Application of metagenomics in understanding oral health and disease

References

• Horz HP, Conrads G. Diagnosis and anti-infective therapy of periodontitis. Expert Rev Anti Infect Ther 2007; 5:703 - 15; http://dx.doi.org/10.1586/14787210.5.4.703; PMID: 17678431
   PubMed Web of Science ®Google Scholar
• Selwitz RH, Ismail AI, Pitts NB. Dental caries. Lancet 2007; 369:51 - 9; http://dx.doi.org/10.1016/S0140-6736(07)60031-2; PMID: 17208642
   PubMed Web of Science ®Google Scholar
• Pihlstrom BL, Michalowicz BS, Johnson NW. Periodontal diseases. Lancet 2005; 366:1809 - 20; http://dx.doi.org/10.1016/S0140-6736(05)67728-8; PMID: 16298220
   PubMed Web of Science ®Google Scholar
• Konopka A. What is microbial community ecology?. ISME J 2009; 3:1223 - 30; http://dx.doi.org/10.1038/ismej.2009.88; PMID: 19657372
   PubMed Web of Science ®Google Scholar
• Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 2005; 43:5721 - 32; http://dx.doi.org/10.1128/JCM.43.11.5721-5732.2005; PMID: 16272510
   PubMed Web of Science ®Google Scholar
• Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG. The human oral microbiome. J Bacteriol 2010; 192:5002 - 17; http://dx.doi.org/10.1128/JB.00542-10; PMID: 20656903
   PubMed Web of Science ®Google Scholar
• Duran-Pinedo AE, Paster B, Teles R, Frias-Lopez J. Correlation network analysis applied to complex biofilm communities. PLoS One 2011; 6:e28438; http://dx.doi.org/10.1371/journal.pone.0028438; PMID: 22163302
   PubMedGoogle Scholar
• Jenkinson HF. Beyond the oral microbiome. Environ Microbiol 2011; 13:3077 - 87; http://dx.doi.org/10.1111/j.1462-2920.2011.02573.x; PMID: 21906224
   PubMed Web of Science ®Google Scholar
• McLean JS, Fansler SJ, Majors PD, McAteer K, Allen LZ, Shirtliff ME, Lux R, Shi W. Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques. PLoS One 2012; 7:e32219; http://dx.doi.org/10.1371/journal.pone.0032219; PMID: 22403637
   PubMed Web of Science ®Google Scholar
• Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, et al. Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One 2012; 7:e37919; http://dx.doi.org/10.1371/journal.pone.0037919; PMID: 22675498
   PubMed Web of Science ®Google Scholar
• Ge X, Rodriguez R, Trinh M, Gunsolley J, Xu P. Oral microbiome of deep and shallow dental pockets in chronic periodontitis. PLoS One 2013; 8:e65520; http://dx.doi.org/10.1371/journal.pone.0065520; PMID: 23762384
   PubMed Web of Science ®Google Scholar
• Wade WG. The oral microbiome in health and disease. Pharmacol Res 2013; 69:137 - 43; http://dx.doi.org/10.1016/j.phrs.2012.11.006; PMID: 23201354
   PubMed Web of Science ®Google Scholar
• Peterson SN, Snesrud E, Schork NJ, Bretz WA. Dental caries pathogenicity: a genomic and metagenomic perspective. Int Dent J 2011; 61:Suppl 1 11 - 22; http://dx.doi.org/10.1111/j.1875-595X.2011.00025.x; PMID: 21726221
   PubMed Web of Science ®Google Scholar
• Takahashi N, Nyvad B. The role of bacteria in the caries process: ecological perspectives. J Dent Res 2011; 90:294 - 303; http://dx.doi.org/10.1177/0022034510379602; PMID: 20924061
   PubMed Web of Science ®Google Scholar
• Jenkinson HF, Lamont RJ. Oral microbial communities in sickness and in health. Trends Microbiol 2005; 13:589 - 95; http://dx.doi.org/10.1016/j.tim.2005.09.006; PMID: 16214341
   PubMed Web of Science ®Google Scholar
• Rickard AH, Gilbert P, High NJ, Kolenbrander PE, Handley PS. Bacterial coaggregation: an integral process in the development of multi-species biofilms. Trends Microbiol 2003; 11:94 - 100; http://dx.doi.org/10.1016/S0966-842X(02)00034-3; PMID: 12598132
   PubMed 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; 95:369 - 80; PMID: 3477852
   PubMedGoogle Scholar
