How has genomics altered our view of caries microbiology?

Caries Research

Volumn 42, Issue 5, 2008, Pages 319-327

  Russell, R R B ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Cariogenic microflora; Genome sequencing; Genomics; Streptococcus mutans

Indexed keywords

ARTICLE; BACTERIAL GENOME; DENTAL CARIES; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; HUMAN; METHODOLOGY; MICROBIOLOGY; STREPTOCOCCUS MUTANS; TOOTH PLAQUE;

DENTAL CARIES; DENTAL PLAQUE; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; GENOMICS; HUMANS; STREPTOCOCCUS MUTANS;

EID: 49149092007     PISSN: 00086568     EISSN: None     Source Type: Journal    
DOI: 10.1159/000151326     Document Type: Article

References (93)

1. Aas JA, Griffen AL, Dardis SR, Lee AM, Olsen I, Dewhirst FE, Leys EJ, Paster BJ: Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol 2008;46:1407-1417.
2. Ahn SJ, Wen ZT, Burne RA: Multilevel control of competence development and stress tolerance in Streptococcus mutans UA159. Infect Immun 2006;74:1631-1642.
3. Ajdic D, McShan WM, McLaughlin RE, Savic G, Chang J, Carson MB, Primeaux C, Tian R, Kenton S, Jia H, Lin S, Qian Y, Li S, Zhu H, Najar F, Lai H, White J, Roe BA, Ferretti JJ: Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc Natl Acad Sci USA 2002;99:14434-14439.
4. Ajdic D, Pham VT: Global transcriptional analysis of Streptococcus mutans sugar transporters using microarrays. J Bacteriol 2007;189:5049-5059.
5. Alam S, Brailsford SR, Adams S, Allison C, Sheehy E, Zoitopoulos L, Kidd EA, Beighton D: Genotypic heterogeneity of Streptococcus oralis and distinct aciduric subpopulations in human dental plaque. Appl Environ Microbiol 2000;66:3330-3336.
6. Banas JA, Vickerman MM: Glucan-binding proteins of the oral streptococci. Crit Rev Oral Biol Med 2003;14:89-99.
7. Becker MR, Paster BJ, Leys EJ, Moeschberger ML, Kenyon SG, Galvin JL, Boches SK, Dewhirst FE, Griffen AL: Molecular analysis of bacterial species associated with childhood caries. J Clin Microbiol 2002;40:1001-1009.
8. Beighton D: The complex oral microflora of high-risk individuals and groups and its role in the caries process. Community Dent Oral Epidemiol 2005;33:248-255.
9. Beighton D, Russell RRB, Whiley RA: A simple biochemical scheme for the differentiation of Streptococcus mutans and Streptococcus sobrinus. Caries Res 1991;25:174-178.
10. Bentley S: Genomic 'valleys of death'. Nat Rev Microbiol 2008;6:260-261.
11. Biswas I, Drake L, Erkina D, Biswas S: Involvement of sensor kinases in the stress tolerance response of Streptococcus mutans. J Bacteriol 2008;190:68-77.
12. Boekhorst J, Siezen RJ, Zwahlen MC, Vilanova D, Pridmore RD, Mercenier A, Kleerebezem M, de Vos WM, Brussow H, Desiere F: The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content. Microbiolog y 2004;150:3601-3611.
13. Bolotin A, Quinquis B, Renault P, Sorokin A, Ehrlich SD, Kulakauskas S, Lapidus A, Golts-man E, Mazur M, Pusch GD, Fonstein M, Overbeek R, Kyprides N, Purnelle B, Prozzi D, Ngui K, Masuy D, Hancy F, Burteau S, Boutry M, Delcour J, Goffeau A, Hols P: Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus. Nat Biotechnol 2004;22:1554-1558.
14. Byun R, Nadkarni MA, Chhour KL, Martin FE, Jacques NA, Hunter N: Quantitative analysis of diverse Lactobacillus species present in advanced dental caries. J Clin Microbiol 2004; 42:3128 -3136.
15. Cai H, Rodriguez BT, Zhang W, Broadbent JR, Steele JL: Genotypic and phenotypic characterization of Lactobacillus casei strains isolated from different ecological niches suggests frequent recombination and niche specificity. Microbiology 2007;153:2655-2665.
