title: Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment.
abstract: Novel approaches using OMICS techniques enable a collective assessment of multiple related biological units, including genes, gene expression, proteins, and metabolites. In the past decade, next-generation sequencing ( NGS) technologies were improved by longer sequence reads and the development of genome databases and user-friendly pipelines for data analysis, all accessible at lower cost. This has generated an outburst of high-throughput data. The application of OMICS has provided more depth to existing hypotheses as well as new insights in the etiology of dental caries. For example, the determination of complete bacterial microbiomes of oral samples rather than selected species, together with oral metatranscriptome and metabolome analyses, supports the viewpoint of dysbiosis of the supragingival biofilms. In addition, metabolome studies have been instrumental in disclosing the contributions of major pathways for central carbon and amino acid metabolisms to biofilm pH homeostasis. New, often noncultured, oral streptococci have been identified, and their phenotypic characterization has revealed candidates for probiotic therapy. Although findings from OMICS research have been greatly informative, problems related to study design, data quality, integration, and reproducibility still need to be addressed. Also, the emergence and continuous updates of these computationally demanding technologies require expertise in advanced bioinformatics for reliable interpretation of data. Despite the obstacles cited above, OMICS research is expected to encourage the discovery of novel caries biomarkers and the development of next-generation diagnostics and therapies for caries control. These observations apply equally to the study of other oral diseases.
authors.affiliation: 1 Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, University of Florida, Gainesville, FL, USA.
authors.forename: M M
authors.initials: MM
authors.lastname: Nascimento
authors.affiliation: 2 Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
authors.forename: E
authors.initials: E
authors.lastname: Zaura
authors.affiliation: 3 Department of Health & Genomics, Center for Advanced Research in Public Health, FISABIO Foundation, Valencia, Spain.
authors.forename: A
authors.initials: A
authors.lastname: Mira
authors.affiliation: 4 Department of Oral Biology, Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan.
authors.forename: N
authors.initials: N
authors.lastname: Takahashi
authors.affiliation: 5 Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, the Netherlands.
authors.forename: J M
authors.initials: JM
authors.lastname: Ten Cate
mesh_terms: D018441:Biofilms; D019295:Computational Biology / Q000379:methods*; D003731:Dental Caries / Q000382:microbiology* / Q000517:prevention & control*; D018865:Dental Research; D004059:Diffusion of Innovation; D023281:Genomics / Q000379:methods; D006801:Humans; D055442:Metabolome; D055432:Metabolomics / Q000379:methods; D054892:Metagenome; D064307:Microbiota; D040901:Proteomics / Q000379:methods
keywords: biofilm; dental caries; genome; metabolome; microbiome; next-generation sequencing