Chapter 4 Metagenomics of Dental Biofilms

Advances in Applied Microbiology

Volumn 64, Issue , 2008, Pages 125-136

  Mullany, Peter ^a   Hunter, Stephanie ^b   Allan, Elaine ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOFILM; DNA EXTRACTION; DNA ISOLATION; GENE LIBRARY; GENOMICS; MOLECULAR CLONING; PHAGE DISPLAY; REVIEW; BACTERIUM; GENETICS; GROWTH, DEVELOPMENT AND AGING; HUMAN; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; MOUTH;

BACTERIAL DNA;

BACTERIA; BIOFILMS; DNA, BACTERIAL; GENOMICS; HUMANS; MOUTH;

EID: 43149103159     PISSN: 00652164     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-2164(08)00404-8     Document Type: Review

References (37)

1. August P.R., Grossman T.H., Minor C., Draper M.P., MacNeil I.A., Pemberton J.M., Call K.M., Holt D., and Osburne M.S. Sequence analysis and functional characterisation of the violacein biosynthetic pathway from Chromobacterium violaceum. J. Mol. Microbiol. Biotechnol. 2 (2000) 513-519
2. Beckmann C., Waggoner J.D., Harris T.O., Tamura G.S., and Rubens C.E. Identification of novel adhesins from Group B streptococci by use of phage display reveals that C5a peptidase mediates fibronectin binding. Infection and Immunity 70 (2002) 2869-2876
3. Béjà O., Suzuki M.T., Koonin E.V., Aravind L., Hadd A., Nguyen L.P., Villacorta R., Amjadi M., Garrigues C., Jovanovich S.B., Feldman R.A., and DeLong E.F. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2 (2000) 516-529
4. Brady S.F., Chao C.J., and Clardy J. Long chain N-Acetyrosine synthases from environmental DNA. Appl. Environ. Microbiol. 70 (2004) 6865-6870
5. Diaz-Torres M.L., McNab R., Spratt D.A., Villedieu A., Hunt N., Wilson M., and Mullany P. Novel tetracycline resistance determinant from the oral Metagenome. Antimicrob. Agents Chemother. 47 (2003) 1430-1432
6. Diaz-Torres M.L., Villedieu A., Hunt N., McNab R., Spratt D.A., Allan E., Mullany P., and Wilson M. Determining the antibiotic resistance potential of the indigenous oral microbiota of humans using a metagenomic approach. FEMS. Microbiol. Lett. 258 (2006) 257-262
7. Easter C.L., Schwab H., and Helinski D.R. Role of the parCBA operon pf the broad-host-range plasmid RK2 in stable plasmid maintenance. J. Bacteriol. 180 (1998) 6023-6030
8. Gabor E.M., Alkema W.B., and Janssen D.B. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ. Microbiol. 6 (2004) 879-886
9. Gafan G.P., and Spratt D.A. Denaturing gradient gel electrophoresis gel expansion (DGGEGE)-An attempt to resolve the limitations of co-migration in the DGGE of complex polymicrobial communities. FEMS Microbiol. Lett. 253 (2005) 303-307
10. Gillespie D.E., Brady S.F., Bettermann A.D., Cianciotto N.P., Liles M.R., Rondon M.R., Clardy J., Goodman R.M., and Handelsman J. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl. Environ. Microbiol. 68 (2002) 4301-4306
11. Henne A., Daniel R., Schmitz R.A., and Gottschalk G. Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilisation of 4-hydroxybutyrate. Appl. Environ. Microbiol. 65 (1999) 3901-3907
12. Jacobsson K., and Frykberg L. Cloning of ligand-binding domains of bacterial receptors by phage display. BioTechniques. 18 (1995) 878-885
13. Jacobsson K., and Frykberg L. Phage Display Shot-Gun Cloning of Ligand-Binding Domains of Prokaryotic Receptors Approaches 100% Correct Clones. BioTechniques. 20 (1996) 1070-1081
14. Jacobsson K., Jonsson H., Lindmark H., Guss B., Lindberg M., and Frykberg L. Shot-gun phage display mapping of two streptococcal cell-surface proteins. Microbiol. Res. 152 (1997) 121-128
15. Jacobsson K., Rosander A., Bjerketorp J., and Frykberg L. Shotgun Phage Display - Selection for Bacterial Receptins or other Exported Proteins. Biological Procedures Online 5 (2003) 123-135
16. Kazor C.E., Mitchell P.M., Lee A.M., Stokes L.N., Loesche W.J., Dewhirst F.E., and Paster B.J. Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J. Clin. Microbiol. 41 (2003) 558-563
