Unveiling Subgingival Oral Microbiota Profile using Next Generation Sequencing Technology
DOI:
https://doi.org/10.22452/adum.vol33.2Keywords:
16s rRNA gene sequencing, periodontitis, subgingival oral microbiotaAbstract
This study aimed to profile the subgingival microbiota of a selected Malaysian population. The subjects consisted of 21 periodontitis, 7 gingivitis and 13 healthy individuals. Subgingival plaque DNA were sequenced using next generation sequencing technology to study the oral microbial profile. In all the 3 groups, bacterial communities comprised 2 clusters whereby the first cluster was according to periodontitis status, while gingivitis and healthy groups clustered together. The phyla that dominated 80% of the bacteria community consisted of Firmicutes, Fusobacteria, Bacteroidetes and Actinobacteria. Among the healthy subjects, the bacterial composition was unique to respective individuals. It was obvious that periodontal condition influences the microenvironment and hence the microbial composition where periodontitis group presented with increased relative abundance in phylum Spirochaetes, Synergistetes, Tenericutes and Chloroflexi. At genus level, the periodontitis group was further represented by the increase in genus Treponema 2, Filifactor, Fretibacterium and Peptostreptococcus. This profiling shows the unique microbial features of a selected Malaysian population with mixed cultural background and habits. The results from this study demonstrates that changes in microbial composition are due to in-situ condition. These results served as a reference for future work related to the subgingival microbiota of Malaysian population.
References
1. Deo PN, Deshmukh R. Oral microbiome: Unveiling the fundamentals. J Oral Maxillofac Pathol. 2019;23(1):122-128. doi: 10.4103/jomfp.JOMFP_304_18.
2. Kilian M, Chapple IL, Hannig M, Marsh PD, Meuric V, Pedersen AM et al. The oral microbiome - an update for oral healthcare professionals. Br Dent J. 2016;221(10):657-666. doi: 10.1038/sj.bdj.2016.865.
3. Griffen AL, Beall CJ, Campbell JH, Firestone ND, Kumar PS, Yang ZK, et al. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J. 2012;6(6):1176-85. doi: 10.1038/ismej.2011.191.
4. Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One. 2012;7(6):e37919. doi: 10.1371/journal.pone.0037919.
5. Abusleme L, Dupuy AK, Dutzan N, Silva N, Burleson JA, Strausbaugh LD, et al. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. ISME J. 2013;7(5):1016-25. doi: 10.1038/ismej.2012.174.
6. Li Y, He J, He Z, Zhou Y, Yuan M, Xu X, et al. Phylogenetic and functional gene structure shifts of the oral microbiomes in periodontitis patients. ISME J. 2014;8(9):1879-91. doi: 10.1038/ismej.2014.28.
7. Vishnu RA, Alamelu S, Arun KV, Sujitha P, Ganesh PR. Comparative evaluation of subgingival microbiome in healthy periodontium and gingivitis using next-generation sequencing technology: A case-control study. J Indian Soc Periodontol. 2022;26(3):224-229. doi: 10.4103/jisp.jisp_837_20. Epub 2022 May 2. PMID: 35602532; PMCID: PMC9118943.
8. Ruan X, Luo J, Zhang P, Howell K. The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations. NPJ Biofilms Microbiomes. 2022;8(1):85. doi: 10.1038/s41522-022-00343-7. PMID: 36266278; PMCID: PMC9584946.
9. Arredondo A, Àlvarez G, Isabal S, Teughels W, Laleman I, Contreras MJ et al. Comparative 16S rRNA gene sequencing study of subgingival microbiota of healthy subjects and patients with periodontitis from four different countries. J Clin Periodontol. 2023;50(9):1176-1187. doi: 10.1111/jcpe.13827. Epub 2023 May 28. PMID: 37246304.
10. Mok SF, Karuthan C, Cheah YK, Ngeow WC, Rosnah Z, Yap SF et al. The oral microbiome community variations associated with normal, potentially malignant disorders and malignant lesions of the oral cavity. Malays J Pathol. 2017;39(1):1-15. PMID: 28413200.
11. Cheah CW, Al-Maleki AR, Vaithilingam RD, Vadivelu J, Sockalingam S, Baharuddin NA et al. Associations between inflammation-related LL-37 with subgingival microbial dysbiosis in rheumatoid arthritis patients. Clin Oral Investig. 2022;26(5):4161-4172. doi: 10.1007/s00784-022-04388-y. Epub 2022 Mar 7. PMID: 35257247.
12. Yeo LF, Aghakhanian FF, Tan JSY, Gan HM, Phipps ME. Health and saliva microbiomes of a semi-urbanized indigenous tribe in Peninsular Malaysia. F1000Res. 2019;8:175. doi: 10.12688/f1000research.17706.3. PMID: 31275564; PMCID: PMC6544134.
