The bacterial microbiome and metabolome in caries progression and arrest

References

• Petersen PE. Challenges to improvement of oral health in the 21st century – the approach of the WHO Global Oral Health Programme. Int Dent J. 2004;54(61):329–15.
   Google Scholar
• Petersen PE. Global policy for improvement of oral health in the 21st century – implications to oral health research of World Health Assembly 2007, World Health Organization. Community Dent Oral Epidemiol. 2009;37(1):1–8.
   Web of Science ®Google Scholar
• Kassebaum NJ, Bernabé E, Dahiya M, et al. Global burden of untreated caries: a systematic review and metaregression. J Dent Res. 2015;94(5):650–658.
   PubMed Web of Science ®Google Scholar
• Centers for Disease Control and Prevention. Oral Health Surveillance Report: trends in Dental Caries and Sealants, Tooth Retention, and Edentulism, USA, 1999–2004 to 2011–2016. Atlanta, GA: Centers for Disease Control and Prevention, US Dept of Health and Human Services; 2019.
   Google Scholar
• Dye BA, Thornton-Evans G, Xianfen L, et al. Dental Caries and Tooth Loss in Adults in the USA, 2011–2012. NCHS Data Brief, no 197. Hyattsville, MD: National Center for Health Statistics; 2015.
   Google Scholar
• Xu H, Hao W, Zhou Q, et al. Plaque Bacterial Microbiome Diversity in Children Younger than 30 Months with or without Caries Prior to Eruption of Second Primary Molars. PLoS One. 2014;9(2):e89269.
   PubMed Web of Science ®Google Scholar
• Thylstrup A. When is caries caries, and what should we do about it? Quintessence Int. 1998;29(9):594–598.
   Web of Science ®Google Scholar
• Nyvad B, Machiulskiene V, Baelum V. Reliability of a New Caries Diagnostic System Differentiating between Active and Inactive Caries Lesions. Caries Res. 1999;33(4):252–260.
   PubMed Web of Science ®Google Scholar
• Carvalho JC, Ekstrand KR, Thylstrup A. Dental plaque and caries on occlusal surfaces of first permanent molars in relation to stage of eruption. J Dent Res. 1989;68(5):773–779.
   PubMed Web of Science ®Google Scholar
• Carvalho JC, Thylstrup A, Ekstrand KR. Results after 3 years of non-operative occlusal caries treatment of erupting permanent first molars. Community Dent Oral Epidemiol. 1992;20(4):187–192.
   Web of Science ®Google Scholar
• Carvalho JC. Caries process on occlusal surfaces: evolving evidence and understanding. Caries Res. 2014;48(4):339–346.
   Web of Science ®Google Scholar
• Takahashi N, Nyvad B. Ecological Hypothesis of Dentin and Root Caries. Caries Res. 2016;50(4):422–431.
   PubMed Web of Science ®Google Scholar
• Peterson SN, Meer T, Su A, et al. Functional expression of dental plaque microbiota. Front Cell Infect Microbiol. 2014;4:108.
   PubMed Web of Science ®Google Scholar
• Simon-Soro A, Guillen-Navarro M, Mira A. Metatranscriptomics reveals overall active bacterial composition in caries lesions. J Oral Microbiol. 2014;6(1):25443.
   PubMed Web of Science ®Google Scholar
• Zaura E. Next-generation Sequencing Approaches to Understanding the Oral Microbiome. Adv Dent Res. 2012;24(2):81–85.
   Google Scholar
• Aas JA, Griffen AL, Dardis SR, et al. Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol. 2008;46(4):1407–1417.
   PubMed Web of Science ®Google Scholar
• Simón-Soro ÁA, Tomás I, Cabrera-Rubio R, et al. Microbial geography of the oral cavity. J Dent Res. 2013;92(7):616–621.
   PubMed Web of Science ®Google Scholar
• Carda-Dieguez M, Bravo-Gonzalez LA, Morata IM, et al. DNA sequencing of microbiota at interproximal sites. J Oral Microbiol. 2019 Nov 11;12(1):1687397.
   Web of Science ®Google Scholar
• Ribeiro AA, Azcarate-Peril MA, Cadenas MB, et al. The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries. PLoS One. 2017;5(7):e0180621.
