Bacterial Community in Dental Biofilms Linked to Periodontal Disease: An Intra-subject Metagenomics Study

Autor/innen

  • Maheen Tariq Universiti Sains Malaysia
  • Wan Nazatul Shima Shahidan
  • Raja Azman Awang

Schlagworte:

Intra-subject, Periodontitis, Gingivitis, Subgingival plaque, 16S RNA Metagenomics.

Abstract

Aims: To study the intra-subject subgingival plaque microbiota composition of gingivitis and periodontitis sites in periodontitis patients using 16s rRNA metagenomics. Methods: Samples of subgingival plaque were collected from 16 periodontitis participants enrolled on the study. The extracted DNA from dental plaque was sent to the Illumina laboratory for 16s rRNA metagenomics. The V₃ and V₄ region of 16s RNA gene were amplified and sequenced using Illumina technology. After quality filtering, 313480 sequences were obtained and arranged in OTU based on the 97% threshold. The reads were assigned to species. Results: The alpha diversity analyses revealed that periodontitis sites had more diverse and rich bacterial communities than gingivitis sites. However, the PCoA analysis (beta diversity) did not reveal any clustering of the bacterial community in gingivitis and periodontitis. Taxonomic analysis verified the presence of 56 known species. However, there was no apparent pattern in the bacterial community between gingivitis and periodontitis sites. Yet, a slight distinction was observed. Species like P. intermedia, R. dentocariosa and P. endodontalis were more abundant in gingivitis sites compared to periodontitis sites, while some other species like V. dispar, C. ochracea and A. segnis were more abundant in periodontitis sites. Conclusion: This study supports the fundamental idea that individual bacterial species are not responsible for the advancement of gingivitis to periodontitis but rather the abundance of bacteria in the bacterial community.

Literaturhinweise

Periodontal diseases. Kinane DF, Stathopoulou PG, Papapanou PN. Nat Rev Dis Prim. England; 2017;3:17038. PMID: 28805207

Defining Metaniches in the Oral Cavity According to Their Microbial Composition and Cytokine Profile. Seidel CL, Gerlach RG, Wiedemann P, Weider M, Rodrian G, Hader M, et al. Int J Mol Sci [Internet]. 2020;21:8218. Available from: https://www.mdpi.com/1422-0067/21/21/8218PMID: 33153049

Comparison of subgingival and buccal mucosa microbiome in chronic and aggressive periodontitis: A pilot study. Wei Y, Shi M, Zhen M, Wang C, Hu W, Nie Y, et al. Front Cell Infect Microbiol. 2019;9:1–11. PMID: 30915280

Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses. Nemoto T, Shiba T, Komatsu K, Watanabe T, Shimogishi M, Shibasaki M, et al. Bik H, editor. mSystems [Internet]. American Society for Microbiology; 2021;6:1–16. Available from: https://journals.asm.org/doi/10.1128/mSystems.00886-21

Periodontal microbial ecology. Socransky SS, Haffajee AD. Periodontol 2000 [Internet]. 2005;38:135–87. Available from: http://www.ncbi.nlm.nih.gov/pubmed/15853940PMID: 15853940

The Oral Microbiome in Periodontal Health. Lenartova M, Tesinska B, Janatova T, Hrebicek O, Mysak J, Janata J, et al. Front Cell Infect Microbiol [Internet]. 2021;11:629723. Available from: https://www.frontiersin.org/articles/10.3389/fcimb.2021.629723/fullPMID: 33828997

Subgingival Microbiota and Cytokines Profile Changes in Patients with Periodontitis: A Pilot Study Comparing Healthy and Diseased Sites in the Same Oral Cavities. Esparbès P, Legrand A, Bandiaky ON, Chéraud-Carpentier M, Martin H, Montassier E, et al. Microorganisms [Internet]. 2021;9:2364. Available from: https://www.mdpi.com/2076-2607/9/11/2364

The prevalence of novel periodontal pathogens and bacterial complexes in Stage II generalized periodontitis based on 16S rRNA next generation sequencing. Abu Fanas S, Brigi C, Varma SR, Desai V, Senok A, D’souza J. J Appl Oral Sci [Internet]. 2021;29:e20200787. Available from: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-77572021000100425&tlng=enPMID: 34008792

QIIME allows analysis of high-throughput community sequencing data. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. Nat Methods [Internet]. 2010/04/11. 2010;7:335–6. Available from: https://pubmed.ncbi.nlm.nih.gov/20383131

PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm. Li Y-L, Weng J-C, Hsiao C-C, Chou M-T, Tseng C-W, Hung J-H. BMC Bioinformatics [Internet]. BioMed Central Ltd; 2015;16 Suppl 1:S2. Available from: http://www.biomedcentral.com/qc/1471-2105/16/S1/S2PMID: 25707528

BBMerge – Accurate paired shotgun read merging via overlap. Bushnell B, Rood J, Singer E. Biggs PJ, editor. PLoS One [Internet]. 2017;12:e0185056. Available from: https://dx.plos.org/10.1371/journal.pone.0185056PMID: 29073143

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Appl Environ Microbiol [Internet]. American Society for Microbiology; 2006;72:5069–72. Available from: https://pubmed.ncbi.nlm.nih.gov/16820507

Nasopharyngeal microbiota in children with invasive pneumococcal disease: Identification of bacteria with potential disease-promoting and protective effects. Camelo-Castillo A, Henares D, Brotons P, Galiana A, Rodríguez JC, Mira A, et al. Front Microbiol. 2019;10.

Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities. Lozupone CA, Hamady M, Kelley ST, Knight R. Appl Environ Microbiol [Internet]. 2007;73:1576–85. Available from: https://europepmc.org/articles/PMC1828774

A new method for non-parametric multivariate analysis of variance. Anderson MJ. Austral Ecol [Internet]. 2001;26:32–46. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1442-9993.2001.01070.pp.x

Substantial differences in the subgingival microbiome measured by 16S metagenomics according to periodontitis status in older women. LaMonte MJ, Genco RJ, Zheng W, McSkimming DI, Andrews CA, Hovey KM, et al. Dent J. 2018;6.

Comparative Analyses of Subgingival Microbiome in Chronic Periodontitis Patients with and Without IgA Nephropathy by High Throughput 16S rRNA Sequencing. Cao Y, Qiao M, Tian Z, Yu Y, Xu B, Lao W, et al. Cell Physiol Biochem [Internet]. 2018;47:774–83. Available from: https://www.karger.com/Article/FullText/490029PMID: 29807361

The Subgingival Microbiome of Periodontal Pockets With Different Probing Depths in Chronic and Aggressive Periodontitis: A Pilot Study. Shi M, Wei Y, Hu W, Nie Y, Wu X, Lu R. Front Cell Infect Microbiol [Internet]. 2018;8:124. Available from: https://www.frontiersin.org/article/10.3389/fcimb.2018.00124

Do different probing depths exhibit striking differences in microbial profiles? Pérez-Chaparro PJ, McCulloch JA, Mamizuka EM, Moraes A da CL, Faveri M, Figueiredo LC, et al. J Clin Periodontol [Internet]. 2018;45:26–37. Available from: http://doi.wiley.com/10.1111/jcpe.12811PMID: 28871594

Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms. Wirth R, Pap B, Maróti G, Vályi P, Komlósi L, Barta N, et al. Front Cell Infect Microbiol. 2021;11:1–13.

Species-Level Salivary Microbial Indicators of Well-Resolved Periodontitis: A Preliminary Investigation. Acharya A, Chen T, Chan Y, Watt RM, Jin L, Mattheos N. Front Cell Infect Microbiol. 2019;9:1–12. PMID: 31681625

Signature of Microbial Dysbiosis in Periodontitis. Meuric V, Le Gall-David S, Boyer E, Acuña-Amador L, Martin B, Fong SB, et al. McBain AJ, editor. Appl Environ Microbiol [Internet]. 2017;83:1–13. Available from: https://journals.asm.org/doi/10.1128/AEM.00462-17PMID: 28476771

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis. Nowicki EM, Shroff R, Singleton JA, Renaud DE, Wallace D, Drury J, et al. Sperandio V, editor. MBio [Internet]. American Society for Microbiology; 2018;9:e00575-18. Available from: https://doi.org/10.1128/mBio.00575-18

Dysbiosis and Alterations in Predicted Functions of the Subgingival Microbiome in Chronic Periodontitis. Kirst ME, Li EC, Alfant B, Chi Y-Y, Walker C, Magnusson I, et al. Drake HL, editor. Appl Environ Microbiol [Internet]. United States: American Society for Microbiology; 2015;81:783–93. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25398868PMID: 25398868

Intra-oral single-site comparisons of periodontal and peri-implant microbiota in health and disease. Yu XL, Chan Y, Zhuang L, Lai HC, Lang NP, Keung Leung W, et al. Clin Oral Implants Res. 2019;30:760–76. PMID: 31102416

Oral Microbiome of Deep and Shallow Dental Pockets In Chronic Periodontitis. Ge X, Rodriguez R, Trinh M, Gunsolley J, Xu P. Burne RA, editor. PLoS One [Internet]. Public Library of Science; 2013;8:e65520. Available from: https://doi.org/10.1371/journal.pone.0065520

Potential Roles of the Free Salivary Microbiome Dysbiosis in Periodontal Diseases. Diao J, Yuan C, Tong P, Ma Z, Sun X. 2021;11:1–11.

Toward Personalized Oral Diagnosis : Distinct Microbiome Clusters in Periodontitis Bio fi lms. Komlo L, Wirth R, Pap B, Maro G, Barta N, Strang O. 2021;11:1–13. Available from: https://www.frontiersin.org/articles/10.3389/fcimb.2021.747814/full

Frequency of periodontal pathogens in equivalent peri- implant and periodontal clinical statuses. Cortelli R, Cavalca S, Oliveira F, Romeiro D, Roberto P, Mendes P, et al. 2012;8:2–9.

Progression of periodontal inflammation in adolescents is associated with increased number of Porphyromonas gingivalis , Prevotella intermedia , Tannerella forsythensis , and Fusobacterium nucleatum. Yang N, Zhang Q, Li J, Yang S, Shi Q. 2013;1–8.

A study of the bacteria associated with advancing periodontitis in man. Tanner AC, Haffer C, Bratthall GT, Visconti RA, Socransky SS. J Clin Periodontol. United States; 1979;6:278–307. PMID: 294457

Toward Personalized Oral Diagnosis: Distinct Microbiome Clusters in Periodontitis Biofilms. Wirth R, Pap B, Maróti G, Vályi P, Komlósi L, Barta N, et al. Front Cell Infect Microbiol [Internet]. 2021;11:1–13. Available from: https://www.frontiersin.org/articles/10.3389/fcimb.2021.747814/full

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Veröffentlicht

2024-08-29

Ausgabe

Bd. 12 Nr. 1 (2024)

Rubrik

Mechanisms of Oral Disease

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Copyright (c) 2024 maheen tariq

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