• Fives-Taylor PM, Meyer DH, Mintz KP, Brissette C. Virulence factors of Actinobacillus actinomycetemcomitans. Periodontol 2000 1999; 20:136 - 67; http://dx.doi.org/10.1111/j.1600-0757.1999.tb00161.x; PMID: 10522226
   PubMed Web of Science ®Google Scholar
• Témoin S, Wu KL, Wu V, Shoham M, Han YW. Signal peptide of FadA adhesin from Fusobacterium nucleatum plays a novel structural role by modulating the filament’s length and width. FEBS Lett 2012; 586:1 - 6; http://dx.doi.org/10.1016/j.febslet.2011.10.047; PMID: 22108653
   PubMed Web of Science ®Google Scholar
• Lamont RJ, Jenkinson HF. Subgingival colonization by Porphyromonas gingivalis. Oral Microbiol Immunol 2000; 15:341 - 9; http://dx.doi.org/10.1034/j.1399-302x.2000.150601.x; PMID: 11154429
   PubMedGoogle Scholar
• Malm S, Jusko M, Eick S, Potempa J, Riesbeck K, Blom AM. Acquisition of complement inhibitor serine protease factor I and its cofactors C4b-binding protein and factor H by Prevotella intermedia. PLoS One 2012; 7:e34852; http://dx.doi.org/10.1371/journal.pone.0034852; PMID: 22514678
   PubMedGoogle Scholar
• Settem RP, Honma K, Stafford GP, Sharma A. Protein-linked glycans in periodontal bacteria: prevalence and role at the immune interface. Front Microbiol 2013; 4:310; http://dx.doi.org/10.3389/fmicb.2013.00310; PMID: 24146665
   PubMed Web of Science ®Google Scholar
• Bian J, Liu X, Cheng YQ, Li C. Inactivation of cyclic Di-GMP binding protein TDE0214 affects the motility, biofilm formation, and virulence of Treponema denticola. J Bacteriol 2013; 195:3897 - 905; http://dx.doi.org/10.1128/JB.00610-13; PMID: 23794624
   PubMed Web of Science ®Google Scholar
• Han YW, Wang X. Mobile microbiome: oral bacteria in extra-oral infections and inflammation. J Dent Res 2013; 92:485 - 91; http://dx.doi.org/10.1177/0022034513487559; PMID: 23625375
   PubMed Web of Science ®Google Scholar
• Hajishengallis G, Darveau RP, Curtis MA. The keystone-pathogen hypothesis. Nat Rev Microbiol 2012; 10:717 - 25; http://dx.doi.org/10.1038/nrmicro2873; PMID: 22941505
   PubMed Web of Science ®Google Scholar
• Paik S, Senty L, Das S, Noe JC, Munro CL, Kitten T. Identification of virulence determinants for endocarditis in Streptococcus sanguinis by signature-tagged mutagenesis. Infect Immun 2005; 73:6064 - 74; http://dx.doi.org/10.1128/IAI.73.9.6064-6074.2005; PMID: 16113327
   PubMed Web of Science ®Google Scholar
• Xu P, Alves JM, Kitten T, Brown A, Chen Z, Ozaki LS, Manque P, Ge X, Serrano MG, Puiu D, et al. Genome of the opportunistic pathogen Streptococcus sanguinis. J Bacteriol 2007; 189:3166 - 75; http://dx.doi.org/10.1128/JB.01808-06; PMID: 17277061
   PubMed Web of Science ®Google Scholar
• Paju S, Scannapieco FA. Oral biofilms, periodontitis, and pulmonary infections. Oral Dis 2007; 13:508 - 12; http://dx.doi.org/10.1111/j.1601-0825.2007.01410a.x; PMID: 17944664
   PubMed Web of Science ®Google Scholar
• Moodley A, Wood NH, Shangase SL. The relationship between periodontitis and diabetes: a brief review. SADJ 2013; 68:260 - , 262-4; PMID: 23971278
   PubMedGoogle Scholar
• Han YW. Oral health and adverse pregnancy outcomes - what’s next?. J Dent Res 2011; 90:289 - 93; http://dx.doi.org/10.1177/0022034510381905; PMID: 21041548
   PubMed Web of Science ®Google Scholar
• Yeoh N, Burton JP, Suppiah P, Reid G, Stebbings S. The role of the microbiome in rheumatic diseases. Curr Rheumatol Rep 2013; 15:314; http://dx.doi.org/10.1007/s11926-012-0314-y; PMID: 23378145
   PubMedGoogle Scholar
• Ismail Y, Mahendran V, Octavia S, Day AS, Riordan SM, Grimm MC, Lan R, Lemberg D, Tran TA, Zhang L. Investigation of the enteric pathogenic potential of oral Campylobacter concisus strains isolated from patients with inflammatory bowel disease. PLoS One 2012; 7:e38217; http://dx.doi.org/10.1371/journal.pone.0038217; PMID: 22666490
