{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T11:22:21Z","timestamp":1787570541327,"version":"build-2736575974"},"reference-count":46,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T00:00:00Z","timestamp":1787270400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Directorate of Research and Community Engagement, Universitas Indonesia","award":["PKS-145\/UN2.RST\/HKP.05.00\/2025"],"award-info":[{"award-number":["PKS-145\/UN2.RST\/HKP.05.00\/2025"]}]},{"award":["PKS-145\/UN2.RST\/HKP.05.00\/2025"],"award-info":[{"award-number":["PKS-145\/UN2.RST\/HKP.05.00\/2025"]}],"id":[{"id":"https:\/\/ror.org\/0116zj450","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Dent. J.","Dentistry Journal"],"abstract":"<jats:p>Background: To date, several studies have confirmed the fact that over 700 species of microbiota interacts with host, modulating immunity, controlling the homeostasis environment, and thus maintaining systemic condition. Dysbiosis in the subgingival biofilm can initiate chronic inflammation of the gingiva, potentially progressing to periodontitis. Advances in DNA sequencing analysis of the subgingival microbial community have shown that periodontal treatment causes a microbial shift in subgingival plaque, affecting the taxonomic composition (disease- and health-associated taxa). Yet, none of these have been investigated in Indonesia. Objective: The objective was to profile the composition of oral microbiome in Indonesian population with healthy, gingivitis, and periodontitis status. Further, we analyzed the subgingival bacterial alteration following the therapy in periodontitis group. Methods: Twelve subjects consisting of healthy, gingivitis, and periodontitis patients were included. Additionally, the periodontitis group was observed at baseline, 1-month, and 3-month. Subgingival dental plaque were sampled and 16S rRNA NGS analysis was performed. Alpha (Chao1, Shannon, and Simpson indices) and beta diversity (PCoA plots based on Bray\u2013Curtis dissimilarity) were observed. Microbiota composition at the genus and species levels was analyzed. Results: No statistically significant differences (p &gt; 0.05) were found for Chao1, Shannon, and Simpson indices amongst groups and in periodontitis patients across the observation. At the genus level, PCoA plots based on Bray\u2013Curtis dissimilarity revealed that the clinical status accounted for 21.9% of the total variation (R2 = 0.219, p = 0.197), while at the species level, it accounted for 19.8% (R2= 0.198, p = 0.281). Periodontitis samples across all timepoints showed no distinct clustering at either the genus 7.6% (R2 = 0.076 p = 0.097) or species levels 9.7% (R2 = 0.097 p = 0.995). Top five subgingival microbiota at the genus and species levels in all groups showed definite pattern of composition. Although no significant association was found (p &gt; 0.05), it described that Veillonella parvula, Campylobacter gracilis, and Capnocytophaga granulosa were more abundant in healthy subjects than in gingivitis and periodontitis. Prevotella oris and Selenomonas noxia were less abundant in healthy subject than in gingivitis and periodontitis. In periodontitis subjects, Prevotella intermedia was increased by the therapy at 1 month and reduced again at 3 months. On the other hand, Capnocytophaga granulosa was increased by the therapy at 1 and 3 months. Hoylesella loescheii was reduced by the time. Porphyromonas gingivalis was reduced at 1 month and increased again at 3 months. Discussion: The result showed that the number of alpha diversity was notably higher in the gingivitis and periodontitis groups compared to health group, supporting a trend toward increased community richness and evenness in diseases states. The microbial richness and evenness remained relatively stable across the evaluated periods within periodontitis cohort. Oral microbial composition defines the periodontal status and disease. More abundance of Red Complex bacteria is associated with disease-associated condition. Pathogen re-colonization may occur 3 months after the therapy. Conclusions: These findings suggest that maintaining health-associated microbiome may be beneficial to the clinical status. Periodontal recall may be addressed from 1 to 3 months after the therapy to avoid bacterial re-colonization. Suppressing bacterial dysbiosis and regulating periodontal homeostasis are the main key in managing periodontal treatment.