Journal of Prevention and Treatment for Stomatological Diseases ›› 2018, Vol. 26 ›› Issue (3): 195-199.doi: 10.12016/j.issn.2096-1456.2018.03.011

• Review Articles • Previous Articles     Next Articles

A multiomics approach to study the associations between microbial communities and functions and dental caries

Yuanyuan HUO(), Xuan HAN, Yuqing LI, Jing ZOU()   

  1. State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China;
  • Received:2017-04-27 Revised:2017-08-24 Online:2018-03-20 Published:2018-08-31

Abstract:

The pathogenic mechanisms by which oral microbial communities affect the occurrence and development of dental caries remain unclear. Applications that make use of high-through put sequencing technologies and metaomics approaches to research dental caries etiology can provide new ideas about disease prevention and treatment. In this article, we review advanced research presented in metaomics studies, including genomic, metagenomic, metatranscriptomic, metaproteomic and metabolomics studies of dental caries.

Key words: Dental caries, Oral microbial community, Micro-ecology, Metagenomics, Metatranscriptomics, Metaproteomics, Metabolomics

CLC Number: 

  • R781
[1] Marsh PD.Are dental diseases examples of ecological catastrophes?[J]. Microbiology, 2003, 149(2): 279-294.
[2] Nyvad B, Crielaard W, Mira A, et al.Dental caries from a molecular microbiological perspective[J]. Caries Res, 2013, 47(2): 89-102.
[3] Tanner AC, Faller LL.Understanding caries from the oral microbiome perspective[J]. J Calif Dent Assoc, 2016, 44(7): 437-446.
[4] Dadi HT.SLIMM: species level identification of microorganisms from metagenomes[J]. Peer J, 2017, 5: e3138.
[5] 凌均棨, 杨芳, 滕飞. 新一代高通量技术在龋病相关的口腔菌群宏基因组学研究中的应用[J]. 中华口腔医学研究杂志电子版, 2011, 5(4): 1-5.
[6] Zhou Q.Genotypic diversity of Streptococcus mutans and Streptococcus sobrinus in 3-4-year-old children with severe caries or without caries[J]. Int J Paediatr Dent, 2011, 21(6): 422-431.
[7] Neves GB.Molecular detection of bacteria associated to caries activity in dentinal lesions[J]. Clin Oral Investig, 2017, 21(6): 2053-2061.
[8] Simon-Soro SA.A tissue-dependent hypothesis of dental caries[J]. Caries Res, 2013, 47(6): 591-600.
[9] Vaishampayan PA.Comparative metagenomics and population dynamics of the gut microbiota in mother and infant[J]. Genome Biol Evol, 2010, 2: 53-66.
[10] Su Z, Fang H, Hong H, et al.An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era[J]. Genome Biol, 2014, 15(12): 523.
[11] Aas JA, Griffen AL, Dardis SR, et al.Bacteria of dental caries in primary and permanent teeth in children and young adults[J]. J Clin Microbiol, 2008, 46(4): 1407-1417.
[12] Belda-Ferre BP.The oral metagenome in health and disease[J]. ISME J, 2012, 6(1): 46-56.
[13] Simon-Soro SA.Microbial geography of the oral cavity[J]. J Dent Res, 2013, 92(7): 616-621.
[14] Gross EL, Beall CJ, Kutsch SR, et al.Beyond streptococcus mutans: dental caries onset linked to multiple species by 16S rRNA community analysis[J]. PLoS One, 2012, 7(10): e47722.
[15] Fejerskov O.Changing paradigms in concepts on dental caries: consequences for oral health care[J]. Caries Res, 2004, 38(3): 182-191.
[16] Kianoush N, Adler CJ, Nguyen KA, et al.Bacterial profile of dentine caries and the impact of pH on bacterial population diversity[J]. PLoS One, 2014, 9(3): e92940.
[17] Benitez-Paez BA.Microbiota diversity and gene expression dynamics in human oral biofilms[J]. BMC Genomics, 2014, 15: 311.
[18] Simon-Soro AG, Mira A.Metatranscriptomics reveals overall active bacterial composition in caries lesions[J]. J Oral Microbiol, 2014, 6: 25443.
[19] Duran-Pinedo AE, Chen T, Teles R, et al.Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis[J]. ISME J, 2014, 8(8): 1659-1672.