16. Caufield PW, Li Y, Dasanayake A, Saxena D: Diversity of lactobacilli in the oral cavities of young women with dental caries. Caries Res 2007a;41:2-8.
17. Caufield PW, Saxena D, Fitch D, Li Y: Population structure of plasmid-containing strains of Streptococcus mutans, a member of the human indigenous biota. J Bacteriol 2007b;189:1238-1243.
18. Chhour KL, Nadkarni MA, Byun R, Martin FE, Jacques NA, Hunter N: Molecular analysis of microbial diversity in advanced caries. J Clin Microbiol 2005;43:843-849.
19. Corby PM, Lyons-Weiler J, Bretz WA, Hart TC, Aas JA, Boumenna T, Goss J, Corby AL, Junior HM, Weyant RJ, Paster BJ: Microbial risk indicators of early childhood caries. J Clin Microbiol 2005;43:5753-5759.
20. Dal Bello F, Hertel C: Oral cavity as natural reservoir for intestinal lactobacilli. Syst Appl Microbiol 2006;29:69-76.
21. Delorme C, Poyart C, Ehrlich SD, Renault P: Extent of horizontal gene transfer in evolution of Streptococci of the salivarius group. J Bacteriol 2007;189:1330-1341.
22. de Soet JJ, Holbrook WP, Magnusdottir MO, De Graaff J: Streptococcus sobrinus and Streptooccus mutans in a longitudinal study of dental caries. Microb EcolHealth Dis 1993;6:237-243.
23. de Soet JJ, Nyvad B, Kilian M: Strain-related acid production by oral streptococci. Caries Res 2000;34:486-490.
24. de Soet JJ, van Loveren C, Lammens AJ, Pavicic MJ, Homburg CH, ten Cate JM, de Graaff J: Differences in cariogenicity between fresh isolates of Streptococcus sobrinus and Streptococcus mutans. Caries Res 1991; 25:116-122.
25. Ehrlich GD, Hu FZ, Shen K, Stoodley P, Post JC: Bacterial plurality as a general mechanism driving persistence in chronic infections. Clin Orthop Relat Res 2005: 20-24.
26. Forney LJ, Zhou X, Brown CJ: Molecular microbial ecology: land of the one-eyed king. Curr Opin Microbiol 2004;7:210-220.
27. Fux CA, Shirtliff M, Stoodley P, Costerton JW: Can laboratory reference strains mirror 'real-world' pathogenesis? Trends Microbiol 2005;13:58-63.
28. Gold OG, Jordan HV, Van Houte J: A selective medium for Streptococcus mutans. Arch Oral Biol 1973;18:1357-1364.
29. Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J, Barbadora K, Klimke W, Dernovoy D, Tatusova T, Parkhill J, Bentley SD, Post JC, Ehrlich GD, Hu FZ: Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol 2007;189:8186-8195.
30. Igarashi T: Deletion in sortase gene of Streptococcus mutans Ingbritt. Oral Microbiol Immunol 2004; 19:210-213.
31. Jakubovics NS, Gill SR, Iobst SE, Vickerman MM, Kolenbrander PE: Regulation of gene expression in a mixed-genus community: stabilized arginine biosynthesis in Streptococcus gordonii by coaggregation with Actinomyces naeslundii. J Bacteriol 2008;190:3646-3657.
32. Jakubovics NS, Stromberg N, van Dolleweerd CJ, Kelly CG, Jenkinson HF: Differential binding specificities of oral streptococcal antigen I/II family adhesins for human or bacterial ligands. Mol Microbiol 2005;55:1591-1605.
33. Juric H, Dukic W, Jankovic B, Karlovic Z, Pavelic B: Suppression of salivary Streptococcus mutans and lactobacilli by topical caries preventive agents. Cent Eur J Public Health 2003;11:219-222.
34. Kilic AO, Honeyman AL, Tao L: Overlapping substrate specificity for sucrose and maltose of two binding protein-dependent sugar uptake systems in Streptococcus mutans. FEMS Microbiol Lett 2007;266:218-223.
