{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T11:06:41Z","timestamp":1784804801568,"version":"3.55.0"},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T00:00:00Z","timestamp":1765584000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T00:00:00Z","timestamp":1768780800000},"content-version":"vor","delay-in-days":37,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/100023003","name":"NITTE University","doi-asserted-by":"publisher","award":["N(DU)\/RD\/NUFR 1Grant\/ABSMIDS\/2021-22\/01-1"],"award-info":[{"award-number":["N(DU)\/RD\/NUFR 1Grant\/ABSMIDS\/2021-22\/01-1"]}],"id":[{"id":"10.13039\/100023003","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Oral Health"],"DOI":"10.1186\/s12903-025-07175-9","type":"journal-article","created":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T09:34:10Z","timestamp":1765618450000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing"],"prefix":"10.1186","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8045-1893","authenticated-orcid":false,"given":"Preethesh","family":"Shetty","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1173-0802","authenticated-orcid":false,"given":"Raksha","family":"Bhat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2851-0080","authenticated-orcid":false,"given":"Shruthi","family":"Padavu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3695-4178","authenticated-orcid":false,"given":"Praveen","family":"Rai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7821-7419","authenticated-orcid":false,"given":"Krishna Kumar","family":"B","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8097-6024","authenticated-orcid":false,"given":"Shishir","family":"Shetty","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,12,13]]},"reference":[{"key":"7175_CR1","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1016\/j.micinf.2015.03.014","volume":"17","author":"AE Duran-Pinedo","year":"2015","unstructured":"Duran-Pinedo AE, Frias-Lopez J. Beyond microbial community composition: functional activities of the oral Microbiome in health and disease. Microbes Infect. 2015;17:505. https:\/\/doi.org\/10.1016\/j.micinf.2015.03.014.","journal-title":"Microbes Infect"},{"key":"7175_CR2","doi-asserted-by":"publisher","first-page":"340","DOI":"10.1016\/0030-4220(65)90166-0","volume":"20","author":"S Kakehashi","year":"1965","unstructured":"Kakehashi S, Stanley HR, Fitzgerald RJ. The effects of surgical exposures of dental pulps in germ-free and conventional laboratory rats. Oral Surg Oral Med Oral Pathol. 1965;20:340. https:\/\/doi.org\/10.1016\/0030-4220(65)90166-0.","journal-title":"Oral Surg Oral Med Oral Pathol"},{"key":"7175_CR3","doi-asserted-by":"publisher","first-page":"216","DOI":"10.4161\/21505594.2014.984567","volume":"6","author":"M Zehnder","year":"2015","unstructured":"Zehnder M, Belibasakis GN. On the dynamics of root Canal infections-what we understand and what we don\u2019t. Virulence. 2015;6:216. https:\/\/doi.org\/10.4161\/21505594.2014.984567.","journal-title":"Virulence"},{"key":"7175_CR4","doi-asserted-by":"publisher","first-page":"1474466","DOI":"10.3389\/fimmu.2024.1474466","volume":"15","author":"S Pohl","year":"2024","unstructured":"Pohl S, Akamp T, Smeda M, Uderhardt S, Besold D, Krastl G, et al. Understanding dental pulp inflammation: from signaling to structure. Front Immunol. 