   PubMedGoogle Scholar
• Castellarin M, Warren RL, Freeman JD, Dreolini L, Krzywinski M, Strauss J, Barnes R, Watson P, Allen-Vercoe E, Moore RA, et al. Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma. Genome Res 2012; 22:299 - 306; http://dx.doi.org/10.1101/gr.126516.111; PMID: 22009989
   PubMed Web of Science ®Google Scholar
• Palmer RJ Jr.. Composition and development of oral bacterial communities. Periodontol 2000 2014; 64:20 - 39; http://dx.doi.org/10.1111/j.1600-0757.2012.00453.x; PMID: 24320954
   PubMed Web of Science ®Google Scholar
• Schultz-Haudt S, Bruce MA, Bibby BG. Bacterial factors in nonspecific gingivitis. J Dent Res 1954; 33:454 - 8; http://dx.doi.org/10.1177/00220345540330040301; PMID: 13184032
   PubMedGoogle Scholar
• MacDonald JB, Sutton RM, Knoll ML, Madlener EM, Grainger RM. The pathogenic components of an experimental fusospirochetal infection. J Infect Dis 1956; 98:15 - 20; http://dx.doi.org/10.1093/infdis/98.1.15; PMID: 13295619
   PubMed Web of Science ®Google Scholar
• Theilade E. The non-specific theory in microbial etiology of inflammatory periodontal diseases. J Clin Periodontol 1986; 13:905 - 11; http://dx.doi.org/10.1111/j.1600-051X.1986.tb01425.x; PMID: 3540019
   PubMed Web of Science ®Google Scholar
• Loesche WJ. Clinical and microbiological aspects of chemotherapeutic agents used according to the specific plaque hypothesis. J Dent Res 1979; 58:2404 - 12; http://dx.doi.org/10.1177/00220345790580120905; PMID: 41862
   PubMed Web of Science ®Google Scholar
• Marsh PD. Microbial ecology of dental plaque and its significance in health and disease. Adv Dent Res 1994; 8:263 - 71; PMID: 7865085
   PubMedGoogle Scholar
• Hajishengallis G, Lamont RJ. Beyond the red complex and into more complexity: the polymicrobial synergy and dysbiosis (PSD) model of periodontal disease etiology. Mol Oral Microbiol 2012; 27:409 - 19; http://dx.doi.org/10.1111/j.2041-1014.2012.00663.x; PMID: 23134607
   PubMed Web of Science ®Google Scholar
• Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307:1915 - 20; http://dx.doi.org/10.1126/science.1104816; PMID: 15790844
   PubMed Web of Science ®Google Scholar
• Savett DA, Progulske-Fox A. Restriction fragment length polymorphism analysis of two hemagglutinin loci, serotyping and agglutinating activity of Porphyromonas gingivalis isolates. Oral Microbiol Immunol 1995; 10:1 - 7; http://dx.doi.org/10.1111/j.1399-302X.1995.tb00110.x; PMID: 7644268
   PubMedGoogle Scholar
• Ménard C, Mouton C. Clonal diversity of the taxon Porphyromonas gingivalis assessed by random amplified polymorphic DNA fingerprinting. Infect Immun 1995; 63:2522 - 31; PMID: 7790065
   PubMed Web of Science ®Google Scholar
• Zijnge V, Harmsen HJ, Kleinfelder JW, van der Rest ME, Degener JE, Welling GW. Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients. Oral Microbiol Immunol 2003; 18:59 - 65; http://dx.doi.org/10.1034/j.1399-302X.2003.180110.x; PMID: 12588461
   PubMedGoogle Scholar
• Blome B, Braun A, Sobarzo V, Jepsen S. Molecular identification and quantification of bacteria from endodontic infections using real-time polymerase chain reaction. Oral Microbiol Immunol 2008; 23:384 - 90; http://dx.doi.org/10.1111/j.1399-302X.2008.00440.x; PMID: 18793361
   PubMedGoogle Scholar
• Colombo AP, Boches SK, Cotton SL, Goodson JM, Kent R, Haffajee AD, Socransky SS, Hasturk H, Van Dyke TE, Dewhirst F, et al. Comparisons of subgingival microbial profiles of refractory periodontitis, severe periodontitis, and periodontal health using the human oral microbe identification microarray. J Periodontol 2009; 80:1421 - 32; http://dx.doi.org/10.1902/jop.2009.090185; PMID: 19722792
