Аннотация
Микробиом полости рта играет решающую роль в поддержании здоровья зубов и слизистой оболочки рта. Изучение видовых и количественных характеристик микробиома в процессе развития воспалительных заболеваний пародонта имеет решающее значение для выявления диагностических и прогностических биомаркеров. Пародонтит является одним из наиболее распространенных инфекционных заболеваний в мире. Это следствие сложных взаимодействий между пародонтальными патогенами и их продуктами, запускающими воспалительную реакцию, хроническое воспаление, разрушение тканей в организме человека.
Цель исследования: изучение видового разнообразия микробиома содержимого пародонтальных карманов у пациентов с хроническим генерализованным пародонтитом легкой и средней степени тяжести.
Материал и методы. Изучался микробиом образцов, взятых из пародонтальных карманов у пациентов с хроническим генерализованным пародонтитом легкой и средней степенями тяжести, с десневой борозды здоровых лиц. Секвенирование проведено в соответствии с протоколом Illumina по подготовке 16S метагеномных библиотек. Биоинформатическая обработка проведена на языках программирования R v.3.6 и Python3.
Результаты и обсуждение. Исследование выявило доминирование Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes в составе микробиоты пациентов с пародонтитом. Установлено, что биоразнообразие микробиома у пациентов с пародонтитом выше, чем у здоровых лиц. У пациентов легкой степени тяжести пародонтита микробиом пародонтальных карманов меняется в сторону образования ассоциаций родов с преобладанием Treponema, Desulfobulbus, Porphyromonas, Filifactor, у пациентов средней степени тяжести преобладают Capnocytophaga spp., Lentimicrobium spр., Fusobacterium spр. Porphyromonas spр., Filifactor spр. Видовое разнообразие характеризуется увеличением таких бактерий, как Phocaeicola abscessus, Leptotrichia wadei, Neisseria meningitidis, Filifactor alocis в группе пациентов с легкой степенью тяжести пародонтита, в группе пациентов со средней степенью тяжести пародонтита видов Capnocytophaga sputigena, Fusobacterium canifelinum, Gemella morbillorum, Filifactor alocis, Porphyromonas gingivalis.
Заключение. В результате проведенного исследования, сравнивающего геномный состав микробиоты десневой борозды у здоровых лиц и содержимого пародонтальных карманов у пациентов с хроническим генерализованным пародонтитом легкой и средней степенями тяжести, выявлены уникальные микробные сообщества, характерные для каждой группы. Полученные данные о специфическом геномном профиле микробиоты открывают перспективы для дальнейшего использования в клинической практике. Установленный уровень геномного разнообразия и выявленные отличительные характеристики микробиоты могут служить ценным инструментом для прогнозирования течения пародонтита и разработки персонализированных стратегий лечения, что способствует улучшению диагностики и эффективности терапевтических вмешательств.
Annotation
The microbiome of the oral cavity plays a crucial role in maintaining the health of teeth and oral mucosa. The study of the qualitative and quantitative characteristics of the microbiome during the development of inflammatory periodontal diseases is crucial for the identification of diagnostic and prognostic biomarkers. Periodontitis is one of the most common infectious diseases in the world. This is a consequence of complex interactions between periodontal pathogens and their products, which trigger an inflammatory response, chronic inflammation and tissue destruction in the human body.
The purpose of this study was to study the species diversity of the microbiome of the contents of periodontal pockets of patients with chronic generalized periodontitis of mild and moderate severity.
Material and methods. The microbiome of samples taken from periodontal pockets of patients with chronic generalized periodontitis of mild and moderate severity, as well as from the gingival sulcus of healthy people, was studied. Sequencing was performed in accordance with the Illumina protocol for the preparation of 16S metagenomic libraries. Bioinformatic processing was carried out in the R v programming languages.3.6 and Python3.
