{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T04:28:29Z","timestamp":1790224109391,"version":"4.1.0"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T00:00:00Z","timestamp":1722384000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T00:00:00Z","timestamp":1722384000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100005957","name":"8020 Promotion Foundation","doi-asserted-by":"publisher","award":["3801"],"award-info":[{"award-number":["3801"]}],"id":[{"id":"10.13039\/501100005957","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005957","name":"8020 Promotion Foundation","doi-asserted-by":"publisher","award":["3801"],"award-info":[{"award-number":["3801"]}],"id":[{"id":"10.13039\/501100005957","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002241","name":"Japan Science and Technology Agency","doi-asserted-by":"publisher","award":["JPMJSP2120"],"award-info":[{"award-number":["JPMJSP2120"]}],"id":[{"id":"10.13039\/501100002241","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["20K09972 and 20KK0209"],"award-info":[{"award-number":["20K09972 and 20KK0209"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Oral Health"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>The global rise in the elderly population has increased the prevalence of root caries. <jats:italic>Streptococcus mutans<\/jats:italic>, <jats:italic>Lactobacilli<\/jats:italic> and <jats:italic>Actinomyces<\/jats:italic> are considered the primary pathogens of dental caries in culture-based studies. This study aimed to investigate bacterial profiles in coronal and root caries lesions and determine the association of specific bacterial genera at each site.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>Dentine samples from carious lesions were collected from 22 extracted teeth using an excavator. Microbial DNA was extracted from the samples using a protocol developed for this study. 16S rRNA gene amplicon sequencing was employed for microbial analysis. PCR amplification targeted the V3-V4 region of the bacterial 16S rRNA, and the amplicon sequencing used an Illumina MiSeq system (2\u2009\u00d7\u2009300\u00a0bp paired-end reads). Statistical analysis was performed by the Phyloseq and DESeq2 packages in R.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>In coronal caries, <jats:italic>Olsenella<\/jats:italic>, <jats:italic>Lactobacillus<\/jats:italic> and <jats:italic>Prevotella<\/jats:italic> were the most prevalent genera, comprising approximately 70% of the microbiome community. In the root caries, however, although <jats:italic>Olsenella<\/jats:italic><jats:italic>, <\/jats:italic><jats:italic>Prevotella<\/jats:italic> and <jats:italic>Lactobacillus<\/jats:italic> remained the dominant genera, they accounted for only half of the microbiome community. This study identified significant differences in alpha diversity indices between the coronal and root caries. LEfSE analysis revealed several unique genera in each caries lesion.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>The microbiome of root caries lesions was richer and more complex than the coronal caries microbiota. The results suggest that lesion-related variations in the oral microflora may be detected in carious dentine.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12903-024-04670-3","type":"journal-article","created":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T19:28:37Z","timestamp":1722454117000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Comparative analysis of microbiome in coronal and root caries"],"prefix":"10.1186","volume":"24","author":[{"given":"Tadamu","family":"Gondo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noriko","family":"Hiraishi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Azusa","family":"Takeuchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Moyes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasushi","family":"Shimada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,7,31]]},"reference":[{"issue":"8","key":"4670_CR1","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1177\/154405910408300810","volume":"83","author":"SO Griffin","year":"2004","unstructured":"Griffin SO, Griffin PM, Swann JL, Zlobin N. Estimating rates of new root caries in older adults. J Dent Res. 2004;83(8):634\u20138.","journal-title":"J Dent