   PubMed Web of Science ®Google Scholar
• Sakamoto M, Umeda M, Benno Y. Molecular analysis of human oral microbiota. J Periodontal Res 2005; 40:277 - 85; http://dx.doi.org/10.1111/j.1600-0765.2005.00793.x; PMID: 15853975
   PubMed Web of Science ®Google Scholar
• Nyvad B, Crielaard W, Mira A, Takahashi N, Beighton D. Dental caries from a molecular microbiological perspective. Caries Res 2013; 47:89 - 102; http://dx.doi.org/10.1159/000345367; PMID: 23207320
   PubMed Web of Science ®Google Scholar
• Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010; 11:31 - 46; http://dx.doi.org/10.1038/nrg2626; PMID: 19997069
   PubMed Web of Science ®Google Scholar
• Zaura E. Next-generation sequencing approaches to understanding the oral microbiome. Adv Dent Res 2012; 24:81 - 5; http://dx.doi.org/10.1177/0022034512449466; PMID: 22899686
   PubMedGoogle Scholar
• Burne RA, Zeng L, Ahn SJ, Palmer SR, Liu Y, Lefebure T, Stanhope MJ, Nascimento MM. Progress dissecting the oral microbiome in caries and health. Adv Dent Res 2012; 24:77 - 80; http://dx.doi.org/10.1177/0022034512449462; PMID: 22899685
   PubMedGoogle Scholar
• Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004; 304:66 - 74; http://dx.doi.org/10.1126/science.1093857; PMID: 15001713
   PubMed Web of Science ®Google Scholar
• Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004; 428:37 - 43; http://dx.doi.org/10.1038/nature02340; PMID: 14961025
   PubMed Web of Science ®Google Scholar
• Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, et al. Comparative metagenomics of microbial communities. Science 2005; 308:554 - 7; http://dx.doi.org/10.1126/science.1107851; PMID: 15845853
   PubMed Web of Science ®Google Scholar
• Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012; 486:207 - 14; http://dx.doi.org/10.1038/nature11234; PMID: 22699609
   PubMed Web of Science ®Google Scholar
• Human Microbiome Project Consortium. A framework for human microbiome research. Nature 2012; 486:215 - 21; http://dx.doi.org/10.1038/nature11209; PMID: 22699610
   PubMed Web of Science ®Google Scholar
• Dark MJ. Whole-genome sequencing in bacteriology: state of the art. Infect Drug Resist 2013; 6:115 - 23; http://dx.doi.org/10.2147/IDR.S35710; PMID: 24143115
   PubMedGoogle Scholar
• Dewhirst FE, Klein EA, Thompson EC, Blanton JM, Chen T, Milella L, Buckley CM, Davis IJ, Bennett ML, Marshall-Jones ZV. The canine oral microbiome. PLoS One 2012; 7:e36067; http://dx.doi.org/10.1371/journal.pone.0036067; PMID: 22558330
   PubMedGoogle Scholar
• Griffen AL, Beall CJ, Campbell JH, Firestone ND, Kumar PS, Yang ZK, Podar M, Leys EJ. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. ISME J 2012; 6:1176 - 85; http://dx.doi.org/10.1038/ismej.2011.191; PMID: 22170420
   PubMed Web of Science ®Google Scholar
• Jiang W, Zhang J, Chen H. Pyrosequencing analysis of oral microbiota in children with severe early childhood dental caries. Curr Microbiol 2013; 67:537 - 42; http://dx.doi.org/10.1007/s00284-013-0393-7; PMID: 23743597
   PubMed Web of Science ®Google Scholar
• Simón-Soro A, Tomás I, Cabrera-Rubio R, Catalan MD, Nyvad B, Mira A. Microbial geography of the oral cavity. J Dent Res 2013; 92:616 - 21; http://dx.doi.org/10.1177/0022034513488119; PMID: 23674263
   PubMed Web of Science ®Google Scholar
• Jiang B, Liang X, Chen Y, Ma T, Liu L, Li J, Jiang R, Chen T, Zhang X, Li S. Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome. Sci Rep 2012; 2:936; PMID: 23226834
   PubMed Web of Science ®Google Scholar