2024;15:1474466. https:\/\/doi.org\/10.3389\/fimmu.2024.1474466.","journal-title":"Front Immunol"},{"key":"7175_CR5","doi-asserted-by":"publisher","first-page":"2099","DOI":"10.1007\/s00784-019-03075-9","volume":"24","author":"N Zargar","year":"2020","unstructured":"Zargar N, Ashraf H, Marashi SMA, Sabeti M, Aziz A. Identification of microorganisms in irreversible pulpitis and primary endodontic infections with respect to clinical and radiographic findings. Clin Oral Investig. 2020;24:2099. https:\/\/doi.org\/10.1007\/s00784-019-03075-9.","journal-title":"Clin Oral Investig"},{"key":"7175_CR6","unstructured":"Trowbridge H, Kim S, Suda H. Structure and functions of the dentin-pulp complex. In: Cohen S, Burns RC, editors. Pathways of the Pulp. 8th ed. St. Louis (MO): Mosby; 2002. p. 411\u2013457. ISBN: 0-323-01162-4."},{"issue":"3","key":"7175_CR7","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1016\/S0099-2399(81)80122-7","volume":"7","author":"G Bergenholtz","year":"1981","unstructured":"Bergenholtz G. Inflammatory response of the dental pulp to bacterial irritation. J Endod. 1981;7(3):100\u20134. https:\/\/doi.org\/10.1016\/S0099-2399(81)80122-7.","journal-title":"J Endod"},{"issue":"11","key":"7175_CR8","doi-asserted-by":"publisher","first-page":"e0167289","DOI":"10.1371\/journal.pone.0167289","volume":"11","author":"DK Rechenberg","year":"2016","unstructured":"Rechenberg DK, Galicia JC, Peters OA. Biological markers for pulpal inflammation: A systematic review. PLoS ONE. 2016;11(11):e0167289. https:\/\/doi.org\/10.1371\/journal.pone.0167289.","journal-title":"PLoS ONE"},{"key":"7175_CR9","doi-asserted-by":"publisher","first-page":"1336","DOI":"10.1111\/iej.12953","volume":"51","author":"G S\u00e1nchez-Sanhueza","year":"2018","unstructured":"S\u00e1nchez-Sanhueza G, Bello-Toledo H, Gonz\u00e1lez-Rocha G, Gon\u00e7alves AT, Valenzuela V, Gallardo-Esc\u00e1rate C. Metagenomic study of bacterial microbiota in persistent endodontic infections using Next-generation sequencing. Int Endod J. 2018;51:1336. https:\/\/doi.org\/10.1111\/iej.12953.","journal-title":"Int Endod J"},{"key":"7175_CR10","doi-asserted-by":"publisher","first-page":"21077","DOI":"10.3402\/jom.v5i0.21077","volume":"5","author":"JF Siqueira Jr","year":"2013","unstructured":"Siqueira JF Jr, R\u00f4\u00e7as IN. As-yet-uncultivated oral bacteria: breadth and association with oral and extra-oral diseases. J Oral Microbiol. 2013;5:21077. https:\/\/doi.org\/10.3402\/jom.v5i0.21077.","journal-title":"J Oral Microbiol"},{"key":"7175_CR11","doi-asserted-by":"publisher","first-page":"922","DOI":"10.1016\/j.joen.2011.04.007","volume":"37","author":"AC Ribeiro","year":"2011","unstructured":"Ribeiro AC, Matarazzo F, Faveri M, Zezell DM, Mayer MP. Exploring bacterial diversity of endodontic microbiota by cloning and sequencing 16S rRNA. J Endod. 2011;37:922. https:\/\/doi.org\/10.1016\/j.joen.2011.04.007.","journal-title":"J Endod"},{"key":"7175_CR12","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1177\/154405910608500814","volume":"85","author":"F Foschi","year":"2006","unstructured":"Foschi F, Izard J, Sasaki H, et al. Treponema denticola in disseminating endodontic infections. J Dent Res. 2006;85:761\u20135. https:\/\/doi.org\/10.1177\/154405910608500814.","journal-title":"J Dent Res"},{"key":"7175_CR13","doi-asserted-by":"publisher","first-page":"1964277","DOI":"10.1080\/20002297.2021.1964277","volume":"13","author":"KS Fakhruddin","year":"2021","unstructured":"Fakhruddin KS, Perera Samaranayake L, Egusa H, Ngo HC, Pesee S. Profuse diversity and acidogenicity of the candida-biome of deep carious lesions of severe early childhood caries (S-ECC). J Oral Microbiol. 