Results and discussion. The study revealed the dominance of Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes in the microbiota of patients with periodontitis. In addition, it was established that the microbiome biodiversity in patients with periodontitis is higher than in healthy people. In patients with mild periodontitis, the microbiome of periodontal pockets changes towards the formation of associations of genera with a predominance of Treponema, Desulfobulbus, Porphyromonas, Filifactor, in patients with moderate severity, Capnocytophaga spp., Lentimicrobium spp., Fusobacterium spp. prevailed. Porphyromonas spp., Filifactor spp. The species diversity was characterized by an increase in bacteria such as Phocaeicola abscessus, Leptotrichia wadei, Neisseria meningitidis, Filifactor alocis in the group of patients with mild periodontitis, and in the group of patients with moderate periodontitis, Capnocytophaga sputigena, Fusobacterium canifelinum, Gemella morbillorum, Filifactor alocis and Porphyromonas gingivalis species.
Conclusion. The study, which compared the genomic composition of the gingival sulcus microbiota in healthy individuals and the contents of periodontal pockets in patients with mild to moderate chronic generalized periodontitis, identified unique microbial communities, which are typical for each group. The obtained data of the microbiota specific genomic profile opens possibilities for further use in clinical practice. The established level of genomic diversity and the identified distinctive characteristics of microbiota can serve as a valuable tool for predicting the course of periodontitis and developing personalized treatment strategies, which contributes to improved diagnostics and effectiveness of therapeutic interventions.
Key words: periodontitis; sequencing; microbiome; periodontal pathogens
Список литературы
ЛИТЕРАТУРА
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REFERENCES
Dewhirst F.E., Chen T., Izard J., Paster B. J., Tanner A. C. R., Yu W. H. et al. The human oral microbiome. J. Bact. 2010; 192(19):5002-17. DOI: 10.1128/jb.00542-10.
Huang Y., Zhao X., Cui L., Huang S. Metagenomic and metatranscriptomic insight into oral biofilms in periodontitis and related systemic diseases. Front. Microbiol. 2021; 12:728585. DOI: 10.3389/fmicb.2021.728585.
Ezzo P.J., Cutler C.W. Microorganisms as risk indicators for periodontal disease. Periodontol. 2000. 2003; 3(1):24-35. DOI: 10.1046/j.0906-6713.2003.03203.x.
Kumar P.S. From focal sepsis to periodontal medicine: a century of exploring the role of the oral microbiome in systemic disease. J. Physiol. 2017; 595:465-76. DOI: 10.1113/JP272427.
Аi D., Huang R., Wen J., Li C., Zhu J., Xia L.C. Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis. BMC Genomics 1. 2017; 8:32545. DOI: 10.1186/s12864-016-3254-5.
Dabdoub S.M., Ganesan S.M., Kumar P.S. Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis. Sci. Rep. 2016; 6:38993. DOI: 10.1038/srep38993.
Altabtbaei K., Maney P., Ganesan S.M., Dabdoub S.M., Nagaraja H.N., Kumar P.S. Anna Karenina and the subgingival microbiome associated with periodontitis. Microbiome. 2021; 9(1):97. DOI: 10.1186/s40168-021-01056-3.
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Ravichandran A., Shobana D., Visudha S., Yazhini, Niveditha S., Saravanan P. Bacterial exopolysaccharides-based nanomaterials for targeting biofilm-associated infections: bacterial nanomaterials. Prabhakar P.K., Prakash A., eds. Cutting-edge applications of nanomaterials in biomedical sciences. IGI Global, Hershey, PA, USA. 2024; 372-86.
Ravichandran A., Sivapackiam J., Periasamy S. Oral bacterial insights from a comparative study between healthy and comorbid diseased human individuals. Microbial. Pathogenesis. 2024; 191:106643. DOI: 10.1016/j.micpath.2024.106643.
Callahan B.J., McMurdie P.J., Rosen M.J., Han A.W., Johnson A.J.A., Holmes S.P. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods. 2016; 13:581-3. DOI: 10.1038/nmeth.3869.
Qiong W., Garrity M.G., Tiedje M.J., Cole R.J. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007; 73:5261-7. DOI: 10.1128/AEM.00062-07.
Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic. Acids Res. 2013; 41(D1):D590-D596. DOI: 10.1093/nar/gks1219.
Love C.J., Gubert C., Kodikara S., Kong G., Cao K.A.L., Hannan A.J. Microbiota DNA isolation, 16S rRNA amplicon sequencing, and bioinformatic analysis for bacterial microbiome profiling of rodent fecal samples. STAR Protoc. 2022; 3(4):101772. DOI: 10.1016/j.xpro.2022.101772.