<\/jats:p>","DOI":"10.3390\/dj14080532","type":"journal-article","created":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T08:14:01Z","timestamp":1787300041000},"page":"532","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Oral Microbiome Signatures in Indonesian Healthy, Gingivitis, and Periodontitis Subjects: A 16S rRNA Next-Generation Sequencing Analysis-Based Exploratory Study"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5976-430X","authenticated-orcid":false,"given":"Benso","family":"Sulijaya","sequence":"first","affiliation":[{"name":"Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Salemba Raya No. 4, Jakarta 10430, Indonesia"},{"name":"Dental Division, Universitas Indonesia Hospital, Depok 16424, Indonesia"},{"name":"Basic, Translational, and Clinical Research in Periodontology Group, Faculty of Dentistry, Universitas Indonesia, Jakarta 10430, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melinda Rabekka","family":"Purba","sequence":"additional","affiliation":[{"name":"Periodontology Specialist Program, Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Jakarta 10430, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mardikacandra Manggala","family":"Putra","sequence":"additional","affiliation":[{"name":"Periodontology Specialist Program, Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Jakarta 10430, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8767-0941","authenticated-orcid":false,"given":"Fatimah Maria","family":"Tadjoedin","sequence":"additional","affiliation":[{"name":"Department of Periodontology, Faculty of Dentistry, Universitas Indonesia, Salemba Raya No. 4, Jakarta 10430, Indonesia"},{"name":"Basic, Translational, and Clinical Research in Periodontology Group, Faculty of Dentistry, Universitas Indonesia, Jakarta 10430, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,21]]},"reference":[{"key":"ref_1","first-page":"S5","article-title":"Principles in prevention of periodontal diseases: Consensus report of group 1 of the 11th European Workshop on Periodontology on effective prevention of periodontal and peri-implant diseases","volume":"42","author":"Tonetti","year":"2015","journal-title":"J. Clin. Periodontol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Lenartova, M., Tesinska, B., Janatova, T., Hrebicek, O., Mysak, J., Janata, J., and Najmanova, L. (2021). The Oral Microbiome in Periodontal Health. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.629723"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1111\/jre.12436","article-title":"Impact of periodontal disease on quality of life: A systematic review","volume":"52","author":"Ferreira","year":"2017","journal-title":"J. Periodontal Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1176","DOI":"10.1038\/ismej.2011.191","article-title":"Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing","volume":"6","author":"Griffen","year":"2012","journal-title":"ISME J."},{"key":"ref_5","first-page":"211","article-title":"Polymicrobial dysbioses: The concepts and the evidence","volume":"19","author":"Hajishengallis","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1111\/j.2041-1014.2012.00663.x","article-title":"Beyond the red complex and into more complexity: The polymicrobial synergy and dysbiosis (PSD) model of periodontal disease etiology","volume":"27","author":"Hajishengallis","year":"2012","journal-title":"Mol. Oral Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1111\/j.1600-051X.1998.tb02419.x","article-title":"Microbial complexes in subgingival plaque","volume":"25","author":"Socransky","year":"1998","journal-title":"J. Clin. Periodontol."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Fernandes, G.V.O., Mosley, G.A., Ross, W., Dagher, A., Martins, B.G.D.S., and Fernandes, J.C.H. (2024). Revisiting Socransky\u2019s Complexes: A Review Suggesting Updated New Bacterial Clusters (GF-MoR Complexes) for Periodontal and Peri-Implant Diseases and Conditions. Microorganisms, 12.","DOI":"10.20944\/preprints202410.1812.v1"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"eaau3333","DOI":"10.1126\/sciadv.aau3333","article-title":"Porphyromonas gingivalis in Alzheimer\u2019s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors","volume":"5","author":"Dominy","year":"2019","journal-title":"Sci. Adv."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1038\/s41396-017-0037-1","article-title":"Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy","volume":"12","author":"Chen","year":"2018","journal-title":"ISME J."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1002\/JPER.22-0749","article-title":"Longitudinal changes in subgingival biofilm composition following periodontal treatment","volume":"94","author":"Johnston","year":"2023","journal-title":"J. Periodontol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1111\/odi.13405","article-title":"Using next-generation sequencing to detect oral microbiome change following periodontal interventions: A systematic review","volume":"27","author":"Zhang","year":"2021","journal-title":"Oral Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1111\/jcpe.13177","article-title":"Microbiome in maintained periodontitis and its shift over a single maintenance interval of 3 months","volume":"46","author":"Lu","year":"2019","journal-title":"J. Clin. Periodontol."