13. Bizzarro S, Laine ML, Buijs MJ, Brandt BW, Crielaard W, Loos BG et al. Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis. Sci Rep. 2016;6:20205. doi: 10.1038/srep20205. PMID: 26830979; PMCID: PMC4735321.
14. Chen L, Zheng T, Yang Y, Chaudhary PP, Teh JPY, Cheon BK et al. Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans. Gut Microbes. 2022;14(1):2070392. doi: 10.1080/19490976.2022.2070392. PMID: 35549618; PMCID: PMC9116421.
15. Takeshita T, Matsuo K, Furuta M, Shibata Y, Fukami K, Shimazaki Y et al. Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults. Sci Rep. 2014;4:6990. doi: 10.1038/srep06990. PMID: 25384884; PMCID: PMC4227031.
16. Singapore Department of Statistics. 2020. Census of Population 2020 Statistical Release 1
17. Bostanci N, Grant M, Bao K, Silbereisen A, Hetrodt F, Manoil D et al. Metaproteome and metabolome of oral microbial communities. Periodontol 2000. 2021;85(1):46-81. Doi: 10.1111/prd.12351. Epub 2020 Nov 23. PMID: 33226703
18. Yost S, Duran-Pinedo AE, Teles R, Krishnan K, Frias-Lopez J. Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis. Genome Med. 2015;7(1):27. doi: 10.1186/s13073-015-0153-3. Erratum in: Genome Med. 2015;7(1):111. doi: 10.1186/s13073-015-0231-6.
19. Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, et al. Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection. Nat Microbiol. 2017;2(11):1493-1499. doi: 10.1038/s41564-017-0021-6. Epub 2017 Sep 18. PMID: 28924191; PMCID: PMC5678995.
20. Yeo LF, Lee SC, Palanisamy UD, Khalid B, Ayub Q, Lim SY et al. The Oral, Gut Microbiota and Cardiometabolic Health of Indigenous Orang Asli Communities. Front Cell Infect Microbiol. 2022;12:812345. doi: 10.3389/fcimb.2022.812345. PMID: 35531342; PMCID: PMC9074829.
21. Payungporn S, Arirachakaran P, Poomipak W, Praianantathavorn K, Charalampakis G, et al. Identification of Bacteria Associated with a Periodontal Disease in Thai Patients Based on Next-Generation Sequencing. Jundishapur J Microbiol. 2017;10(6):e13646. doi: https://doi.org/10.5812/jjm.13646
22. Takeshita T, Nakano Y, Kumagai T, Yasui M, Kamio N, Shibata Y et al. The ecological proportion of indigenous bacterial populations in saliva is correlated with oral health status. ISME J. 2009;3(1):65-78. doi: 10.1038/ismej.2008.91. Epub 2008 Oct 2. PMID: 18830275.
23. Eng CW, Lim SC, Ngongo C, Sham ZH, Kataria I, Chandran A et al. Dietary practices, food purchasing, and perceptions about healthy food availability and affordability: a cross-sectional study of low-income Malaysian adults. BMC Public Health. 2022;22(1):192. doi: 10.1186/s12889-022-12598-y. PMID: 35090429; PMCID: PMC8795714.
24. Nemoto T, Shiba T, Komatsu K, Watanabe T, Shimogishi M, Shibasaki M et al. Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses. mSystems. 2021;6(6):e0088621. doi: 10.1128/mSystems.00886-21. Epub 2021 Oct 26. PMID: 34698525; PMCID: PMC8547322.
25. Balan P, Chong YS, Umashankar S, Swarup S, Loke WM, Lopez V et al. Keystone Species in Pregnancy Gingivitis: A Snapshot of Oral Microbiome During Pregnancy and Postpartum Period. Front Microbiol. 2018;9:2360. doi: 10.3389/fmicb.2018.02360. PMID: 30356676; PMCID: PMC6189292.
26. Li X, Liu Y, Yang X, Li C, Song Z. The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions. Front Microbiol. 2022 Apr 29;13:895537. doi: 10.3389/fmicb.2022.895537. PMID: 35572634; PMCID: PMC9100676.
27. Rungrueang K, Yuma S, Tantipoj C, Khovidhunkit SP, Fuangtharnthip P, Thuramonwong T et al. Oral Bacterial Microbiomes in Association with Potential Prediabetes Using Different Criteria of Diagnosis. Int J Environ Res Public Health. 2021;18(14):7436. doi: 10.3390/ijerph18147436. PMID: 34299886; PMCID: PMC8307246.
28. Tan YWB, Lau JH, AshaRani PV, Roystonn K, Devi F, Lee YY et al. Dietary patterns of persons with chronic conditions within a multi-ethnic population: results from the nationwide Knowledge, Attitudes and Practices survey on diabetes in Singapore. Arch Public Health. 2022;80(1):62. doi: 10.1186/s13690-022-00817-2. PMID: 35189947; PMCID: PMC8862351.
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