Colombo A.P.V., Tanner A.C.R. The role of bacterial biofilms in dental caries and periodontal and peri-implant diseases: a historical perspective. J. Dent. Res. 2019; 98(4):373-85. DOI: 10.1177/0022034519830686.
Ravichandran A., Sivapackiam J., Periasamy S. Oral bacterial insights from a comparative study between healthy and comorbid diseased human individuals. Microb. Pathog. 2024; 191:106643. DOI: 10.1016/j.micpath.2024.106643.
Griffen A.L., Beall C.J., Campbell J.H., Firestone N.D., Kumar P.S., Yang Z.K. et al. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J. 2012; 6:1176-85. DOI: 10.1038/ismej.2011.191.
Cai Z., Lin S., Hu S., Zhao L. Structure and function of Oral microbial Community in Periodontitis Based on integrated data. Front. Cell. Infect. Microbiol. 2021; 11:663756. DOI: 10.3389/fcimb.2021.663756.
Sedghi L.M., Bacino M., Kapila Y.L. Periodontal disease: the good, the bad, and the unknown. Front. Cell. Infect. Microbiol. 2021; 11:766944. DOI: 10.3389/fcimb.2021.766944.
Kaur K., Khatri I., Akhtar A., Subramanian S., Ramya T.N.C. Metagenomics analysis reveals features unique to Indian distal gut microbiota. PLoS One. 2020; 15(4):e0231197. DOI: 10.1371/journal.pone.0231197.
Narayanan A., Söder B., Meurman J., Lundmark A., Hu Y.O.O., Neogi U. et al. Composition of subgingival microbiota associated with periodontitis and diagnosis of malignancy-a cross-sectional study. Front. Microbiol. 2023; 14:1172340. DOI: 10.3389/fmicb.2023.1172340.
Mombelli A. Microbial colonization of the periodontal pocket and its significance for periodontal therapy. Periodontol. 2000. 2018; 76(1):85-96. DOI: 10.1111/prd.12147.
Abusleme L., Dupuy A.K., Dutzan N., Silva N., Burleson J.A., Strausbaugh L.D. et al. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J. 2013; 7:1016-25. DOI: 10.1038/ismej.2012.174.
Shi B., Chang M., Martin J., Mitreva M., Lux R., Klokkevold P. et al. Dynamic changes in the subgingival microbiome and their potential for diagnosis and prognosis of periodontitis. MBio. 2015; 6:e01926-14. DOI: 10.1128/mBio.01926-14.
Zhou P., Manoil D., Belibasakis G.N., Kotsakis G.A. Veillonellae: beyond bridging species in oral biofilm ecology. Front. Oral. Health. 2021; 2:774115. DOI: 10.3389/froh.2021.774115.
Hoare A., Wang H., Meethil A., Abusleme L., Hong B.Y., Moutsopoulos N.M. et al. A cross-species interaction with a symbiotic commensal enables cell-density-dependent growth and in vivo virulence of an oral pathogen. ISME J. 2021; 15:1490-1504. DOI: 10.1101/2020.09.30.320770.
Cross K.L., Chirania P., Xiong W., C.J. Beall, J.G. Elkins, Giannone R.J. et al. Insights into the evolution of host association through the isolation and characterization of a novel human periodontal pathobiont, Desulfobulbus oralis. mBio. 2018; 9(2):e02061-17. DOI: 10.1128/mBio.02061-17.
Oliveira R.R., Fermiano D., Feres M., Figueiredo L.C., Teles F.R., Soares G.M. et al. Levels of candidate periodontal pathogens in subgingival biofilm. J. Dent. Res. 2016; 95(6):711-8. DOI: 10.1177/0022034516634619.
Lafaurie G.I., Neuta Y., Ríos R., Pacheco-Montealegre M., Pianeta R., Castillo D.M. et al. Differences in the subgingival microbiome according to stage of periodontitis: A comparison of two geographic regions. PLoS One. 2022; 17(8):e0273523. DOI: 10.1371/journal.pone.0273523.
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