{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T01:49:39Z","timestamp":1784166579530,"version":"3.55.0"},"reference-count":52,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T00:00:00Z","timestamp":1726012800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Early childhood caries (ECC) are a prevalent chronic disease in young children. However, there has been limited research on the microbiota in different tissue levels of the same tooth in children with ECC. This study aimed to investigate the dynamic changes in bacterial diversity during the progression of Severe Early Childhood Caries (S-ECC) within the same tooth, from the tooth surface to the root canal, by collecting tissue samples from different areas of the affected tooth.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Twenty primary teeth with periapical periodontitis were selected from 20 children aged 3\u20135\u2009years, with 100 samples collected from the different layers: uncavitated buccal enamel surface without white spot lesion (surface), the outermost layer of the dentin carious lesion (superficial), the inner layer of carious dentin (deep), necrotic pulp tissue (pulp), and root exudate (exudate). The taxonomy of each OTU representative sequence was analyzed against the 16S rRNA database. Comparisons of alpha diversity between groups were performed. The number of shared and unique genera between groups counted. Beta diversity was contrasted to evaluate differences in bacterial community composition, and the relationships between the microbiota and samples were analyzed. The heatmap analysis of the 30 most abundant genera was used, which highlighted their relative distribution and abundance. The significantly abundant taxa (phylum to genera) of bacteria among the different groups were identified. The differences of relative abundance between bacterial genera among the five groups were analyzed. Significant Spearman correlations were noted, and visualization of the co-occurrence network was conducted.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Bacterial 16S rRNA gene sequencing showed that most genera were present in all layers, with the number of shared genera increasing as the disease advanced. The bacterial communities and core genera in the co-occurrence network changed with progression to severe ECC.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>An increase in both the quantity and complexity of bacterial interactions was observed. This study emphasized the importance of paying attention to the relationship between microbial species rather than just checking changes in bacterial species structure when investigating the role of bacteria in disease progression.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2024.1418261","type":"journal-article","created":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T04:29:47Z","timestamp":1726028987000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":13,"title":["Bacterial dynamics in the progression of caries to apical periodontitis in primary teeth of children with severe early childhood caries"],"prefix":"10.3389","volume":"15","author":[{"given":"Bichen","family":"Lin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinfeng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2024,9,11]]},"reference":[{"key":"ref1","first-page":"52","article-title":"Policy on early childhood caries (ECC): classifications, consequences, and preventive strategies","volume":"38","year":"2016","journal-title":"Pediatr. Dent."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41579-018-0024-1","article-title":"Keystone taxa as drivers of microbiome structure and functioning","volume":"16","author":"Banerjee","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1016\/j.tim.2017.09.008","article-title":"Oral biofilms: pathogens, matrix, and polymicrobial interactions in microenvironments","volume":"26","author":"Bowen","year":"2018","journal-title":"Trends Microbiol."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1016\/j.joen.2022.11.015","article-title":"Endodontic microbial communities in apical periodontitis","volume":"49","author":"Buonavoglia","year":"2023","journal-title":"J. Endod."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"25951","DOI":"10.3402\/jom.v7.25951","article-title":"Pulp and plaque microbiotas of children with severe early childhood caries","volume":"7","author":"Chalmers","year":"2015","journal-title":"J. Oral Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one fastq preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1109\/TMI.2020.3027500","article-title":"Laplacian flow dynamics on geometric graphs for anatomical modeling of cerebrovascular networks","volume":"40","author":"Damseh","year":"2021","journal-title":"IEEE Trans. Med. Imaging"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"10932","DOI":"10.1038\/s41598-020-67828-3","article-title":"The apical root canal system microbial communities determined by next-generation sequencing","volume":"10","author":"de Brito","year":"2020","journal-title":"Sci. Rep."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1111\/iej.13424","article-title":"A macroscopic and histological analysis of radiographically well-defined deep and extremely deep carious lesions: carious lesion characteristics as indicators of the level of bacterial penetration and pulp response","volume":"54","author":"Demant","year":"2021","journal-title":"Int. Endod. J."