2021;13:1964277. https:\/\/doi.org\/10.1080\/20002297.2021.1964277.","journal-title":"J Oral Microbiol"},{"key":"7175_CR14","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","volume":"20","author":"CY Chiu","year":"2019","unstructured":"Chiu CY, Miller SA. Clinical metagenomics. Nat Rev Genet. 2019;20:341\u201355. https:\/\/doi.org\/10.1038\/s41576-019-0113-7.","journal-title":"Nat Rev Genet"},{"issue":"Suppl 1","key":"7175_CR15","doi-asserted-by":"publisher","first-page":"5","DOI":"10.4137\/EBO.S36436","volume":"12","author":"V Aguiar-Pulido","year":"2016","unstructured":"Aguiar-Pulido V, Huang W, Suarez-Ulloa V, Cickovski T, Mathee K, Narasimhan G. Metagenomics, Metatranscriptomics, and metabolomics approaches for Microbiome analysis. Evol Bioinform Online. 2016;12(Suppl 1):5\u201316. https:\/\/doi.org\/10.4137\/EBO.S36436.","journal-title":"Evol Bioinform Online"},{"key":"7175_CR16","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1038\/s41597-022-01762-z","volume":"9","author":"V Meslier","year":"2022","unstructured":"Meslier V, Quinquis B, Da Silva K, et al. Benchmarking second and third-generation sequencing platforms for microbial metagenomics. Sci Data. 2022;9:694. https:\/\/doi.org\/10.1038\/s41597-022-01762-z.","journal-title":"Sci Data"},{"key":"7175_CR17","doi-asserted-by":"publisher","first-page":"1482","DOI":"10.1111\/iej.13542","volume":"54","author":"V Nagendrababu","year":"2021","unstructured":"Nagendrababu V, Murray PE, Ordinola-Zapata R, Peters OA, R\u00f4\u00e7as IN, Siqueira JF Jr, et al. PRILE 2021 guidelines for reporting laboratory studies in endodontology: A consensus-based development. Int Endod J. 2021;54:1482. https:\/\/doi.org\/10.1111\/iej.13542.","journal-title":"Int Endod J"},{"key":"7175_CR18","doi-asserted-by":"publisher","first-page":"1491","DOI":"10.1111\/iej.13565","volume":"54","author":"V Nagendrababu","year":"2021","unstructured":"Nagendrababu V, Murray PE, Ordinola-Zapata R, Peters OA, R\u00f4\u00e7as IN, Siqueira JF Jr, et al. PRILE 2021 guidelines for reporting laboratory studies in endodontology: explanation and elaboration. Int Endod J. 2021;54:1491. https:\/\/doi.org\/10.1111\/iej.13565.","journal-title":"Int Endod J"},{"key":"7175_CR19","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1016\/j.joen.2020.12.009","volume":"47","author":"S Zahran","year":"2021","unstructured":"Zahran S, Witherden E, Mannocci F, Koller G. Characterization of root Canal microbiota in teeth diagnosed with irreversible pulpitis. J Endod. 2021;47:415\u201323. https:\/\/doi.org\/10.1016\/j.joen.2020.12.009.","journal-title":"J Endod"},{"key":"7175_CR20","doi-asserted-by":"publisher","unstructured":"Glickman GN. AAE Consensus Conference on Diagnostic Terminology: background and perspectives. J Endod. 2009;35:1619.\u00a0https:\/\/doi.org\/10.1016\/j.joen.2009.09.029.","DOI":"10.1016\/j.joen.2009.09.029"},{"issue":"8","key":"7175_CR21","doi-asserted-by":"publisher","first-page":"1411","DOI":"10.1093\/bioinformatics\/btx617","volume":"34","author":"N Weber","year":"2018","unstructured":"Weber N, Liou D, Dommer J, et al. Nephele: a cloud platform for simplified, standardized and reproducible Microbiome data analysis. Bioinformatics. 