[20] Teng F, Yang F, Huang S, et al.Prediction of early childhood caries via spatial-temporal variations of oral microbiota[J]. Cell Host Microbe, 2015, 18(3): 296-306.
[21] Schwanhaeusser B, Busse D, Li N, et al.Global quantification of mammalian gene expression control[J]. Nature, 2011, 473(7347): 337-342.
[22] Grassl N, Kulak NA, Pichler G, et al.Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome[J]. Genome Med, 2016, 8(1): 44.
[23] Belda-Ferre P, Williamson J, Simón-Soro Á, et al.The human oral metaproteome reveals potential biomarkers for caries disease[J]. Proteomics, 2015, 15(20): 3497-3507.
[24] Edlund A, Yang Y, Yooseph S, et al.Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism[J]. ISME J, 2015, 9(12): 2605-2619.
[25] Agnello M.Arginine improves pH homeostasis via metabolism and microbiome modulation[J]. J Dent Res, 2017, 96(8): 924-930.
[26] Zhou Y.Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls[J]. Peer J, 2016, 4: e2433.
[27] Morou-Bermudez ME.Urease and dental plaque microbial profiles in children[J]. PLoS One, 2015, 10(9): e0139315.
[28] Morou-Bermudez ME.Urease activity in dental plaque and saliva of children during a three-year study period and its relationship with other caries risk factors[J]. Arch Oral Biol, 2011, 56(11): 1282-1289.
[29] Morou-Bermudez ME.Urease activity as a risk factor for caries development in children during a three-year study period: a survival analysis approach[J]. Arch Oral Biol, 2011, 56(12): 1560-1568.
[30] Gomez A, Nelson KE.The oral microbiome of children:development, disease, and implications beyond oral health[J]. Microb Ecol, 2017, 73(2): 492-503.
[31] Ogbaga CC, Stepien P, Dyson BC, et al.Biochemical analyses of sorghum varieties reveal differential responses to drought[J]. PLoS One, 2016, 11(5): e0154423.
[32] Takahashi N, Nyvad B.The role of bacteria in the caries process: ecological perspectives[J]. J Dent Res, 2011, 90(3): 294-303.
[33] Fidalgo TS, Freitas-Fernandes LB, Angeli R, et al.Salivary metabolite signatures of children with and without dental caries lesions[J]. Metabolomics, 2013, 9(3): 657-666.
[34] Fidalgo TS, Freitas-Fernandes LB, Almeida FL, et al.Longitudinal evaluation of salivary profile from children with dental caries before and after treatment[J]. Metabolomics, 2015, 11(3): 583-593.
[35] Takahashi NW, Mayanagi G.Metabolomics of supragingival plaque and oral bacteria[J]. J Dent Res, 2010, 89(12): 1383-1388.
[1] HUANG Shaohong,WU Linmei. The prevalence of dental caries in urban areas is lower than that in rural areas--analysis of changes in the epidemiological characteristics of caries in urban and rural areas [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2020, 28(5): 273-278.
[2] HE Yuanli,REN Biao,CHEN Xuan,ZOU Ling. Mechanism research of srtA gene on the oxidation tolerance of Streptococcus mutans [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2020, 28(5): 292-297.
[3] WU Hongyu,MA Xiaoxin,LU Haixia,FENG Xiping,GU Qin,YE Wei,XIE Yingxin,XIE Danshu,WANG Wenji. Investigation of dental caries and periodontal conditions in maintenance hemodialysis patients [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2020, 28(5): 313-317.
[4] LIU Haotian,LI Huihui,LIU Shanshan. Research progress on the relationship between enamel-related gene polymorphisms and caries susceptibility [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2020, 28(2): 123-126.
[5] FU Zhuohui,DENG Jiaxin,CHEN Yuan,WANG Yan. Research progress into probiotics for the prevention of dental caries [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2019, 27(9): 603-608.
[6] LI Jiatong,ZHOU Xuedong,XU Xin,WANG Yan. Research progress of probiotics in the prevention and treatment of oral infectious diseases [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2019, 27(9): 598-601.