• Kraneveld EA, Buijs MJ, Bonder MJ, Visser M, Keijser BJ, Crielaard W, Zaura E. The relation between oral Candida load and bacterial microbiome profiles in Dutch older adults. PLoS One 2012; 7:e42770; http://dx.doi.org/10.1371/journal.pone.0042770; PMID: 22900048
   PubMed Web of Science ®Google Scholar
• Hsiao WW, Li KL, Liu Z, Jones C, Fraser-Liggett CM, Fouad AF. Microbial transformation from normal oral microbiota to acute endodontic infections. BMC Genomics 2012; 13:345; http://dx.doi.org/10.1186/1471-2164-13-345; PMID: 22839737
   PubMed Web of Science ®Google Scholar
• Pinto AJ, Raskin L. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One 2012; 7:e43093; http://dx.doi.org/10.1371/journal.pone.0043093; PMID: 22905208
   PubMed Web of Science ®Google Scholar
• Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504 - 9; http://dx.doi.org/10.1016/j.mib.2007.08.006; PMID: 17923431
   PubMed Web of Science ®Google Scholar
• Faruque SM, Mekalanos JJ. Pathogenicity islands and phages in Vibrio cholerae evolution. Trends Microbiol 2003; 11:505 - 10; http://dx.doi.org/10.1016/j.tim.2003.09.003; PMID: 14607067
   PubMed Web of Science ®Google Scholar
• Lesic B, Carniel E. Horizontal transfer of the high-pathogenicity island of Yersinia pseudotuberculosis. J Bacteriol 2005; 187:3352 - 8; http://dx.doi.org/10.1128/JB.187.10.3352-3358.2005; PMID: 15866919
   PubMed Web of Science ®Google Scholar
• Malachowa N, DeLeo FR. Mobile genetic elements of Staphylococcus aureus. Cell Mol Life Sci 2010; 67:3057 - 71; http://dx.doi.org/10.1007/s00018-010-0389-4; PMID: 20668911
   PubMed Web of Science ®Google Scholar
• Thomas T, Gilbert J, Meyer F. Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2012; 2:3; http://dx.doi.org/10.1186/2042-5783-2-3; PMID: 22587947
   PubMedGoogle Scholar
• Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. [see comments] Science 1995; 269:496 - 512; http://dx.doi.org/10.1126/science.7542800; PMID: 7542800
   PubMed Web of Science ®Google Scholar
• Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE. The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford) 2010; 2010:baq013; http://dx.doi.org/10.1093/database/baq013; PMID: 20624719
   PubMed Web of Science ®Google Scholar
• Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 2005; 102:13950 - 5; http://dx.doi.org/10.1073/pnas.0506758102; PMID: 16172379
   PubMed Web of Science ®Google Scholar
• Cornejo OE, Lefébure T, Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, et al. Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol 2013; 30:881 - 93; http://dx.doi.org/10.1093/molbev/mss278; PMID: 23228887
   PubMed Web of Science ®Google Scholar
• Xie G, Chain PS, Lo CC, Liu KL, Gans J, Merritt J, Qi F. Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Mol Oral Microbiol 2010; 25:391 - 405; http://dx.doi.org/10.1111/j.2041-1014.2010.00587.x; PMID: 21040513
   PubMed Web of Science ®Google Scholar
• Wang J, Qi J, Zhao H, He S, Zhang Y, Wei S, Zhao F. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep 2013; 3:1843; PMID: 23673380
   PubMed Web of Science ®Google Scholar
• Yoshino T, Laine ML, van Winkelhoff AJ, Dahlén G. Genotype variation and capsular serotypes of Porphyromonas gingivalis from chronic periodontitis and periodontal abscesses. FEMS Microbiol Lett 2007; 270:75 - 81; http://dx.doi.org/10.1111/j.1574-6968.2007.00651.x; PMID: 17439635
   PubMed Web of Science ®Google Scholar
• Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simón-Soro A, Pignatelli M, Mira A. The oral metagenome in health and disease. ISME J 2012; 6:46 - 56; http://dx.doi.org/10.1038/ismej.2011.85; PMID: 21716308
   PubMed Web of Science ®Google Scholar