35. Kleinberg I: A mixed-bacteria ecological approach to understanding the role of the oral bacteria in dental caries causation: an alternative to Streptococcus mutans and the specific-plaque hypothesis. Crit Rev Oral Biol Med 2002;13:108-125.
36. Kolenbrander PE, Andersen RN, Blehert DS, Eg-land PG, Foster JS, Palmer RJ: Communication among oral bacteria. Microbiol Mol Biol Rev 2002;66:486-505.
37. Kreth J, Merritt J, Zhu L, Shi W, Qi F: Cell density- and ComE-dependent expression of a group of mutacin and mutacin-like genes in Streptococcus mutans. FEMS Microbiol Lett 2006;265:11-17.
38. Lefébure T, Stanhope MJ: Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol 2007;8:R71.
39. Len AC, Harty DW, Jacques NA: Proteome analysis of Streptococcus mutans metabolic phenotype during acid tolerance. Microbiology 2004a;150: 1353-1366.
40. Len AC, Harty DW, Jacques NA: Stress-responsive proteins are upregulated in Streptococcus mutans during acid tolerance. Microbiology 2004b;150:1339-1351.
41. Lévesque CM, Mair RW, Perry JA, Lau PC, Li YH, Cvitkovitch DG: Systemic inactivation and phenotypic characterization of two-component systems in expression of Streptococcus mutans virulence properties. Lett Appl Microbiol 2007;45:398-404.
42. Lévesque CM, Voronejskaia E, Huang YC, Mair RW, Ellen R P, Cvitkovitch DG: Involvement of sortase anchoring of cell wall proteins in biofilm formation by Streptococcus mutans. Infect Immun 2005;73:3773-3777.
43. Li Y, Caufield PW: Arbitrarily primed polymerase chain reaction fingerprinting for the genotypic identification of mutans streptococci from humans. Oral Microbiol Immunol 1998;13:17-22.
44. Loesche WJ: Role of Streptococcus mutans in human dental decay. Microbiol Rev 1986;50:353-380.
45. Luppens SB, Kara D, Bandounas L, Jonker MJ, Wittink FR, Bruning O, Breit TM, Ten Cate JM, Crielaard W: Effect of Veillonella parvula on the antimicrobial resistance and gene expression of Streptococcus mutans grown in a dual-species biofilm. Oral Microbiol Immunol 2008;23:183-189.
46. Makinen KK, Alanen P, Isokangas P, Isotupa K, Soderling E, Makinen P-L, Wenhui W, Weijian W, Xiaochi C, Yi W, Boxue Z: Thirty-nine-month xylitol chewing-gum programme in initially 8-year-old school children: a feasibility study focusing on mutans streptococci and lactobacilli. Int Dent J 2008;58:41-50.
47. Marri PR, Hao W, Golding GB: Gene gain and gene loss in streptococcus: is it driven by habitat? Mol Biol Evol 2006;23:2379-2391.
48. Marsh PD: Are dental diseases examples of ecological catastrophes? Microbiology 2003;149:279-294.
49. Motegi M, Takagi Y, Yonezawa H, Hanada N, Terajima J, Watanabe H, Senpuku H: Assessment of genes associated with Streptococcus mutans biofilm morphology. Appl Environ Microbiol 2006;72:6277-6287.
50. Munson MA, Banerjee A, Watson TF, Wade WG: Molecular analysis of the microflora associated with dental caries. J Clin Microbiol 2004;42:3023-3029.
51. Murakami Y, Nakano Y, Yamashit a Y, Koga T: Identification of a frameshift mutation resulting in premature termination and loss of cell wall anchoring of the PAc antigen of Streptococcu s mutans GS -5. Infect Immun 1997;65:794-797.
52. Nakano K, Lapirattanakul J, Nomura R, Nemoto H, Alaluusua S, Gronroos L , Vaara M, Hamada S, Ooshima T, Nakagawa I: Streptococcus mutans clonal variation revealed by multilocus sequence typing. J Clin Microbiol 2007;45:2616-2625.
53. Nakano K, Tsuji M, Nishimura K, Nomura R, Ooshima T: Contribution of cell surface protein antigen PAc of Streptococcus mutans to bacteremia. Microbes Infect 2006;8:114-121.
