editors).
   Google Scholar
• Rawlings JO, Pantula SG, Dickey DA. Collinearity. In: Casella G, Fienberg S, and Olkin I, editors. Applied regression analysis : a research tool. Second ed. Springer. 1998; p. 433–462.
   Google Scholar
• Savitt ED, Darack AP, Killoy WJ, et al. Site selection criteria for microbiological testing of periodontal microorganisms. J Periodontol. 1991;62(9):558–561.
   PubMed Web of Science ®Google Scholar
• Camelo-Castillo A, Novoa L, Balsa-Castro C, et al. Relationship between periodontitis-associated subgingival microbiota and clinical inflammation by 16S pyrosequencing. J Clin Periodontol. 2015;42(12):1074–1082.
   PubMed Web of Science ®Google Scholar
• Tomás I, Arias-Bujanda N, Alonso-Sampedro M, et al. Cytokine-based predictive models to estimate the probability of chronic periodontitis: development of diagnostic nomograms. Sci Rep. 2017;7(1):1–15.
   PubMedGoogle Scholar
• Yost S, Duran-Pinedo AE, Teles R, et al. Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis. Genome Med. 2011;7(1). DOI:10.1186/s13073-015-0153-3
   Google Scholar
• He J, Li Y, Cao Y, et al. The oral microbiome diversity and its relation to human diseases. Folia Microbiol (Praha). 2015;60(1):69–80.
   PubMed Web of Science ®Google Scholar
• United Nations Development Programme. United nations development programm. Human development report 2020; 2020 [cited 2022 Aug 17]. Available from: https://hdr.undp.org/content/human-development-report-2020
   Google Scholar
• Pérez-Chaparro PJ, Gonçalves C, Figueiredo LC, et al. Newly identified pathogens associated with periodontitis: a systematic review. J Dent Res. 2014;93(9):846–858.
   PubMed Web of Science ®Google Scholar
• Lamont RJ, Hajishengallis G. Polymicrobial synergy and dysbiosis in inflammatory disease. Trends Mol Med. 2015;21(3):172–183. Published online. doi:10.1016/j.molmed.2014.11.004.
   PubMed Web of Science ®Google Scholar
• Ikeda E, Shiba T, Ikeda Y, et al. Japanese subgingival microbiota in health vs disease and their roles in predicted functions associated with periodontitis. Odontology. 2019;108(2):280–291.
   PubMed Web of Science ®Google Scholar
• Ye C, Xia Z, Tang J, et al. Unculturable and culturable periodontal-related bacteria are associated with periodontal inflammation during pregnancy and with preterm low birth weight delivery. Sci Rep. 2020;10(1):15807.
   PubMed Web of Science ®Google Scholar
• Hiranmayi K, Sirisha K, Ramoji Rao M, et al. Novel pathogens in periodontal microbiology. J Pharm Bioallied Sci. 2017;9(3):155.
   PubMedGoogle Scholar
• Armitage GC. Development of a classification system for periodontal diseases and conditions. Ann Periodontol. 1999;4(1):1–6.
   PubMedGoogle Scholar