Res"},{"key":"4670_CR2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jdent.2018.06.013","volume":"77","author":"N Hariyani","year":"2018","unstructured":"Hariyani N, Setyowati D, Spencer AJ, Luzzi L, Do LG. Root caries incidence and increment in the population - A systematic review, meta-analysis and meta-regression of longitudinal studies. J Dent. 2018;77:1\u20137.","journal-title":"J Dent"},{"issue":"1","key":"4670_CR3","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1186\/s12903-021-01520-4","volume":"21","author":"M Usuga-Vacca","year":"2021","unstructured":"Usuga-Vacca M, Marin-Zuluaga DJ, Castellanos JE, Martignon S. Association between root\/coronal caries and individual factors in institutionalised elderly using ICDAS severity and activity. BMC Oral Health. 2021;21(1):146.","journal-title":"BMC Oral Health"},{"key":"4670_CR4","doi-asserted-by":"publisher","first-page":"103166","DOI":"10.1016\/j.jdent.2019.07.004","volume":"89","author":"J Zhang","year":"2019","unstructured":"Zhang J, Leung KCM, Sardana D, Wong MCM, Lo ECM. Risk predictors of dental root caries: A systematic review. J Dent. 2019;89:103166.","journal-title":"J Dent"},{"issue":"6","key":"4670_CR5","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1159\/000501588","volume":"53","author":"H Meyer-Lueckel","year":"2019","unstructured":"Meyer-Lueckel H, Machiulskiene V, Giacaman RA. How to Intervene in the Root Caries Process? Systematic Review and Meta-Analyses. Caries Res. 2019;53(6):599\u2013608.","journal-title":"Caries Res"},{"issue":"1","key":"4670_CR6","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/s10266-021-00637-w","volume":"110","author":"KJ Park","year":"2022","unstructured":"Park KJ, Mei\u00dfner T, G\u00fcnther E, Schmalz G, Kottmann T, Krause F, et al. Arrest of root caries with an adjuvant chlorhexidine-fluoride varnish over a 12-months observation period: a QLF-analyzed, placebo-controlled, randomized, clinical trial (RCT). Odontology. 2022;110(1):193\u2013202.","journal-title":"Odontology"},{"key":"4670_CR7","doi-asserted-by":"publisher","first-page":"895537","DOI":"10.3389\/fmicb.2022.895537","volume":"13","author":"X Li","year":"2022","unstructured":"Li X, Liu Y, Yang X, Li C, Song Z. The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions. Front Microbiol. 2022;13:895537.","journal-title":"Front Microbiol"},{"issue":"3","key":"4670_CR8","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1159\/000261021","volume":"21","author":"HM Keltjens","year":"1987","unstructured":"Keltjens HM, Schaeken MJ, van der Hoeven JS, Hendriks JC. Microflora of plaque from sound and carious root surfaces. Caries Res. 1987;21(3):193\u20139.","journal-title":"Caries Res"},{"issue":"9","key":"4670_CR9","doi-asserted-by":"publisher","first-page":"1525","DOI":"10.1177\/00220345990780090701","volume":"78","author":"SR Brailsford","year":"1999","unstructured":"Brailsford SR, Tregaskis RB, Leftwich HS, Beighton D. The predominant Actinomyces spp. isolated from infected dentin of active root caries lesions. J Dent Res. 1999;78(9):1525\u201334.","journal-title":"J Dent Res."},{"issue":"19","key":"4670_CR10","doi-asserted-by":"publisher","first-page":"5002","DOI":"10.1128\/JB.00542-10","volume":"192","author":"FE Dewhirst","year":"2010","unstructured":"Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, et al. The human oral microbiome. J Bacteriol. 2010;192(19):5002\u201317.","journal-title":"J Bacteriol"},{"issue":"5","key":"4670_CR11","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1007\/s10096-008-0662-8","volume":"28","author":"D Preza","year":"2009","unstructured":"Preza D, Olsen I, Willumsen T, Boches SK, Cotton SL, Grinde B, et al. Microarray analysis of the microflora of root caries in elderly. Eur J Clin Microbiol Infect Dis. 2009;28(5):509\u201317.","journal-title":"Eur J Clin Microbiol Infect Dis"},{"issue":"6","key":"4670_CR12","doi-asserted-by":"publisher","first-page":"2015","DOI":"10.1128\/JCM.02411-07","volume":"46","author":"D Preza","year":"2008","unstructured":"Preza D, Olsen I, Aas JA, Willumsen T, Grinde B, Paster BJ. Bacterial profiles of root caries in elderly patients. J Clin Microbiol. 