54. Nakano Y, Shibata Y, Kawada M, Kojima M, Fukamachi H, Shibata Y, Okano S, Matsushima K, Abiko Y, Yamashita Y: A searchable database for proteomes of oral microorganisms. Oral Microbiol Immunol 2005;20:344-348.
55. Napimoga MH, Kamiya RU, Rosa RT, Rosa EA, Hofling JF, Mattos-Graner RO, Goncalves RB: Genotypic diversity and virulence traits of Streptococcus mutans in caries-free and caries-active individuals. J Med Microbiol 2004;53:697-703.
56. Okada M, Soda Y, Hayashi F, Doi T, Suzuki J, Miura K, Kozai K: Longitudinal study of dental caries incidence associated with Streptococcus mutans and Streptococcus sobrinus in pre-school children. J Med Microbiol 2005;54:661-665.
57. Old LA, Lowes S, Russell RRB: Genomic variation in Streptococcus mutans: deletions affecting the multiple pathways of β-glucoside metabolism. Oral Microbiol Immunol 2006;21:21-27.
58. Parche S, Amon J, Jankovic I, Rezzonico E, Beleut M, Barutcu H, Schendel I, Eddy MP, Burkovski A, Arigoni F, Titgemeyer F: Sugar transport systems of Bifidobacterium longum NCC2705. J Mol Microbiol Biotechnol 2007;12:9-19.
59. Petersen FC, Fimland G, Scheie AA: Purification and functional studies of a potent modified quorum-sensing peptide and a two-peptide bacteriocin in Streptococcus mutans. Mol Microbiol 2006;61:1322-1334.
60. Petersen FC, Tao L, Scheie AA: DNA binding-uptake system: a link between cell-to-cell communication and biofilm formation. J Bacteriol 2005;187:4392-4400.
61. Rathsam C, Eaton RE, Simpson CL, Browne GV, Berg T, Harty DW, Jacques NA: Up-regulation of competence- but not stress-responsive proteins accompanies an altered metabolic phenotype in Streptococcus mutans biofilms. Microbiology 2005a;151:1823-1837.
62. Rathsam C, Eaton RE, Simpson CL, Browne GV, Valova VA, Harty DW, Jacques NA: Two-dimensional fluorescence difference gel electrophoretic analysis of Streptococcus mutans biofilms. J Proteome Res 2005b;4: 2161-2173.
63. Robinson WG, Old LA, Shah DSH, Russell RRB: Chromosomal insertions and deletions in Streptococcus mutans . Caries Res 2003;37:148-156.
64. Rupf S, Merte K, Eschrich K, Kneist S: Streptococcus sobrinus in children and its influence on caries activity. Eur Arch Paediatr Dent 2006;7:17-22.
65. Russell MW, Bergmeier LA, Zanders ED, Lehner T: Protein antigens of Streptococcus mutans: purification and properties of a double antigen and its protease-resistant component. Infect Immun 1980;28:486-493.
66. Russell RRB: Wall-associated protein antigens of Streptococcus mutans. J Gen Microbiol 1979;114:109-115.
67. Russell RRB: The application of molecular genetics to the microbiology of dental caries. Caries Res 1994;28:69-82.
68. Russell RRB: The Molecular Biology of Cario-genic Bacteria; in AH Rogers (ed): Molecular Oral Microbiology. Norwich, Caister Academic Press, 2008, pp 109-133.
69. Sansone C, Van Houte J, Joshipura K, Kent R, Margolis HC: The association of mutans streptococci and non-mutans streptococci capable of acidogenesis at a low pH with dental caries on enamel and root surfaces. J Dent Res 1993;72:508-516.
70. Sato Y, Okamoto K, Kizaki H: gbpC and pac gene mutations detected in Streptococcus mutans strain GS-5. Oral Microbiol Immunol 2002;17:263-266.
71. Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F: The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc Natl Acad Sci USA 2002;99:14422-14427.
72. Shah DS, Joucla G, Remaud-Simeon M, Russell RRB: Conserved repeat motifs and glucan binding by glucansucrases of oral streptococci and Leuconostoc mesenteroides. J Bacteriol 2004;186:8301-8308.