2018;34(8):1411\u20133. https:\/\/doi.org\/10.1093\/bioinformatics\/btx617.","journal-title":"Bioinformatics"},{"key":"7175_CR22","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/s41597-023-02877-7","volume":"11","author":"EM Valencia","year":"2024","unstructured":"Valencia EM, Maki KA, Dootz JN, Barb JJ. Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines. Sci Data. 2024;11:81. https:\/\/doi.org\/10.1038\/s41597-023-02877-7.","journal-title":"Sci Data"},{"key":"7175_CR23","doi-asserted-by":"publisher","first-page":"2445","DOI":"10.1128\/AEM.01754-09","volume":"76","author":"D Nichols","year":"2010","unstructured":"Nichols D, Cahoon N, Trakhtenberg EM, Pham L, Mehta A, Belanger A, et al. Use of Ichip for high-throughput in situ cultivation of uncultivable microbial species. Appl Environ Microbiol. 2010;76:2445. https:\/\/doi.org\/10.1128\/AEM.01754-09.","journal-title":"Appl Environ Microbiol"},{"key":"7175_CR24","doi-asserted-by":"publisher","first-page":"e28088","DOI":"10.1371\/journal.pone.0028088","volume":"6","author":"AL Santos","year":"2011","unstructured":"Santos AL, Siqueira JF Jr, R\u00f4\u00e7as IN, Jesus EC, Rosado AS, Tiedje JM. Comparing the bacterial diversity of acute and chronic dental root Canal infections. PLoS ONE. 2011;6:e28088. https:\/\/doi.org\/10.1371\/journal.pone.0028088.","journal-title":"PLoS ONE"},{"key":"7175_CR25","doi-asserted-by":"publisher","first-page":"1499","DOI":"10.1016\/j.joen.2011.08.012","volume":"37","author":"JF Siqueira Jr","year":"2011","unstructured":"Siqueira JF Jr, Alves FR, R\u00f4\u00e7as IN. Pyrosequencing analysis of the apical root Canal microbiota. J Endod. 2011;37:1499. https:\/\/doi.org\/10.1016\/j.joen.2011.08.012.","journal-title":"J Endod"},{"key":"7175_CR26","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1016\/j.joen.2015.03.010","volume":"41","author":"GN Tzanetakis","year":"2015","unstructured":"Tzanetakis GN, Azcarate-Peril MA, Zachaki S, Panopoulos P, Kontakiotis EG, Madianos PN, et al. Comparison of bacterial community composition of primary and persistent endodontic infections using pyrosequencing. J Endod. 2015;41:1226. https:\/\/doi.org\/10.1016\/j.joen.2015.03.010.","journal-title":"J Endod"},{"issue":"Suppl 2","key":"7175_CR27","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1186\/s12864-019-5474-y","volume":"20","author":"W Qian","year":"2019","unstructured":"Qian W, Ma T, Ye M, Li Z, Liu Y, Hao P. Microbiota in the apical root Canal system of tooth with apical periodontitis. BMC Genomics. 2019;20(Suppl 2):189. https:\/\/doi.org\/10.1186\/s12864-019-5474-y.","journal-title":"BMC Genomics"},{"key":"7175_CR28","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1016\/j.joen.2020.05.004","volume":"46","author":"LCL Nardello","year":"2020","unstructured":"Nardello LCL, Amado PPP, Franco DC, Cazares RXR, Nogales CG, Mayer MPA, et al. Next-Generation sequencing to assess potentially active bacteria in endodontic infections. J Endod. 2020;46:1105. https:\/\/doi.org\/10.1016\/j.joen.2020.05.004.","journal-title":"J Endod"},{"key":"7175_CR29","doi-asserted-by":"publisher","first-page":"e15406","DOI":"10.1371\/journal.pone.0015406","volume":"5","author":"GB Gloor","year":"2010","unstructured":"Gloor GB, Hummelen R, Macklaim JM, Dickson RJ, Fernandes AD, MacPhee R, et al. Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products. PLoS ONE. 2010;5:e15406. https:\/\/doi.org\/10.1371\/journal.pone.0015406.","journal-title":"PLoS ONE"},{"key":"7175_CR30","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1111\/j.2041-1014.2012.00642.x","volume":"27","author":"PI Diaz","year":"2012","unstructured":"Diaz PI, Dupuy AK, Abusleme L, Reese B, Obergfell C, Choquette L, et al. Using high throughput sequencing to explore the biodiversity in oral bacterial communities. Mol Oral Microbiol. 2012;27:182. https:\/\/doi.org\/10.1111\/j.2041-1014.2012.00642.x.","journal-title":"Mol Oral Microbiol"},{"key":"7175_CR31","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1016\/j.mimet.2013.08.011","volume":"95","author":"JM Di Bella","year":"2013","unstructured":"Di Bella JM, Bao Y, Gloor GB, Burton JP, Reid G. High throughput sequencing methods and analysis for Microbiome research. J Microbiol Methods. 2013;95:401. https:\/\/doi.org\/10.1016\/j.mimet.2013.08.011.","journal-title":"J Microbiol Methods"},{"key":"7175_CR32","doi-asserted-by":"publisher","first-page":"100391","DOI":"10.1016\/j.crmeth.2022.100391","volume":"3","author":"CC Sollecito","year":"2023","unstructured":"Sollecito CC, Vazquez-Baeza Y, Shaffer JP, Gellman MD, Talavera GA, Daviglus ML, et al. Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies. Cell Rep Methods. 2023;3:100391. https:\/\/doi.org\/10.1016\/j.crmeth.2022.100391.","journal-title":"Cell Rep Methods"},{"key":"7175_CR33","doi-asserted-by":"publisher","first-page":"e1900060","DOI":"10.1002\/prca.201900060","volume":"14","author":"D Manoil","year":"2020","unstructured":"Manoil D, Al-Manei K, Belibasakis GN. A systematic review of the root Canal microbiota associated with apical periodontitis: lessons from Next-Generation sequencing. Proteom Clin Appl. 2020;14:e1900060. https:\/\/doi.org\/10.1002\/prca.201900060.","journal-title":"Proteom Clin Appl"},{"key":"7175_CR34","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1111\/j.1365-2591.2011.02006.x","volume":"45","author":"AR Ozok","year":"2012","unstructured":"Ozok AR, Persoon IF, Huse SM, Keijser BJ, Wesselink PR, Crielaard W, et al. Ecology of the Microbiome of the infected root Canal system: a comparison between apical and coronal root segments. Int Endod J. 2012;45:530. https:\/\/doi.org\/10.1111\/j.1365-2591.2011.02006.x.","journal-title":"Int Endod J"},{"key":"7175_CR35","doi-asserted-by":"publisher","first-page":"1975","DOI":"10.1016\/j.joen.2015.08.022","volume":"41","author":"BP Gomes","year":"2015","unstructured":"Gomes BP, Berber VB, Kokaras AS, Chen T, Paster BJ. Microbiomes of Endodontic-Periodontal lesions before and after chemomechanical Preparation. J Endod. 2015;41:1975. https:\/\/doi.org\/10.1016\/j.joen.2015.08.022.","journal-title":"J Endod"},{"key":"7175_CR36","doi-asserted-by":"publisher","first-page":"e0162887","DOI":"10.1371\/journal.pone.0162887","volume":"11","author":"JF Siqueira Jr","year":"2016","unstructured":"Siqueira JF Jr, Antunes HS, R\u00f4\u00e7as IN, Rachid CT, Alves FR. Microbiome in the apical root Canal system of teeth with Post-Treatment apical periodontitis. PLoS ONE. 2016;11:e0162887. https:\/\/doi.org\/10.1371\/journal.pone.0162887.","journal-title":"PLoS ONE"},{"key":"7175_CR37","doi-asserted-by":"publisher","first-page":"1080","DOI":"10.1016\/j.joen.2018.04.003","volume":"44","author":"JM Shin","year":"2018","unstructured":"Shin JM, Luo T, Lee KH, Guerreiro D, Botero TM, McDonald NJ, et al. Deciphering endodontic microbial communities by Next-generation sequencing. J Endod. 