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Lei XU


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Journal of Zhejiang University SCIENCE B 2021 Vol.22 No.4 P.285-294


High-throughput sequencing identifies salivary microbiota in Chinese caries-free preschool children with primary dentition

Author(s):  Lei XU, Zhifang WU, Yuan WANG, Sa WANG, Chang SHU, Zhuhui DUAN, Shuli DENG

Affiliation(s):  The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, and Key Laboratory of Oral Biomedical Research of Zhejiang Province, Hangzhou 310006, China; more

Corresponding email(s):   dengshuli@zju.edu.cn

Key Words:  Salivary microbiota, Caries-free, Preschool children, Primary dentition, Illumina MiSeq, 16S rDNA V3-V4 hypervariable regions

Lei XU, Zhifang WU, Yuan WANG, Sa WANG, Chang SHU, Zhuhui DUAN, Shuli DENG. High-throughput sequencing identifies salivary microbiota in Chinese caries-free preschool children with primary dentition[J]. Journal of Zhejiang University Science B, 2021, 22(4): 285-294.

@article{title="High-throughput sequencing identifies salivary microbiota in Chinese caries-free preschool children with primary dentition",
author="Lei XU, Zhifang WU, Yuan WANG, Sa WANG, Chang SHU, Zhuhui DUAN, Shuli DENG",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T High-throughput sequencing identifies salivary microbiota in Chinese caries-free preschool children with primary dentition
%A Lei XU
%A Zhifang WU
%A Yuan WANG
%A Chang SHU
%A Zhuhui DUAN
%A Shuli DENG
%J Journal of Zhejiang University SCIENCE B
%V 22
%N 4
%P 285-294
%@ 1673-1581
%D 2021
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B2000554

T1 - High-throughput sequencing identifies salivary microbiota in Chinese caries-free preschool children with primary dentition
A1 - Lei XU
A1 - Zhifang WU
A1 - Yuan WANG
A1 - Sa WANG
A1 - Chang SHU
A1 - Zhuhui DUAN
A1 - Shuli DENG
J0 - Journal of Zhejiang University Science B
VL - 22
IS - 4
SP - 285
EP - 294
%@ 1673-1581
Y1 - 2021
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B2000554

ObjectivesThe study aimed at identifying salivary microbiota in caries-free Chinese preschool children using high-throughput sequencing.
MethodsSaliva samples were obtained from 35 caries-free preschool children (18 boys and 17 girls) with primary dentition, and 16S ribosomal DNA (rDNA) V3–V4 hypervariable regions of the microorganisms were analyzed using illumina MiSeq.
ResultsAt 97% similarity level, all of these reads were clustered into 334 operational taxonomic units (OTUs). Among these, five phyla (Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Candidate division TM7) and 13 genera (Streptococcus, Rothia, Granulicatella, Prevotella, Enterobacter, Veillonella, Neisseria, Staphylococcus, Janthinobacterium, Pseudomonas, Brevundimonas, Devosia, and Gemella) were the most dominant, constituting 99.4% and 89.9% of the salivary microbiota, respectively. The core salivary microbiome comprised nine genera (Actinomyces, Capnocytophaga, Gemella, Granulicatella, Lachnoanaerobaculum, Neisseria, Porphyromonas, Rothia, and Streptococcus). Analysis of microbial diversity and community structure revealed a similar pattern between male and female subjects. The difference in microbial community composition between them was mainly attributed to Neisseria (P=0.023). Furthermore, functional prediction revealed that the most abundant genes were related to amino acid transport and metabolism.
ConclusionsOur results revealed the diversity and composition of salivary microbiota in caries-free preschool children, with little difference between male and female subjects. Identity of the core microbiome, coupled with prediction of gene function, deepens our understanding of oral microbiota in caries-free populations and provides basic information for associating salivary microecology and oral health.