73. Shah DS, Russell RRB: A novel glucan-binding protein with lipase activity from the oral pathogen Streptococcus mutans. Microbiology 2004;150:1947-1956.
74. Sipahi Ogretme M, Do T, Gilbert S, Clark D, Wade WG, Beig hton D: Mult i locus se quence typing (MLST) of Streptococcus mutans. Caries Res 2006;40:350.
75. Svensater G, Borgstrom M, Bowden GH, Edwardsson S: The acid-tolerant microbiota associated with plaque from initial caries and healthy tooth surfaces. Caries Res 2003;37:395-403.
76. Takahashi N, Nyvad B: Caries ecology revisited: microbial dynamics and the caries process. Caries Res 2008, in press.
77. Tanzer JM: Quantitative considerations in microbiological evaluations for caries: risks for type II errors resulting from use of MSB agar. Oral Microbiol Immunol 1986;1:28-30.
78. Tanzer JM, Livingston J, Thompson AM: The microbiolog y of primar y dental caries in humans. J Dent Educ 2001;65:1028-1037.
79. 2: a possible counteroffensive strategy for interspecies competition. Mol Microbiol 2007;63:872-880.
80. van der Ploeg JR: Regulation of bacteriocin production in Streptococcus mutans by the quorum-sensing system required for development of genetic competence. J Bacteriol 2005;187:3980-3989.
81. van Hijum SA, Kralj S, Ozimek LK, Dijkhuizen L, van Geel-Schutten IG: Structure-function relationships of glucansucrase and fructan-sucrase enzymes from lactic acid bacteria. Microbiol Mol Biol Rev 2006;70:157-176.
82. van Houte J: Role of micro-organisms in caries etiology. J Dent Res 1994;73:672-681.
83. Van Palenstein Helderman WH, Ijsseldijk M, Huis in 't Veld JH:A selective medium for the two major subgroups of the bacterium Streptococcus mutans isolated from human dental plaque and saliva. Arch Oral Biol 1983;28:599-603.
84. Waterhouse JC, Russell RRB: Dispensable genes and foreign DNA in Streptococcus mutans. Microbiolog y 2006;152:1777-1788.
85. Waterhouse JC, Swan DC, Russell RRB: Comparative genome hybridisation of Streptococcus mutans strains. Oral Microbiol Immunol 2007;22:103-110.
86. Webb AJ, Homer KA, Hosie AH: A phosphoenolpyruvate-dependent phosphotransfer-ase system is the principal maltose transporter in Streptococcus mutans. J Bacteriol 2007;189:3322-3327.
87. Webb AJ, Homer KA, Hosie AH: Two closely related ABC transporters in Streptococcus mutans are involved in disaccharide and/or oligosaccharide uptake. J Bacteriol 2008;190:168-178.
88. Wen ZT, Baker HV, Burne RA: Influence of BrpA on critical viru lence attributes of Streptococcus mutans. J Bacteriol 2006;188:2983-2992.
89. Whiley RA, Beighton D: Current classification of the oral streptococci. Oral Microbiol Immunol 1998;13:195-216.
90. Wilkins JC, Homer KA, Beighton D: Analysis of Streptococcus mutans proteins modulated by culture under acidic conditions. Appl Environ Microbiol 2002;68:2382-2390.
91. Wright WG, Thelwell C, Svensson B, Russell RRB: Inhibition of catalytic and glucan-binding activities of a streptococcal GTF forming insoluble glucans. Caries Res 2002;36:353-359.
92. Yoo SY, Kim PS, Hwang HK, Lim SH, Kim KW, Choe SJ, Min BM, Kook JK: Identification of non-mutans streptococci organisms in dental plaques recovering on mitis-salivarius bacitracin agar medium. J Microbiol 2005;43:204-208.
93. Zhu L, Kreth J, Cross SE, Gimzewski JK, Shi W, Qi F: Functional characterization of cell wall associated protein WapA in Streptococcus mutans . Microbiolog y 2006;152:2395-2404.