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Original Research

Open Access

Oral microbiome characteristics in children with and without early childhood caries

  • Xianyin Xu1,†
  • Baokun Shan2,3,†
  • Qiuxiang Zhang2,3,*,
  • Wenwei Lu2,3
  • Jianxin Zhao2,3
  • Hao Zhang2,3,4
  • Wei Chen2,3,5

1Department of Stomatology, Wuxi Children’s Hospital, 214023 Wuxi, Jiangsu, China

2State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, Jiangsu, China

3School of Food Science and Technology, Jiangnan University, 214122 Wuxi, Jiangsu, China

4Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, 214122 Wuxi, Jiangsu, China

5National Engineering Research Center for Functional Food, Jiangnan University, 214122 Wuxi, Jiangsu, China

DOI: 10.22514/jocpd.2023.012 Vol.47,Issue 2,March 2023 pp.58-67

Submitted: 14 October 2022 Accepted: 05 December 2022

Published: 03 March 2023

*Corresponding Author(s): Qiuxiang Zhang E-mail:

† These authors contributed equally.


Objective: Early childhood caries (ECC) negatively affects children’s growth due to its close relation to an imbalance of the oral microbiota. This study aimed to evaluate the distribution of the oral microbiota in children with ECC and healthy individuals. Methods: The oral microbiota of 20 children with dental caries from both carious teeth (CC cohort) and healthy teeth (CH cohort), and the oral microbiota of 20 healthy control children (HH cohort) were subjected to 16S rDNA sequencing. Results: The results revealed significant differences between the microbial structure of the CC and CH cohorts of every child with ECC. The most common microbes were Streptococcus, Neisseria, Leptotrichia, Lautropia and Haemophilus. Specifically, the CC cohort contained Lactobacillus, Veillonella, and Prevotella 7, the CH cohort contained Actinomyces, Bifidobacterium and Abiotrophia, and the HH cohort mainly contained Neisseria, Leptotrichia, Porphyromonas and Gemella. Lastly, we established a random forest model consisting of 10 genera (Prevotella 7, Actinobacillus, etc.) which demonstrated promising clinical diagnostic ability (area under the curve (AUC) = 89.8%). These findings indicate that oral microbiota can potentially be used as therapeutic targets or diagnostic markers for the early prediction and prevention of caries in children.


Early childhood caries; Oral microbiota; 16S rDNA sequencing; Randomforest model; Biomarker

Cite and Share

Xianyin Xu,Baokun Shan,Qiuxiang Zhang,Wenwei Lu,Jianxin Zhao,Hao Zhang,Wei Chen. Oral microbiome characteristics in children with and without early childhood caries. Journal of Clinical Pediatric Dentistry. 2023. 47(2);58-67.


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