2018;44:1080. https:\/\/doi.org\/10.1016\/j.joen.2018.04.003.","journal-title":"J Endod"},{"key":"7175_CR38","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1016\/j.joen.2012.06.037","volume":"38","author":"MH Saber","year":"2012","unstructured":"Saber MH, Schwarzberg K, Alonaizan FA, Kelley ST, Sedghizadeh PP, Furlan M, et al. Bacterial flora of dental periradicular lesions analyzed by the 454-pyrosequencing technology. J Endod. 2012;38:1484. https:\/\/doi.org\/10.1016\/j.joen.2012.06.037.","journal-title":"J Endod"},{"key":"7175_CR39","doi-asserted-by":"publisher","first-page":"31","DOI":"10.4161\/bact.1.1.14942","volume":"1","author":"MR Clokie","year":"2011","unstructured":"Clokie MR, Millard AD, Letarov AV, Heaphy S. Phages in nature. Bacteriophage. 2011;1:31. https:\/\/doi.org\/10.4161\/bact.1.1.14942.","journal-title":"Bacteriophage"},{"key":"7175_CR40","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1177\/0022034517731758","volume":"97","author":"L Eriksson","year":"2018","unstructured":"Eriksson L, Lif Holgerson P, Esberg A, Johansson I. Microbial complexes and caries in 17-Year-Olds with and without Streptococcus mutans. J Dent Res. 2018;97:275. https:\/\/doi.org\/10.1177\/0022034517731758.","journal-title":"J Dent Res"},{"key":"7175_CR41","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1159\/000344022","volume":"47","author":"D Wolff","year":"2013","unstructured":"Wolff D, Frese C, Maier-Kraus T, Krueger T, Wolff B. Bacterial biofilm composition in caries and caries-free subjects. Caries Res. 2013;47:69. https:\/\/doi.org\/10.1159\/000344022.","journal-title":"Caries Res"},{"key":"7175_CR42","doi-asserted-by":"publisher","first-page":"e103712","DOI":"10.1371\/journal.pone.0103712","volume":"9","author":"J Obata","year":"2014","unstructured":"Obata J, Takeshita T, Shibata Y, Yamanaka W, Unemori M, Akamine A, et al. Identification of the microbiota in carious dentin lesions using 16S rRNA gene sequencing. PLoS ONE. 2014;9:e103712. https:\/\/doi.org\/10.1371\/journal.pone.0103712.","journal-title":"PLoS ONE"},{"key":"7175_CR43","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.joen.2018.11.017","volume":"45","author":"J Zheng","year":"2019","unstructured":"Zheng J, Wu Z, Niu K, Xie Y, Hu X, Fu J, et al. Microbiome of deep dentinal caries from reversible pulpitis to irreversible pulpitis. J Endod. 2019;45:302. https:\/\/doi.org\/10.1016\/j.joen.2018.11.017.","journal-title":"J Endod"},{"key":"7175_CR44","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1016\/j.joen.2020.02.011","volume":"46","author":"C Sun","year":"2020","unstructured":"Sun C, Xie Y, Hu X, Fu J, Zhou J, Wu L. Relationship between clinical symptoms and the microbiota in advanced caries. J Endod. 2020;46:763. https:\/\/doi.org\/10.1016\/j.joen.2020.02.011.","journal-title":"J Endod"},{"key":"7175_CR45","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1111\/j.1399-302X.2006.00270.x","volume":"21","author":"M Sakamoto","year":"2006","unstructured":"Sakamoto M, R\u00f4\u00e7as IN, Siqueira JF Jr, Benno Y. Molecular analysis of bacteria in asymptomatic and symptomatic endodontic infections. Oral Microbiol Immunol. 