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"25","DOI":"10.3389\/fcimb.2015.00025","article-title":"Transcriptomic analysis of three veillonella spp. present in carious dentine and in the saliva of caries-free individuals","volume":"5","author":"Do","year":"2015","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1111\/iej.13080","article-title":"European Society of Endodontology position statement: management of deep caries and the exposed pulp","volume":"52","author":"Duncan","year":"2019","journal-title":"Int. Endod. J."},{"key":"ref12","first-page":"200","article-title":"Prevalence and measurement of dental caries in young children","volume":"37","author":"Dye","year":"2015","journal-title":"Pediatr. Dent."},{"key":"ref13","first-page":"1","article-title":"Trends in oral health status: United States, 1988-1994 and 1999-2004","author":"Dye","year":"2007","journal-title":"Vital Health Stat 11"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"Uparse: highly accurate otu sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1368848","DOI":"10.1080\/20002297.2017.1368848","article-title":"Leptotrichia species in human infections ii","volume":"9","author":"Eribe","year":"2017","journal-title":"J. Oral Microbiol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"538","DOI":"10.1038\/nrmicro2832","article-title":"Microbial interactions: from networks to models","volume":"10","author":"Faust","year":"2012","journal-title":"Nat. Rev. Microbiol."},{"key":"ref9003","doi-asserted-by":"crossref","first-page":"141","DOI":"10.3389\/fpubh.2020.00141","article-title":"Editorial: Country profile of the epidemiology and clinical management of early childhood caries","volume":"8","author":"Folayan","year":"2020","journal-title":"Front Public Health."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1016\/j.joen.2008.01.016","article-title":"Microbial analysis of canals of root-filled teeth with periapical lesions using polymerase chain reaction","volume":"34","author":"Gomes","year":"2008","journal-title":"J. Endod."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1111\/omi.12152","article-title":"Advances in the microbial etiology and pathogenesis of early childhood caries","volume":"32","author":"Hajishengallis","year":"2017","journal-title":"Mol Oral Microbiol"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1016\/j.joen.2013.05.001","article-title":"Microbial analysis in primary and persistent endodontic infections by using pyrosequencing","volume":"39","author":"Hong","year":"2013","journal-title":"J. Endod."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1186\/1471-2164-13-345","article-title":"Microbial transformation from normal oral microbiota to acute endodontic infections","volume":"13","author":"Hsiao","year":"2012","journal-title":"BMC Genomics"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"ref9001","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1111\/j.1752-7325.1999.tb03267.x","article-title":"A systematic review of clinical diagnostic criteria of early childhood caries","volume":"59","author":"Ismail","year":"1999","journal-title":"J. Public Health Dent."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"1495976","DOI":"10.1080\/20002297.2018.1495976","article-title":"Functional profiles of coronal and dentin caries in children","volume":"10","author":"Kressirer","year":"2018","journal-title":"J. Oral Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1111\/aej.12728","article-title":"Effectiveness of probiotics in apical periodontitis progression: a scoping review and implications for research","volume":"49","author":"La Rosa","year":"2023","journal-title":"Aust. Endod. J."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1177\/0022034520913248","article-title":"Structural and functional characteristics of the microbiome in deep-dentin caries","volume":"99","author":"Liu","year":"2020","journal-title":"J. Dent. Res."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"2433","DOI":"10.1099\/mic.0.048314-0","article-title":"Differential response of streptococcus mutans towards friend and foe in mixed-species cultures","volume":"157","author":"Liu","year":"2011","journal-title":"Microbiology"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1038\/s41522-024-00488-7","article-title":"How probiotics, prebiotics, synbiotics, and postbiotics prevent dental caries: an oral microbiota perspective","volume":"10","author":"Luo","year":"2024","journal-title":"NPJ Biofilms Microbiomes"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"691092","DOI":"10.3389\/fcimb.2021.691092","article-title":"Oral microbiota composition and function changes during chronic erythematous candidiasis","volume":"11","author":"Lyu","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"Flash: fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Mago\u010d","year":"2011","journal-title":"Bioinformatics (Oxford, England)"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"7857","DOI":"10.1038\/s41598-022-11979-y","article-title":"Child saliva microbiota and caries: a randomized controlled maternal education trial in rural Uganda","volume":"12","author":"Muhoozi","year":"2022","journal-title":"Sci. Rep."