2008;46(6):2015\u201321.","journal-title":"J Clin Microbiol"},{"key":"4670_CR13","doi-asserted-by":"crossref","unstructured":"Nyvad B, Crielaard W, Mira A, Takahashi N, Beighton D. Dental caries from a molecular microbiological perspective. Caries Res. 2013;47(2):89\u2013102.","DOI":"10.1159\/000345367"},{"key":"4670_CR14","doi-asserted-by":"crossref","unstructured":"Fakhruddin K, Samaranayake L, Hamoudi R, Ngo H, Egusa H. Diversity of site-specific microbes of occlusal and proximal lesions in severe- early childhood caries (S-ECC). J Oral Microbiol. 2022;14(1):2037832.","DOI":"10.1080\/20002297.2022.2037832"},{"key":"4670_CR15","doi-asserted-by":"crossref","unstructured":"Takenaka S, Edanami N, Komatsu Y, Nagata R, Naksagoon T, Sotozono M, et al. Periodontal pathogens inhabit root caries lesions extending beyond the gingival margin: a next-generation sequencing analysis. Microorganisms. 2021;9(11):2349.","DOI":"10.3390\/microorganisms9112349"},{"issue":"8","key":"4670_CR16","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(8):e103712.","journal-title":"PLoS ONE"},{"issue":"6","key":"4670_CR17","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1177\/0022034520913248","volume":"99","author":"G Liu","year":"2020","unstructured":"Liu G, Wu C, Abrams WR, Li Y. Structural and Functional Characteristics of the Microbiome in Deep-Dentin Caries. J Dent Res. 2020;99(6):713\u201320.","journal-title":"J Dent Res"},{"issue":"4","key":"4670_CR18","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1159\/000447309","volume":"50","author":"N Takahashi","year":"2016","unstructured":"Takahashi N, Nyvad B. Ecological Hypothesis of Dentin and Root Caries. Caries Res. 2016;50(4):422\u201331.","journal-title":"Caries Res"},{"key":"4670_CR19","doi-asserted-by":"crossref","unstructured":"Ptasiewicz M, B\u0119bnowska D, Ma\u0142kowska P, Sierawska O, Poniewierska-Baran A, Hrynkiewicz R, et al. Immunoglobulin disorders and the oral cavity: a narrative review. J Clin Med. 2022;11(16):4873.","DOI":"10.3390\/jcm11164873"},{"issue":"3","key":"4670_CR20","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1128\/JCM.40.3.1001-1009.2002","volume":"40","author":"MR Becker","year":"2002","unstructured":"Becker MR, Paster BJ, Leys EJ, Moeschberger ML, Kenyon SG, Galvin JL, et al. Molecular analysis of bacterial species associated with childhood caries. J Clin Microbiol. 2002;40(3):1001\u20139.","journal-title":"J Clin Microbiol"},{"issue":"12","key":"4670_CR21","doi-asserted-by":"publisher","first-page":"1218","DOI":"10.1177\/00220345830620120901","volume":"62","author":"F Brudevold","year":"1983","unstructured":"Brudevold F, Tehrani A, Attarzadeh F, van Houte J, Russo J. Enamel demineralization potential of dietary carbohydrates. J Dent Res. 1983;62(12):1218\u201320.","journal-title":"J Dent Res"},{"issue":"4","key":"4670_CR22","doi-asserted-by":"publisher","first-page":"1407","DOI":"10.1128\/JCM.01410-07","volume":"46","author":"JA Aas","year":"2008","unstructured":"Aas JA, Griffen AL, Dardis SR, Lee AM, Olsen I, Dewhirst FE, et al. Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol. 2008;46(4):1407\u201317.","journal-title":"J Clin Microbiol"},{"key":"4670_CR23","doi-asserted-by":"publisher","first-page":"604596","DOI":"10.3389\/fcimb.2020.604596","volume":"10","author":"S Saito","year":"2020","unstructured":"Saito S, Aoki Y, Tamahara T, Goto M, Matsui H, Kawashima J, et al. Oral Microbiome Analysis in Prospective Genome Cohort Studies of the Tohoku Medical Megabank Project. Front Cell Infect Microbiol. 2020;10:604596.","journal-title":"Front Cell Infect Microbiol"},{"issue":"1","key":"4670_CR24","doi-asserted-by":"publisher","first-page":"414","DOI":"10.1038\/s41598-017-18677-0","volume":"8","author":"T Ogawa","year":"2018","unstructured":"Ogawa T, Hirose Y, Honda-Ogawa M, Sugimoto M, Sasaki S, Kibi M, et al. Composition of salivary microbiota in elderly subjects. Sci Rep. 2018;8(1):414.","journal-title":"Sci Rep"},{"issue":"11","key":"4670_CR25","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1177\/0810761","volume":"81","author":"MA Munson","year":"2002","unstructured":"Munson MA, Pitt-Ford T, Chong B, Weightman A, Wade WG. Molecular and cultural analysis of the microflora associated with endodontic infections. J Dent Res. 2002;81(11):761\u20136.","journal-title":"J Dent Res"},{"issue":"Pt 5","key":"4670_CR26","doi-asserted-by":"publisher","first-page":"1797","DOI":"10.1099\/00207713-51-5-1797","volume":"51","author":"FE Dewhirst","year":"2001","unstructured":"Dewhirst FE, Paster BJ, Tzellas N, Coleman B, Downes J, Spratt DA, et al. Characterization of novel human oral isolates and cloned 16S rDNA sequences that fall in the family Coriobacteriaceae: description of olsenella gen. nov., reclassification of Lactobacillus uli as Olsenella uli comb. nov. and description of Olsenella profusa sp. nov. Int J Syst Evol Microbiol. 