方法:我们采集了来自35名无龋学龄前乳牙列儿童的口腔唾液样本,其中包括18名男孩和17名女孩。利用Illumina MiSeq平台对微生物样本的16S rDNA V3-V4高变区进行测序分析,从而分析获得的微生物群落特征。

关键词:唾液微生物群落;无龋;学龄前儿童;乳牙列;MiSeq测序;16S rDNA V3-V4高变区

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1]AbouNE, AljaboA, StrangeA, et al., 2016. Demineralizationremineralization dynamics in teeth and bone. Int J Nanomed, 11:4743-4763.

[2]AndersonM, GrindefjordM, DahllöfG, et al., 2016. Oral microflora in preschool children attending a fluoride varnish program: a cross-sectional study. BMC Oral Health, 16:130.

[3]Belda-FerreP, AlcarazLD, Cabrera-RubioR, et al., 2012. The oral metagenome in health and disease. ISME J, 6(1):46-56.

[4]BennA, HengN, BroadbentJM, et al., 2018. Studying the human oral microbiome: challenges and the evolution of solutions. Aust Dent J, 63(1):14-24.

[5]CampiscianoG, ToschettiA, ComarM, et al., 2017. Shifts of subgingival bacterial population after nonsurgical and pharmacological therapy of localized aggressive periodontitis, followed for 1 year by Ion Torrent PGM platform. Eur J Dent, 11(1):126-129.

[6]ClaessonMJ, WangQ, O'SullivanO, et al., 2010. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res, 38(22):e200.

[7]CogenAL, NizetV, GalloRL, 2008. Skin microbiota: a source of disease or defence? Br J Dermatol, 158(3):442-455.

[8]DeutscherJ, FranckeC, PostmaPW, 2006. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev, 70(4):939-1031.

[9]DewhirstFE, ChenT, IzardJ, et al., 2010. The human oral microbiome. J Bacteriol, 192(19):5002-5017.

[10]FadroshDW, MaB, GajerP, et al., 2014. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome, 2:6.

[11]FeatherstoneJDB, LussiA, 2006. Understanding the chemistry of dental erosion. Monogr Oral Sci, 20:66-76.

[12]FranzosaEA, MorganXC, SegataN, et al., 2014. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci USA, 111(22):E2329-E2338.

[13]GillSR, PopM, DeboyRT, et al., 2006. Metagenomic analysis of the human distal gut microbiome. Science, 312(5778):1355-1359.

[14]GriceEA, SegreJA, 2012. The human microbiome: our second genome. Annu Rev Genomics Hum Genet, 13:151-170.

[15]HaraAT, ZeroDT, 2010. The caries environment: saliva, pellicle, diet, and hard tissue ultrastructure. Dent Clin North Am, 54(3):455-467.

[16]IsmailAS, BehrendtCL, HooperLV, 2009. Reciprocal interactions between commensal bacteria and γδ intraepithelial lymphocytes during mucosal injury. J Immunol, 182(5):3047-3054.

[17]JiangS, GaoXL, JinLJ, et al., 2016. Salivary microbiome diversity in caries-free and caries-affected children. Int J Mol Sci, 17(12):1978.

[18]JiangW, JiangYT, LiCL, et al., 2011. Investigation of supragingival plaque microbiota in different caries status of Chinese preschool children by denaturing gradient gel electrophoresis. Microb Ecol, 61(2):342-352.

[19]JiangW, ZhangJ, ChenH, 2013. Pyrosequencing analysis of oral microbiota in children with severe early childhood dental caries. Curr Microbiol, 67(5):537-542.

[20]KaplanJB, RagunathC, VelliyagounderK, et al., 2004. Enzymatic detachment of Staphylococcus epidermidis biofilms. Antimicrob Agents Chemother, 48(7):2633-2636.

[21]KauAL, AhernPP, GriffinNW, et al., 2011. Human nutrition, the gut microbiome and the immune system. Nature, 474(7351):327-336.

[22]LeeSE, NamOH, LeeHS, et al., 2016. Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing. Acta Odontol Scand, 74(5):335-336.

[23]LingZX, KongJM, JiaP, et al., 2010. Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb Ecol, 60(3):677-690.

[24]LingZX, LiuX, ChengYW, et al., 2015. Decreased diversity of the oral microbiota of patients with hepatitis B virus-induced chronic liver disease: a pilot project. Sci Rep, 5:17098.