[7] GUO Xiao,DU Xinmei,CHENG Lei,ZHOU Xuedong,LI Mingyun. Research progress on the function and metabolism of d-alanine in bacteria [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2019, 27(4): 264-267.
[8] YANG Ting,ZHANG Wanting,LI Beibei,DONG Ying,CAO Hongfei,ZHAO Jin. Distribution of oral Streptococcus mutans and its correlation with dental caries in children of Bortala Mongolian Autonomous Prefecture [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2019, 27(4): 219-225.
[9] ZHANG Fan,REN Weiwei,GUAN Qin,ZHAO Hui,LI Shouhong. The management of dental fear symptoms in children in a coparticipation model [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2019, 27(2): 104-106.
[10] Xuan HAN, Yuanyuan HUO, Qiong ZHANG, Yuqing LI, Jing ZOU. Research progress of microbial biomarkers of early childhood caries [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2018, 26(6): 391-395.
[11] Yuan CHEN,Zhuohui FU,Yue CHEN,Jiaxin DENG,Yan WANG,Jing ZOU. Analysis of risk factors for dental caries in deciduous teeth among preschool children [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2018, 26(10): 652-656.
[12] Bei-si CHEN, Qiu-lin LIU, Bo-lin CHEN, Wei WU, Xue-ling MA, Xiao-juan ZENG. Effect analysis of topical fluoride varnish on caries prevention of first permanent molars in school-age children [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(4): 254-257.
[13] Rong LIN, Wei LIU, Li-hua XIONG, Wei-jia LIU, Chong-shan GUO, Kun-cai CHEN. Analysis of influencing factors of dental caries in first permanent molars among children aged 10-12 years old in Guangzhou [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(3): 183-187.
[14] Mengqi LI, Hai LAN. The research progress of anti-caries materials [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(10): 668-671.
[15] LI Chun,LI Yan-hong,LIU Juan. Application of probiotics for dental caries prevention in children [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2016, 24(9): 558-560.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
[1] Hong-chang LAI,Jun-yu SHI. Maxillary sinus floor elevation[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(1): 8 -12 .
[2] Pin ZHOU, Yang-fei LI. MRI study of temporomandibular joint disc position in asymptomatic volunteers[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(4): 239 -244 .
[3] Xinxin XIA, Fang FANG, Lijuan CHENG. Shaping ability of Pathfile and WaveOne in simulated root canals[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(6): 365 -368 .
[4] Yuanhong LI, Xinyi FANG, Yu QIU, Lei CHENG. Experimental study on the effects of green tea on salivary flow rate and pH value[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(9): 560 -564 .
[5] Chengzhang LI. Masticatory muscles in occlusion[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(12): 755 -760 .
[6] . [J]. Journal of Prevention and Treatment for Stomatological Diseases, 2018, 26(1): 1 .
[7] Zhirong WU, Shiguang Huang. Research progress on the etiology, clinical examination and treatment of peri-implantitis[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2018, 26(6): 401 -405 .
[8] Xiaowu YAO, Shisheng CHEN, Zizheng LU, Minxiao LIN. Clinical report and literature review on the amyloidosis of salivary glands[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2018, 26(8): 533 -536 .
[9] Lan LIAO, Lijun ZENG. Updated research on digitalization in aesthetic restoration[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2018, 26(7): 409 -414 .
[10] Yu LU, Chengxia LIU, Zhongjun LIU. Role of TRAF6 in inflammatory responses of human osteoblast-like cells with Enterococcusfaecalis[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2017, 25(7): 420 -425 .
This work is licensed under a Creative Commons Attribution 3.0 License.