2001;51(Pt 5):1797\u2013804.","journal-title":"Int J Syst Evol Microbiol."},{"issue":"Pt 4","key":"4670_CR27","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1099\/ijs.0.022954-0","volume":"61","author":"M Kraatz","year":"2011","unstructured":"Kraatz M, Wallace RJ, Svensson L. Olsenella umbonata sp. Nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa. Int J Syst Evol Microbiol. 2011;61(Pt 4):795\u2013803.","journal-title":"Int J Syst Evol Microbiol."},{"issue":"3","key":"4670_CR28","doi-asserted-by":"publisher","first-page":"e32219","DOI":"10.1371\/journal.pone.0032219","volume":"7","author":"JS McLean","year":"2012","unstructured":"McLean JS, Fansler SJ, Majors PD, McAteer K, Allen LZ, Shirtliff ME, et al. Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques. PLoS ONE. 2012;7(3):e32219.","journal-title":"PLoS ONE"},{"issue":"6","key":"4670_CR29","doi-asserted-by":"publisher","first-page":"321","DOI":"10.3109\/00016357.2011.568962","volume":"69","author":"LG Petersson","year":"2011","unstructured":"Petersson LG, Magnusson K, Hakestam U, Baigi A, Twetman S. Reversal of primary root caries lesions after daily intake of milk supplemented with fluoride and probiotic lactobacilli in older adults. Acta Odontol Scand. 2011;69(6):321\u20137.","journal-title":"Acta Odontol Scand"},{"key":"4670_CR30","doi-asserted-by":"publisher","first-page":"105204","DOI":"10.1016\/j.archoralbio.2021.105204","volume":"129","author":"D Bhaumik","year":"2021","unstructured":"Bhaumik D, Manikandan D, Foxman B. Cariogenic and oral health taxa in the oral cavity among children and adults: A scoping review. Arch Oral Biol. 2021;129:105204.","journal-title":"Arch Oral Biol"},{"issue":"7597","key":"4670_CR31","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1038\/nature17625","volume":"532","author":"DL Moyes","year":"2016","unstructured":"Moyes DL, Wilson D, Richardson JP, Mogavero S, Tang SX, Wernecke J, et al. Candidalysin is a fungal peptide toxin critical for mucosal infection. Nature. 2016;532(7597):64\u20138.","journal-title":"Nature"},{"issue":"12","key":"4670_CR32","doi-asserted-by":"publisher","first-page":"e1007342","DOI":"10.1371\/journal.ppat.1007342","volume":"14","author":"H Koo","year":"2018","unstructured":"Koo H, Andes DR, Krysan DJ. Candida-streptococcal interactions in biofilm-associated oral diseases. PLoS Pathog. 2018;14(12):e1007342.","journal-title":"PLoS Pathog"},{"key":"4670_CR33","doi-asserted-by":"crossref","unstructured":"Alves R, Sousa-Silva M, Vieira D, Soares P, Chebaro Y, Lorenz MC, et al. Carboxylic acid transporters in candida pathogenesis. mBio. 2020;11(3):e00156\u201320.","DOI":"10.1128\/mBio.00156-20"}],"container-title":["BMC Oral Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12903-024-04670-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12903-024-04670-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12903-024-04670-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T19:28:49Z","timestamp":1722454129000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcoralhealth.biomedcentral.com\/articles\/10.1186\/s12903-024-04670-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,31]]},"references-count":33,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["4670"],"URL":"https:\/\/doi.org\/10.1186\/s12903-024-04670-3","relation":{},"ISSN":["1472-6831"],"issn-type":[{"value":"1472-6831","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,31]]},"assertion":[{"value":"20 April 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 July 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 July 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The study design and sample collection were approved by the Ethical Committee of the Tokyo Medical and Dental University Graduate School of Medical and Dental Science (approval number: D2021-034). The informed consent was obtained from all subjects involved in the study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"869"}}