[25]LiuB, FallerLL, KlitgordN, et al., 2012. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS ONE, 7(6):e37919.

[26]LoescheWJ, 1986. Role of Streptococcus mutans in human dental decay. Microbiol Rev, 50(4):353-380.

[27]LussiA, HellwigE, KlimekJ, 2012. Fluorides—mode of action and recommendations for use. Schweiz Monatsschr Zahnmed, 122(11):1030-1042.

[28]MeyerF, AmaechiBT, FabritiusHO, et al., 2018. Overview of calcium phosphates used in biomimetic oral care. Open Dent J, 12:406-423.

[29]PereiraJV, LeomilL, Rodrigues-AlbuquerqueF, et al., 2012. Bacterial diversity in the saliva of patients with different oral hygiene indexes. Braz Dent J, 23(4):409-416.

[30]PetersonJ, GargesS, GiovanniM, et al., 2009. The NIH Human Microbiome Project. Genome Res, 19(12):2317-2323.

[31]QuX, ZhouXD, 2020. Novel insights on the etiology, diagnosis and prevention of dental erosion. Chin J Stomatol, 55(5):289-295 (in Chinese).

[32]RitzS, HahnD, WamiHT, et al., 2020. Gut microbiome as a response marker for pancreatic enzyme replacement therapy in a porcine model of exocrine pancreas insufficiency. Microb Cell Fact, 19:221.

[33]RudneyJD, XieH, RhodusNL, et al., 2010. A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry. Mol Oral Microbiol, 25(1):38-49.

[34]SaidHS, SudaW, NakagomeS, et al., 2014. Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers. DNA Res, 21(1):15-25.

[35]SenderR, FuchsS, MiloR, 2016. Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell, 164(3):337-340.

[36]StruzyckaI, 2014. The oral microbiome in dental caries. Pol J Microbiol, 63(2):127-135.

[37]TaoL, SutcliffeIC, RussellRRB, et al., 1993. Transport of sugars, including sucrose, by the msm transport system of Streptococcus mutans. J Dent Res, 72(10):1386-1390.

[38]TappendenKA, DeutschAS, 2007. The physiological relevance of the intestinal microbiota-contributions to human health. J Am Coll Nutr, 26(6):679S-683S.

[39]TurnbaughPJ, LeyRE, HamadyM, et al., 2007. The Human Microbiome Project. Nature, 449(7164):804-810.

[40]VadeboncoeurC, PelletierM, 1997. The phosphoenolpyruvate: sugar phosphotransferase system of oral streptococci and its role in the control of sugar metabolism. FEMS Microbiol Rev, 19(3):187-207.

[41]WadeWG, 2013. The oral microbiome in health and disease. Pharmacol Res, 69(1):137-143.

[42]WebbAJ, HomerKA, HosieAH, 2008. Two closely related ABC transporters in Streptococcus mutans are involved in disaccharide and/or oligosaccharide uptake. J Bacteriol, 190(1):168-178.

[43]XinBC, LuoAH, QinJ, et al., 2013. Microbial diversity in the oral cavity of healthy Chinese Han children. Oral Dis, 19(4):401-405.

[44]XuH, HaoWJ, ZhouQ, et al., 2014. Plaque bacterial microbiome diversity in children younger than 30 months with or without caries prior to eruption of second primary molars. PLoS ONE, 9(2):e89269.

[45]YeDD, FanMM, GuanQ, et al., 2012. A review on the bioinformatics pipelines for metagenomic research. Zool Res, 33(6):574-585 (in Chinese).

[46]ZauraE, KeijserBJF, HuseSM, et al., 2009. Defining the healthy "core microbiome" of oral microbial communities. BMC Microbiol, 9:259.

[47]ZhangF, LiY, XunZ, et al., 2017. A preliminary study on the relationship between iron and black extrinsic tooth stain in children. Lett Appl Microbiol, 64(6):424-429.

[48]ZhouJ, ZhangY, CuiP, et al., 2020. Gut microbiome changes associated with HIV infection and sexual orientation. Front Cell Infect Microbiol, 10:434.

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