2006;21:112. https:\/\/doi.org\/10.1111\/j.1399-302X.2006.00270.x.","journal-title":"Oral Microbiol Immunol"},{"key":"7175_CR46","doi-asserted-by":"publisher","first-page":"11253","DOI":"10.1038\/s41598-025-95522-9","volume":"15","author":"DH Park","year":"2025","unstructured":"Park DH, Tak EJ, Park OJ, Perinpanayagam H, Yoo YJ, Lee HJ, et al. Association between root canals and gingival sulci microbiota in secondary and persistent endodontic infections. Sci Rep. 2025;15:11253. https:\/\/doi.org\/10.1038\/s41598-025-95522-9.","journal-title":"Sci Rep"},{"key":"7175_CR47","doi-asserted-by":"publisher","first-page":"995","DOI":"10.1007\/s00784-023-04882-x","volume":"27","author":"B Kesim","year":"2023","unstructured":"Kesim B, \u00dclger ST, Aslan G, Cudal H, \u00dcst\u00fcn Y, K\u00fc\u00e7\u00fck M\u00d6. Amplicon-based next-generation sequencing for comparative analysis of root Canal Microbiome of teeth with primary and persistent\/secondary endodontic infections. Clin Oral Investig. 2023;27:995. https:\/\/doi.org\/10.1007\/s00784-023-04882-x.","journal-title":"Clin Oral Investig"},{"key":"7175_CR48","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1016\/j.joen.2017.03.019","volume":"43","author":"C Keskin","year":"2017","unstructured":"Keskin C, Demiry\u00fcrek E\u00d6, Onuk EE. Pyrosequencing analysis of cryogenically ground samples from primary and Secondary\/Persistent endodontic infections. J Endod. 2017;43:1309. https:\/\/doi.org\/10.1016\/j.joen.2017.03.019.","journal-title":"J Endod"},{"key":"7175_CR49","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1067\/moe.2000.106576","volume":"89","author":"JF Siqueira Jr","year":"2000","unstructured":"Siqueira JF Jr, R\u00f4\u00e7as IN, Souto R, de Uzeda M, Colombo AP. Checkerboard DNA-DNA hybridization analysis of endodontic infections. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 2000;89:744. https:\/\/doi.org\/10.1067\/moe.2000.106576.","journal-title":"Oral Surg Oral Med Oral Pathol Oral Radiol Endod"},{"key":"7175_CR50","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1034\/j.1600-9657.2000.016005191.x","volume":"16","author":"PT Sunde","year":"2000","unstructured":"Sunde PT, Tronstad L, Eribe ER, Lind PO, Olsen I. Assessment of periradicular microbiota by DNA-DNA hybridization. Endod Dent Traumatol. 2000;16:191. https:\/\/doi.org\/10.1034\/j.1600-9657.2000.016005191.x.","journal-title":"Endod Dent Traumatol"},{"key":"7175_CR51","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1046\/j.1365-2591.1997.00092.x","volume":"30","author":"U Sj\u00f6gren","year":"1997","unstructured":"Sj\u00f6gren U, Figdor D, Persson S, Sundqvist G. Influence of infection at the time of root filling on the outcome of endodontic treatment of teeth with apical periodontitis. Int Endod J. 1997;30:297. https:\/\/doi.org\/10.1046\/j.1365-2591.1997.00092.x.","journal-title":"Int Endod J"},{"key":"7175_CR52","doi-asserted-by":"publisher","first-page":"e84960","DOI":"10.1371\/journal.pone.0084960","volume":"8","author":"AC Anderson","year":"2013","unstructured":"Anderson AC, Al-Ahmad A, Elamin F, Jonas D, Mirghani Y, Schilhabel M, et al. Comparison of the bacterial composition and structure in symptomatic and asymptomatic endodontic infections associated with root-filled teeth using pyrosequencing. PLoS ONE. 2013;8:e84960. https:\/\/doi.org\/10.1371\/journal.pone.0084960.","journal-title":"PLoS ONE"},{"key":"7175_CR53","doi-asserted-by":"publisher","first-page":"2374","DOI":"10.3389\/fmicb.2018.02374","volume":"9","author":"S Bouillaguet","year":"2018","unstructured":"Bouillaguet S, Manoil D, Girard M, Louis J, Ga\u00efa N, Leo S, et al. Root microbiota in primary and secondary apical periodontitis. Front Microbiol. 