   Google Scholar
• Fidalgo TKS, Freitas-Fernandes LB, Angeli R, et al. Salivary metabolite signatures of children with and without dental caries lesions. Metabolomics 2013;9(3):657–666.
   Web of Science ®Google Scholar
• Fidalgo TKS, Freitas-Fernandes LB, Almeida FL, et al. Longitudinal evaluation of salivary profile from children with dental caries before and after treatment. Metabolomics 2015;11(3):780–785.
   Web of Science ®Google Scholar
• Belda-Ferre P, Williamson J, Simón-Soro Á, et al. The human oral metaproteome reveals potential biomarkers for caries disease. Proteomics. 2015;15(20):3497–3507.
   PubMed Web of Science ®Google Scholar
• Belstrøm D, Constancias F, Liu Y, et al. Metagenomic and metatranscriptomic analysis of saliva reveals disease associated microbiota in patients with periodontitis and dental caries. NPJ Biofilms Microbiomes. 2017;3(1):23.
   Google Scholar
• Al-Hebshi NN, Baraniya D, Chen T, et al. Metagenome sequencing-based strain-level and functional characterization of supragingival microbiome associated with dental caries in children. J Oral Microbiol. 2018;11(1):1557986.
   Web of Science ®Google Scholar
• Holmen L, Mejare I, Malmgren B, et al. The effect of regular professional plaque removal on dental caries in vivo. A polarized light and scanning electron microscope study. Caries Res. 1988;22(4):250–256.
   Web of Science ®Google Scholar
• Paim S, Modesto A, Cury JA, et al. Development and control of caries lesions on the occlusal surface using a new in vivo caries model. Pesqui Odontol Bras. 2003;17(2):189–195.
   Google Scholar
• Torlakovic L, Klepac-Ceraj V, Ogaard B, et al. Microbial community succession on developing lesions on human enamel. J Oral Microbiol. 2012;4(1):16125.
   Google Scholar
• Nakata K, Nikaido T, Nakashima S, et al. An approach to normalizing micro-CT depth profiles of mineral density for monitoring enamel remineralization progress. Dental Materials J. 2012;31(4):533–540.
   Web of Science ®Google Scholar
• Jones RB, Zhu X, Moan E, et al. Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples. Sci Rep. 2018;8(1):4139.
   Google Scholar
• Edwards U, Rogall T, Blocker H, et al. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res. 1989;17(19):7843–7853.
   PubMed Web of Science ®Google Scholar
• Thompson AL, Monteagudo-Mera A, Cadenas MB, et al. Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome. Front Cell Infect Microbiol. 2015;5:5.
   Web of Science ®Google Scholar
• Callahan BJ, McMurdie PJ, Rosen MJ, et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583.
   PubMed Web of Science ®Google Scholar
• Al-Hebshi NN, Nasher AT, Idris AM, et al. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples. J Oral Microbiol. 2015;7(1):28934.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Schwartz S, Wagner L, et al. A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000;7(1–2):203–214.
   PubMed Web of Science ®Google Scholar
• Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–336.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780.
   PubMed Web of Science ®Google Scholar
• Ramadan Z, Jacobs D, Grigorov M, et al. Metabolic profiling using principal component analysis, discriminant partial least squares, and genetic algorithms. Talanta. 2006;68(5):1683–1691.
   PubMed Web of Science ®Google Scholar
• Almeida PA, Fidalgo TKS, Freitas-Fernandes LB, et al. Salivary metabolic profile of children and adolescents after hemodialysis. Metabolomics. 2017;13(11):141.
   Web of Science ®Google Scholar
• Van Velzen EJ, Westerhuis JA, Van Duynhoven JP, et al. Multilevel data analysis of a crossover designed human nutritional intervention study. J Proteome Res. 2008;7(10):4483–4491.
   Web of Science ®Google Scholar
• Silwood CJ, Lynch E, Claxson AW, et al. 1h and (13)c nmr spectroscopic analysis of human saliva. J Dent Res. 2002;81(6):422–427.