• Noorda WD, Purdell-Lewis DJ, van Montfort AM, Weerkamp AH. Monobacterial and mixed bacterial plaques of Streptococcus mutans and Veillonella alcalescens in an artificial mouth: development, metabolism, and effect on human dental enamel. Caries Res 1988; 22:342 - 7; http://dx.doi.org/10.1159/000261134; PMID: 3214847
   PubMed Web of Science ®Google Scholar
• Gross EL, Leys EJ, Gasparovich SR, Firestone ND, Schwartzbaum JA, Janies DA, Asnani K, Griffen AL. Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol 2010; 48:4121 - 8; http://dx.doi.org/10.1128/JCM.01232-10; PMID: 20826648
   PubMed Web of Science ®Google Scholar
• Merritt J, Qi F. The mutacins of Streptococcus mutans: regulation and ecology. Mol Oral Microbiol 2012; 27:57 - 69; http://dx.doi.org/10.1111/j.2041-1014.2011.00634.x; PMID: 22394465
   PubMed Web of Science ®Google Scholar
• Campan P, Planchand PO, Duran D. Pilot study on n-3 polyunsaturated fatty acids in the treatment of human experimental gingivitis. J Clin Periodontol 1997; 24:907 - 13; http://dx.doi.org/10.1111/j.1600-051X.1997.tb01210.x; PMID: 9442428
   PubMed Web of Science ®Google Scholar
• Kesavalu L, Bakthavatchalu V, Rahman MM, Su J, Raghu B, Dawson D, Fernandes G, Ebersole JL. Omega-3 fatty acid regulates inflammatory cytokine/mediator messenger RNA expression in Porphyromonas gingivalis-induced experimental periodontal disease. Oral Microbiol Immunol 2007; 22:232 - 9; http://dx.doi.org/10.1111/j.1399-302X.2007.00346.x; PMID: 17600534
   PubMedGoogle Scholar
• Jain S, Darveau RP. Contribution of Porphyromonas gingivalis lipopolysaccharide to periodontitis. Periodontol 2000 2010; 54:53 - 70; http://dx.doi.org/10.1111/j.1600-0757.2009.00333.x; PMID: 20712633
   PubMed Web of Science ®Google Scholar
• Caufield PW, Dasanayake AP, Li Y, Pan Y, Hsu J, Hardin JM. Natural history of Streptococcus sanguinis in the oral cavity of infants: evidence for a discrete window of infectivity. Infect Immun 2000; 68:4018 - 23; http://dx.doi.org/10.1128/IAI.68.7.4018-4023.2000; PMID: 10858217
   PubMed Web of Science ®Google Scholar
• Kreth J, Merritt J, Shi W, Qi F. Competition and coexistence between Streptococcus mutans and Streptococcus sanguinis in the dental biofilm. J Bacteriol 2005; 187:7193 - 203; http://dx.doi.org/10.1128/JB.187.21.7193-7203.2005; PMID: 16237003
   PubMed Web of Science ®Google Scholar
• Chen L, Ge X, Dou Y, Wang X, Patel JR, Xu P. Identification of hydrogen peroxide production-related genes in Streptococcus sanguinis and their functional relationship with pyruvate oxidase. Microbiology 2011; 157:13 - 20; http://dx.doi.org/10.1099/mic.0.039669-0; PMID: 20847003
   PubMed Web of Science ®Google Scholar
• Jagtap P, McGowan T, Bandhakavi S, Tu ZJ, Seymour S, Griffin TJ, Rudney JD. Deep metaproteomic analysis of human salivary supernatant. Proteomics 2012; 12:992 - 1001; http://dx.doi.org/10.1002/pmic.201100503; PMID: 22522805
   PubMed Web of Science ®Google Scholar
• Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biol 2007; 8:R10; http://dx.doi.org/10.1186/gb-2007-8-1-r10; PMID: 17224063
   PubMedGoogle Scholar
• Hunter SJ, Easton S, Booth V, Henderson B, Wade WG, Ward JM. Selective removal of human DNA from metagenomic DNA samples extracted from dental plaque. J Basic Microbiol 2011; 51:442 - 6; http://dx.doi.org/10.1002/jobm.201000372; PMID: 21298692
   PubMed Web of Science ®Google Scholar
• Mullany P, Hunter S, Allan E. Metagenomics of dental biofilms. Adv Appl Microbiol 2008; 64:125 - 36; http://dx.doi.org/10.1016/S0065-2164(08)00404-8; PMID: 18485283
   PubMed Web of Science ®Google Scholar
• Segata N, Boernigen D, Tickle TL, Morgan XC, Garrett WS, Huttenhower C. Computational meta’omics for microbial community studies. Mol Syst Biol 2013; 9:666; http://dx.doi.org/10.1038/msb.2013.22; PMID: 23670539
   PubMed Web of Science ®Google Scholar