2018;9:2374. https:\/\/doi.org\/10.3389\/fmicb.2018.02374.","journal-title":"Front Microbiol"},{"key":"7175_CR54","doi-asserted-by":"publisher","first-page":"1778","DOI":"10.1016\/j.joen.2014.06.017","volume":"40","author":"V Vengerfeldt","year":"2014","unstructured":"Vengerfeldt V, \u0160pilka K, Saag M, Preem JK, Oopkaup K, Truu J, et al. Highly diverse microbiota in dental root canals in cases of apical periodontitis (data of illumina sequencing). J Endod. 2014;40:1778. https:\/\/doi.org\/10.1016\/j.joen.2014.06.017.","journal-title":"J Endod"},{"key":"7175_CR55","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1016\/j.joen.2017.11.019","volume":"44","author":"H Zandi","year":"2018","unstructured":"Zandi H, Kristoffersen AK, \u00d8rstavik D, R\u00f4\u00e7as IN, Siqueira JF Jr. Microbial analysis of endodontic infections in Root-filled teeth with apical periodontitis before and after irrigation using pyrosequencing. J Endod. 2018;44:372. https:\/\/doi.org\/10.1016\/j.joen.2017.11.019.","journal-title":"J Endod"},{"key":"7175_CR56","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1111\/j.1365-2591.2008.01537.x","volume":"42","author":"M Zehnder","year":"2009","unstructured":"Zehnder M, Guggenheim B. The mysterious appearance of enterococci in filled root canals. Int Endod J. 2009;42:277. https:\/\/doi.org\/10.1111\/j.1365-2591.2008.01537.x.","journal-title":"Int Endod J"},{"key":"7175_CR57","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1016\/j.joen.2013.05.001","volume":"39","author":"BY Hong","year":"2013","unstructured":"Hong BY, Lee TK, Lim SM, Chang SW, Park J, Han SH, et al. Microbial analysis in primary and persistent endodontic infections by using pyrosequencing. J Endod. 2013;39:1136. https:\/\/doi.org\/10.1016\/j.joen.2013.05.001.","journal-title":"J Endod"}],"container-title":["BMC Oral Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12903-025-07175-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12903-025-07175-9","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12903-025-07175-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T19:35:36Z","timestamp":1768851336000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s12903-025-07175-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,13]]},"references-count":57,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["7175"],"URL":"https:\/\/doi.org\/10.1186\/s12903-025-07175-9","relation":{},"ISSN":["1472-6831"],"issn-type":[{"value":"1472-6831","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,13]]},"assertion":[{"value":"26 May 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 October 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 December 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Ethical clearance was obtained from the Institutional ethical committee of AB Shetty Memorial Institute of Dental Sciences, Nitte DU (ETHICS\/ABSMIDS\/180\/2021). Informed consent was obtained from all patients participating in the study. Written informed consent was obtained from participants in accordance with the Declaration of Helsinki.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"<!--Emphasis Type='Bold' removed-->Ethics approval and consent to participate"}},{"value":"Not Applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"<!--Emphasis Type='Bold' removed-->Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"<!--Emphasis Type='Bold' removed-->Competing interests"}}],"article-number":"118"}}