Chapter 3 : Genomes of and

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This chapter talks about the closest relatives of that are the commensals , , and, in particular, the important pathogen and the still relatively unknown . The genetic diversity among strains may have important consequences in the oral cavity. Draft genomes display an artificially high total number of genes and number of paralogs due to sequencing errors and gaps leading to gene fragmentation, as well as low-quality redundant sequences at contig ends. The verification results in the conclusion that this observation is not due to the fact that (i) all but one of the non- genomes studied are draft genomes, and (ii) gene prediction standards differ among sequencing centers. First, the closed B6 genome displays a higher coding percentage. Second, the coding density was measured in three unpublished draft genomes obtained from three different sequencing centers, and the average coding percentage was 84.9%. The previous observation that virtually every independent isolate of represents a distinct species according to traditional taxonomic principles is supported by our multigenome analysis. The significant sharing of core genes between and reinforces the conclusion that is one lineage of the complex.

Citation: Tettelin H, Kilian M. 2011. Genomes of and , p 37-42. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch3
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1. Bek-Thomsen, M.,, H. Tettelin,, I. Hance,, K. E. Nelson, and, M. Kilian. 2008. Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a non-culture strategy. Infect. Immun. 76: 18891896.
2. Bishop, C. J.,, D. M. Aanensen,, G. E. Jordan,, M. Kilian,, W. P. Hanage, and, B. G. Spratt. 2009. Assigning strains to bacterial species via the internet. BMC Biol. 7: 3.
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5. DeSoet, J. J.,, B. Nyvad, and, M. Kilian. 2000. Strain-related acid production by oral streptococci. Caries Res. 34: 486490.
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7. Dowson, C. G.,, T. J. Coffey, and, B. G. Spratt. 1994. Origin and molecular epidemiology of penicillin-binding-protein-mediated resistance to beta-lactam antibiotics. Trends Microbiol. 2: 361366.
8. Fitzsimmons, S.,, M. Evans,, C. Pearce,, M. J. Sheridan,, R. Wientzen,, G. Bowden, and, M. F. Cole. 1996. Clonal diversity of Streptococcus mitis biovar 1 isolates from the oral cavity of human neonates. Clin. Diagn. Lab. Immunol. 3: 517522.
9. Hakenbeck, R.,, N. Balmelle,, B. Weber,, C. Gardes,, W. Keck, and, A. de Saizieu. 2001. Mosaic genes and mosaic chromosomes: intra-and interspecies genomic variation of Streptococcus pneumoniae. Infect. Immun. 69: 24772486.
10. Håvarstein, L. S.,, R. Hakenbeck, and, P. Gaustad. 1997. Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges. J. Bacteriol. 179: 65896594.
11. Hohwy, J.,, and M. Kilian. 1995. Clonal diversity of the Streptococcus mitis biovar 1 population in the human oral cavity and pharynx. Oral Microbiol. Immunol. 10: 1925.
12. Hohwy, J.,, J. Reinholdt, and, M. Kilian. 2001. Population dynamics of Streptococcus mitis in its natural habitat. Infect. Immun. 69: 60556063.
13. Hoshino, T.,, T. Fujiwara, and, M. Kilian. 2005. Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients. J. Clin. Microbiol. 43: 60736085.
14. Kawamura, Y.,, X. G. Hou,, F. Sultana,, H. Miura, and, T. Ezaki. 1995. Determination of 16S rRNA sequences of Streptococcus mitis and Streptococcus gordonii and phylogenetic relationships among members of the genus Streptococcus. Int. J. Syst. Bacteriol. 45: 406408.
15. Kilian, M. 2005. Streptococcus and Lactobacillus, p. 833–881. In P. Borriello,, P. R. Murray, and, G. Funke (ed.), Topley and Wilson’s Microbiology and Microbial Infections. Hodder Arnold Health Sciences, Washington, DC.
16. Kilian, M.,, K. Poulsen,, T. Blomqvist,, L. S. Håvarstein,, M. Bek-Thomsen,, H. Tettelin, and, U. B. Sorensen. 2008. Evolution of Streptococcus pneumoniae and its close commensal relatives. PLoS One 3: e2683.
17. Martin, B.,, O. Humbert,, M. Camara,, E. Guenzi,, J. Walker,, T. Mitchell,, P. Andrew,, M. Prudhomme,, G. Alloing,, R. Hakenbeck,, D. A. Morrison,, G. J. Boulnois, and, J. P. Claverys. 1992. A highly conserved repeated DNA element located in the chromosome of Streptococcus pneumoniae. Nucleic Acids Res. 20: 34793483.
18. Nyvad, B.,, and M. Kilian. 1990. Comparison of the initial streptococcal microflora on dental enamel in caries-active and in caries-inactive individuals. Caries Res. 24: 267272.
19. Pearce, C.,, G. H. Bowden,, M. Evans,, S. P. Fitzsimmons,, J. Johnson,, M. J. Sheridan,, R. Wientzen, and, M. F. Cole. 1995. Identification of pioneer viridans streptococci in the oral cavity of human neonates. J. Med. Microbiol. 42: 6772.
20. Poulsen, K.,, J. Reinholdt,, C. Jespersgaard,, K. Boye,, T. A. Brown,, M. Hauge, and, M. Kilian. 1998. A comprehensive genetic study of streptococcal immunoglobulin A1 proteases: evidence for recombination within and between species. Infect. Immun. 66: 181190.
21. Whatmore, A. M.,, A. Efstratiou,, A. P. Pick-erill,, K. Broughton,, G. Woodard,, D. Sturgeon,, R. George, and, C. G. Dowson. 2000. Genetic relationships between clinical isolates of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus mitis: characterization of “atypical” pneumococci and organisms allied to S. mitis harboring S. pneumoniae virulence factor-encoding genes. Infect. Immun. 68: 13741382.
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23. Yoshida, Y.,, J. Yang,, P. E. Peaker,, H. Kato,, C. A. Bush, and, J. O. Cisar. 2008. Molecular and antigenic characterization of a Streptococcus oralis coaggregation receptor polysaccharide by carbohydrate engineering in Streptococcus gordonii. J. Biol. Chem. 283: 1265412664.


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Salient features of genomes analyzed

Citation: Tettelin H, Kilian M. 2011. Genomes of and , p 37-42. In Kolenbrander P (ed), Oral Microbial Communities. ASM Press, Washington, DC. doi: 10.1128/9781555817107.ch3

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