Dental plaque development on a hydroxyapatite disk in young adults observed by using a barcoded pyrosequencing approach

Filoche, S., Wong, L. & Sissons, C. H. Oral biofilms: emerging concepts in microbial ecology. J Dent Res 89, 8–18 (2010).

Rickard, A. H., Gilbert, P., High, N. J., Kolenbrander, P. E. & Handley, P. S. Bacterial coaggregation: an integral process in the development of multi-species biofilms. Trends Microbiol 11, 94–100 (2003).

Marsh, P. D. Dental plaque as a biofilm and a microbial community - implications for health and disease. BMC Oral Health 6 Suppl 1S14 (2006).

Ritz, H. L. Microbial population shifts in developing human dental plaque. Arch Oral Biol 12, 1561–1568 (1967).

Kolenbrander, P. E. et al. Communication among oral bacteria. Microbiol Mol Biol Rev 66, 486–505 (2002).

Langfeldt, D. et al. Composition of microbial oral biofilms during maturation in young healthy adults. PLoS One 9, e87449 (2014).

Kolenbrander, P. E. et al. Bacterial interactions and successions during plaque development. Periodontol 2000 42, 47–79 (2006).

Kolenbrander, P. E., Palmer, R. J., Jr, Periasamy, S. & Jakubovics, N. S. Oral multispecies biofilm development and the key role of cell-cell distance. Nat Rev Microbiol 8, 471–480 (2010).

Gross, E. L. et al. Beyond Streptococcus mutans: dental caries onset linked to multiple species by 16S rRNA community analysis. PLoS One 7, e47722 (2012).

Aas, J. A. et al. Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol 46, 1407–1417 (2008).

Tanner, A. C. et al. Cultivable anaerobic microbiota of severe early childhood caries. J Clin Microbiol 49, 1464–1474 (2011).

Gross, E. L. et al. Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol 48, 4121–4128 (2010).

Bender, R. & Lange, S. Adjusting for multiple testing--when and how? J Clin Epidemiol 54, 343–349 (2001).

Simon-Soro, A. et al. Microbial geography of the oral cavity. J Dent Res 92, 616–621 (2013).

Takeshita, T., Nakano, Y. & Yamashita, Y. Improved accuracy in terminal restriction fragment length polymorphism phylogenetic analysis using a novel internal size standard definition. Oral Microbiol Immunol 22, 419–428 (2007).

Takeshita, T. et al. The ecological proportion of indigenous bacterial populations in saliva is correlated with oral health status. ISME J 3, 65–78 (2009).

Takeshita, T. et al. Enteral tube feeding alters the oral indigenous microbiota in elderly adults. Appl Environ Microbiol 77, 6739–6745 (2011).

Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460–2461 (2010).

Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335–336 (2010).

Caporaso, J. G. et al. PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26, 266–267 (2010).

DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 5069–5072 (2006).

Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21, 494–504 (2011).

Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26, 1641–1650 (2009).

Lozupone, C. & Knight, R. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71, 8228–8235 (2005).

Chen, T. et al. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database 2010

10.1093/database/baq013 (2010).