17. Kumar P.S., Griffen A.L., Barton J.A., Paster B.J., Moeschberger M.L., and Leys E.J. New bacterial species associated with chronic periodontitis. J. Dent. Res. 82 (2003) 338-344
18. Lämmle K., Zipper H., Breuer M., Hauer B., Buta C., Brunner H., and Rupp S. Identification of novel enzymes with different hydrolytic activities by metagenomic expression cloning. J. Biotechnnol. 127 (2007) 575-592
19. Leggewie C., Henning H., Schmeisser C., Streit W.R., and Jaeger K.E. A novel transposon for functional expression of DNA libraries. J. Biotechnnol. 123 (2006) 281-287
20. MacNeil I.A., Tiong C.L., Minor C., August P.R., Grossman T.H., Loiacono K.A., Lynch B.A., Phillips T., Narula S., Sundaramoorthi R., Tyler A., Aldredge T., et al. Expression and isolation of antimicrobial small molecules from soil DNA libraries. J. Mol. Microbiol. Biotechnol. 3 (2001) 301-308
21. Mullen L.M., Nair S.P., Ward J.M., Rycroft A.N., Williams R.J., and Henderson B. Comparative functional genomic analysis of Pasteurellaceae adhesins using phage display. Veterinary Microbiol. 122 (2007) 123-134
22. Nilsson M., Bjerketorp J., Wiebensjö A., and Ljungh A. A von Willebrand factor-binding protein from Staphylococcus lugdunensis. FEMS. Microbiol. Lett. 234 (2004) 155-161
23. Quaiser A., Ochsenreiter T., Klenk H.P., Kletzin A., Treusch A.H., Meurer G., Eck J., Sensen C.W., and Schleper C. First insight into the genome of an uncultivated crenarchaeote from soil. Environ. Microbiol. 4 (2002) 603-611
24. Ready D., Pratten J., Roberts A.P., Bedi R., Mullany P., and Wilson M. Potential role of Veillonella spp. as a reservoir of transferable tetracycline resistance in the oral cavity. Antimicrob. Agents Chemother. 50 (2006) 2866-2868
25. Riesenfeld C.S., Goodman R.M., and Handelsman J. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6 (2004) 981-989
26. Roberts A.P., and Mullany P. Genetic basis of horizontal gene transfer among oral bacteria. Periodontology 2000. 42 (2006) 36-46
27. Rondot S., Koch J., Breitling F., and Dübel S. A helper phage to improve single-chain antibody presentation in phage display. Nature Biotechnol. 19 (2001) 75-78
28. Scannapieco F.A. Saliva-bacterium interactions in oral microbial ecology. Crit. Rev. Oral Bio. Med. 5 (1994) 203-248
29. Shizuya H., Birren B., Kim U.J., Mancino V., Slepak T., Tachiiri Y., and Simon M. Cloning and stable maintainance of 300 kilobase pair fragments of human DNA in Escherichia coli using an F-factor based vector. Proc. Natl. Acad. Sci. USA 89 (1992) 8794-8797
30. Shizuya H., and Kouros-Mehr H. The development and applications of the bacterial artificial chromosome cloning system. Keio. J. Med. 50 (2001) 26-30
31. Syed S.A., and Loesche W.J. Survival of Human dental plaque flora in various transport media. Appl. Microbiol. 24 (1972) 638-644
32. Treusch A.H., Kletzin A., Raddatz G., Ochsenreiter T., Quaiser A., Meurer G., Schuster S.C., and Schleper C. Characterisation of large insert DNA libraries from soil for environmental genomic studies of Archaea. Environ. Microbiol. 6 (2004) 970-980
33. Villedieu A., Roberts A.P., Allan E., Hussain H., McNab R., Spratt D.A., Wilson M., and Mullany P. Determination of the genetic support for tet(W) in oral bacteria. Antimicrob. Agents Chemother. 51 (2007) 2195-2197
34. Voget S., Leggewie C., Uesbeck A., Raasch C., Jaeger K.E., and Streit W.R. Prospecting for novel biocatalysts in a soil metagenome. Appl. Environ. Microbiol. 69 (2003) 6235-6242
35. Williams R.J., Henderson B., Sharp L.J., and Nair S.P. Identification of a fibronectic-Binding Protein from Staphylococcus epidermis. Infection and Immunity. 70 (2002) 6805-6810
36. Wilson M. Microbial Inhabitants of Humans: Their Ecology and Role in Health and Disease (2005), Cambridge University Press, Cambridge, UK
37. Zoetendal E.G., Cheng B., Koike S., and Mackie R.I. Molecular microbial ecology of the gastrointestinal tract: From phylogeny to function. Curr. Issues Intest. Microbiol. 5 (2004) 31-47