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Golub, L.M., Lee, H.M., Bacigalupo, J., and Gu, Y. (2024). Host modulation therapy in periodontitis, diagnosis and treatment-status update. Front. Dent. Med., 5.","DOI":"10.3389\/fdmed.2024.1423401"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/jcpe.12650","article-title":"Risk factors in periodontology: A conceptual framework","volume":"44","author":"Bouchard","year":"2017","journal-title":"J. Clin. Periodontol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"S74","DOI":"10.1002\/JPER.17-0719","article-title":"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","volume":"89","author":"Chapple","year":"2018","journal-title":"J. Periodontol."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"S106","DOI":"10.1902\/jop.2013.1340011","article-title":"Diabetes and periodontal diseases: Consensus report of the Joint EFP\/AAP Workshop on Periodontitis and Systemic Diseases","volume":"84","author":"Chapple","year":"2013","journal-title":"J. Periodontol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/nri3785","article-title":"Periodontitis: From Microbial Immune Subversion to Systemic Inflammation","volume":"15","author":"Hajishengallis","year":"2015","journal-title":"Nat. Rev. Immunol."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Chatzopoulos, G.S., Jiang, Z., Marka, N., and Wolff, L.F. (2023). Relationship of Medication Intake and Systemic Conditions with Periodontitis: A Retrospective Study. J. Pers. Med., 13.","DOI":"10.3390\/jpm13101480"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Kopra, E., Lahdentausta, L., Pieti\u00e4inen, M., Buhlin, K., M\u00e4ntyl\u00e4, P., H\u00f6rkk\u00f6, S., Persson, R., Paju, S., Sinisalo, J., and Salminen, A. (2021). Systemic Antibiotics Influence Periodontal Parameters and Oral Microbiota, But Not Serological Markers. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.774665"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"16870","DOI":"10.1038\/s41598-021-96495-1","article-title":"Oral microflora and pregnancy: A systematic review and meta-analysis","volume":"11","author":"Jang","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1111\/prd.12386","article-title":"Oral microbiome shifts during pregnancy and adverse pregnancy outcomes: Hormonal and Immunologic changes at play","volume":"87","author":"Ye","year":"2021","journal-title":"Periodontology"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1111\/1758-2229.12684","article-title":"Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment","volume":"11","author":"Bahram","year":"2019","journal-title":"Environ. Microbiol. Rep."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1186\/s13059-019-1727-y","article-title":"Performance of neural network basecalling tools for Oxford Nanopore sequencing","volume":"20","author":"Wick","year":"2019","journal-title":"Genome Biol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2666","DOI":"10.1093\/bioinformatics\/bty149","article-title":"NanoPack: Visualizing and processing long-read sequencing data","volume":"34","author":"Schultz","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3209","DOI":"10.1038\/s41598-020-59771-0","article-title":"A preliminary study on the potential of nanopore minion and illumina miseq 16S rRNA gene sequencing to characterize building-dust microbiomes","volume":"10","author":"Nygaard","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1093\/bioinformatics\/btz715","article-title":"Pavian: Interactive analysis of metagenomics data for micro-biome studies and pathogen identification","volume":"36","author":"Breitwieser","year":"2020","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Ondov, B.D., Bergman, N.H., and Phillippy, A.M. (2011). Interactive metagenomic visualization in a web browser. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-385"},{"key":"ref_29","unstructured":"Oksanen, J., Simpson, G.L., Blanchet, F.G., Kindt, R., Legendre, P., Minchin, P.R., Friendly, M., McGlin, D., O\u2019Hara, R.B., and Solymos, P. (2025, November 01). Vegan: Community Ecology Package. R Package Version 2.4-3. Available online: https:\/\/www.researchgate.net\/publication\/323265822_vegan_Community_Ecology_Package_R_package_version_24-3_2017_accessed_2016_Jan_1."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"R\u00f8sland, A., Amin, H., Lie, S.A., Malinovschi, A., Bun\u00e6s, D.F., and Bertelsen, R.J. (2025). Effect of periodontal therapy on the oral microbiome and lung function: An intervention study. Front. Cell. Infect. Microbiol., 16.","DOI":"10.3389\/fcimb.2026.1725666"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Ham, H., and Park, T. (2022). Combining p-values from various statistical methods for microbiome data. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.990870"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1186\/s13059-016-1086-x","article-title":"Tiny microbes, enormous impacts: What matters in gut microbiome studies?","volume":"17","author":"Debelius","year":"2016","journal-title":"Genome Biol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Jiang, L., Zhang, J., Fang, M., Qin, Y., Huang, Y., and Tao, R. (2022). Analysis of subgingival micro-organisms based on multi-omics and Treg\/Th17 balance in type 2 diabetes with\/without periodontitis. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.939608"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1111\/jre.12645","article-title":"No differences in microbiome changes between anti-adhesive and antibacterial ingredients in toothpastes during periodontal therapy","volume":"54","author":"Hagenfeld","year":"2019","journal-title":"J. Periodontal Res."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Rajasekaran, J.J., Krishnamurthy, H.K., Bosco, J., Jayaraman, V., Krishna, K., Wang, T., and Bei, K. (2024). Oral microbiome: A review of its impact on oral and systemic health. Microorganisms, 12.","DOI":"10.20944\/preprints202406.1923.v1"},{"key":"ref_36","first-page":"437","article-title":"Understanding caries from the oral microbiome perspective","volume":"44","author":"Tanner","year":"2016","journal-title":"J. Calif. Dent. Assoc."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e163","DOI":"10.52225\/narra.v3i2.163","article-title":"Clinical and oral microbiome pattern of halitosis patients with periodontitis and gingivitis","volume":"3","author":"Ningsih","year":"2023","journal-title":"Narra J."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1111\/jre.70046","article-title":"Oral Microbiome Signatures in Periodontitis and Edentulism-A Population-Based Study","volume":"60","author":"Balan","year":"2025","journal-title":"J. Periodontal Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2372206","DOI":"10.1080\/20002297.2024.2372206","article-title":"Effect of mobile app-based oral hygiene instructions on clinical parameters, oral bacterial diversity, and composition of subgingival microbiota in periodontitis patients","volume":"16","author":"Purba","year":"2024","journal-title":"J. Oral Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"\u0141asica, A., Golec, P., Laskus, A., Zalewska, M., G\u0119daj, M., and Popowska, M. (2024). Periodontitis: Etiology, conventional treatments, and emerging bacteriophage and predatory bacteria therapies. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1469414"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Cui, Z., Wang, P., and Gao, W. (2025). Microbial dysbiosis in periodontitis and peri-implantitis: Pathogenesis, immune responses, and therapeutic. Front. Cell. Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1517154"},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Wang, J., Geng, Y., Guo, J., Peng, J., Xu, H., Zhao, B., Huang, S., Qin, M., Du, W., and Tian, J. (2025). The Subgingival Microbial Composition in Health and Periodontitis with Different Probing Depths. Microorganisms, 13.","DOI":"10.3390\/microorganisms13040930"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Amato, M., Polizzi, A., Viglianisi, G., Leonforte, F., Mascitti, M., and Isola, G. (2025). Impact of periodontitis and oral dysbiosis metabolites in the modulation of accelerating ageing and human senescence. Metabolites, 15.","DOI":"10.3390\/metabo15010035"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Mehrnia, A. (2025). Microbial dysbiosis and immune dysregulation in periodontitis and peri-implantitis. Front. Cell. Infect. Microbiol., 15.","DOI":"10.3389\/fcimb.2025.1678163"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"S173","DOI":"10.1002\/JPER.17-0721","article-title":"Periodontitis: Consensus report of workgroup 2 of the 2017 World Workshop on the Classification of Periodontal and Peri-Implant Diseases and Conditions","volume":"89","author":"Papapanou","year":"2018","journal-title":"J. Periodontol."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Zhao, Z.Z., Shan, W., Sun, X., Cheng, T., Zhang, J., and Chu, C.H. (2025). Quorum-Quenching AHL-Lactonase Est816 Inhibits Polymicrobial Subgingival-Plaque-Derived Biofilm Formation. Dent. J., 13.","DOI":"10.3390\/dj13080372"}],"container-title":["Dentistry Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-6767\/14\/8\/532\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T10:37:49Z","timestamp":1787567869000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-6767\/14\/8\/532"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,21]]},"references-count":46,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["dj14080532"],"URL":"https:\/\/doi.org\/10.3390\/dj14080532","relation":{},"ISSN":["2304-6767"],"issn-type":[{"value":"2304-6767","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,21]]}}}