   Web of Science ®Google Scholar
• Hals E, Simonsen LT. Histopathology of experimental in vivo caries around silver amalgam fillings. Caries Res. 1972;6(1):16–33.
   Web of Science ®Google Scholar
• Silverstone LM. Structure of carious enamel, including the early lesion. Oral Sci Rev. 1973;3:100–160.
   PubMedGoogle Scholar
• Holmen AL, Thylstrup A, Artun J. Clinical and histological features observed during arrestment of active enamel carious lesions in vivo. Caries Res. 1987;21(6):546–554.
   Web of Science ®Google Scholar
• Holmen AL, Thylstrup A, Artun J. Surface changes during the arrest of active enamel carious lesions in vivo a scanning electron microscope study. Acta Odontol Scand. 1987;45(6):383–390.
   PubMed Web of Science ®Google Scholar
• Dewhirst FE, Chen T, Izard J, et al. The Human Oral Microbiome. J Bacteriol. 2010;192(19):5002–5017.
   PubMed Web of Science ®Google Scholar
• Li Y, Ge Y, Saxena D, et al. Genetic profiling of the oral microbiota associated with severe early-childhood caries. J Clin Microbiol. 2007;45(1):81–87.
   Web of Science ®Google Scholar
• Bik EM, Long CD, Armitage GC, et al. Bacterial diversity in the oral cavity of 10 healthy individuals. Isme J. 2010;4(8):962–974.
   PubMed Web of Science ®Google Scholar
• Peterson SN, Snesrud E, Liu J, et al. The dental plaque microbiome in health and disease. PLoS One. 2013;8(3):e58487.
   PubMed Web of Science ®Google Scholar
• Carda-Diéguez M, Bravo-González LA, Morata IM, et al. High-throughput DNA sequencing of microbiota at interproximal sites. J Oral Microbiol. 2019;12(1):1687397.
   Web of Science ®Google Scholar
• Nyvad B, Kilian M. Microbiology of the early colonization of human enamel and root surfaces in vivo. Scand J Dent Res. 1987;95(5):369–380.
   Google Scholar
• Nyvad B, Kilian M. Comparison of the initial streptococcal microflora on dental enamel in caries-active and in caries-inactive individuals. Caries Res. 1990;24(4):267–272.
   PubMed Web of Science ®Google Scholar
• Li J, Helmerhorst EJ, Leone CW, et al. Identification of early microbial colonizers in human dental biofilm. J Appl Microbiol. 2004;97(6):1311–1318.
   PubMed Web of Science ®Google Scholar
• Jiang S, Gao X, Jin L, et al. Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children. Int J Mol Sci. 2016;17(12):1978.
   PubMed Web of Science ®Google Scholar
• Li Y, Zou CG, Fu Y, Li Y, Zhou Q, Liu B, Zhang Z, Liu J, et al. Oral microbial community typing of caries and pigment in primary dentition. BMC Genomics. 2016 Aug 5;17:558.
   Google Scholar
• Kressirer CA, Chen T, Harriman KL, et al. Functional profiles of coronal and dentin caries in children. J Oral Microbiol. 2018;10(1):1495976.
   PubMed Web of Science ®Google Scholar
• Preza D, Olsen I, Aas JA, et al. Bacterial profiles of root caries in elderly patients. J Clin Microbiol. 2008;46(6):2015–2021.
   PubMed Web of Science ®Google Scholar
• Merritt J, Qi F. The mutacins of Streptococcus mutans: regulation and ecology. Mol Oral Microbiol. 2012;27(2):57–69.
   PubMed Web of Science ®Google Scholar
• Takeda I, Stretch C, Barnaby P, et al. Understanding the human salivary metabolome. NMR Biomed. 2009;22(6):577–584.
   PubMed Web of Science ®Google Scholar
• Hojo K, Nagaoka S, Ohshima T, et al. Bacterial interactions in dental biofilm development. J Dent Res. 2009;88(11):982–990.
   PubMed Web of Science ®Google Scholar
• Van Houte J, Russo J, Prostak KS. Increased pH-lowering ability of Streptococcus mutans cell masses associated with extracellular glucan-rich matrix material and the mechanisms involved. J Dent Res. 1989;68(3):451–459.
   Web of Science ®Google Scholar