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1111\/iej.13911","article-title":"The root canal microbiome diversity and function. A whole-metagenome shotgun analysis","volume":"57","author":"Ordinola-Zapata","year":"2023","journal-title":"Int. Endod. J."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"1264619","DOI":"10.3389\/fmicb.2023.1264619","article-title":"Effects of long-term metal exposure on the structure and co-occurrence patterns of the oral microbiota of residents around a mining area","volume":"14","author":"Pei","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref9002","doi-asserted-by":"crossref","first-page":"328","DOI":"10.3389\/fpubh.2019.00328","article-title":"The burden of early childhood caries in canadian children and associated risk factors","volume":"7","author":"Pierce","year":"2019","journal-title":"Front Public Health."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1186\/s12903-015-0134-3","article-title":"Genotypic diversity and cariogenicity of candida albicans from children with early childhood caries and caries-free children","volume":"15","author":"Qiu","year":"2015","journal-title":"BMC Oral Health"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1159\/000314675","article-title":"Association of oral candidal carriage with dental caries in children","volume":"44","author":"Raja","year":"2010","journal-title":"Caries Res."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1038\/s41579-018-0089-x","article-title":"The oral microbiota: dynamic communities and host interactions","volume":"16","author":"Richard","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e00106-17","DOI":"10.1128\/IAI.00106-17","article-title":"Microbiomes of site-specific dental plaques from children with different caries status","volume":"85","author":"Richards","year":"2017","journal-title":"Infect. Immun."},{"key":"ref36","first-page":"118","article-title":"Assessment of the microbiota in root canals of human primary teeth by checkerboard DNA-DNA hybridization","volume":"74","author":"Ruvi\u00e9re","year":"2007","journal-title":"J. Dent. Child. (Chic.)"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1038\/nature10072","article-title":"Detection of prokaryotic mrna signifies microbial viability and promotes immunity","volume":"474","author":"Sander","year":"2011","journal-title":"Nature"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"e28088","DOI":"10.1371\/journal.pone.0028088","article-title":"Comparing the bacterial diversity of acute and chronic dental root canal infections","volume":"6","author":"Santos","year":"2011","journal-title":"PLoS ONE"},{"key":"ref9004","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1633194","DOI":"10.1080\/20002297.2019.1633194","article-title":"Bacterial biofilm composition in healthy subjects with and without caries experience","volume":"11","author":"Schoilew","year":"2019","journal-title":"J. Oral Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1016\/j.tripleo.2009.01.042","article-title":"Bacteria in the apical root canal of teeth with primary apical periodontitis","volume":"107","author":"Siqueira","year":"2009","journal-title":"Oral Surg. Oral Med. Oral Pathol. Oral Radiol. Endod."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"713","DOI":"10.1038\/nm.4142","article-title":"The microbiome in early life: implications for health outcomes","volume":"22","author":"Tamburini","year":"2016","journal-title":"Nat. Med."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"778","DOI":"10.1038\/ismej.2013.190","article-title":"Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered antarctic lakes","volume":"8","author":"Vick-Majors","year":"2014","journal-title":"ISME J."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive bayesian classifier for rapid assignment of rrna sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1468","DOI":"10.1177\/0022034518790941","article-title":"Association between oral candida and bacteriome in children with severe ecc","volume":"97","author":"Xiao","year":"","journal-title":"J. Dent. Res."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1159\/000481833","article-title":"Candida albicans and early childhood caries: a systematic review and meta-analysis","volume":"52","author":"Xiao","year":"","journal-title":"Caries Res."},{"key":"ref47","doi-asserted-by":"publisher","first-page":"2377","DOI":"10.3389\/fmicb.2017.02377","article-title":"Soil bacterial community structure and co-occurrence pattern during vegetation restoration in karst rocky desertification area","volume":"8","author":"Xue","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"2307416","DOI":"10.1080\/20002297.2024.2307416","article-title":"Manipulating the diseased oral microbiome: the power of probiotics and prebiotics","volume":"16","author":"Yu","year":"2024","journal-title":"J. Oral Microbiol."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1418261\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T04:29:55Z","timestamp":1726028995000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1418261\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9,11]]},"references-count":52,"alternative-id":["10.3389\/fmicb.2024.1418261"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1418261","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,9,11]]},"article-number":"1418261"}}