T-RFLP-based differences in oral microbial communities as risk factor for development of oral diseases under stress

Environmental Microbiology Reports

Volumn 4, Issue 4, 2012, Pages 390-397

  Horz, H P ^a   Ten Haaf, A ^a   Kessler, O ^a   Said Yekta, S ^a   Seyfarth, I ^a   Hettlich, M ^b   Lampert, F ^a   Kupper T ^b   Conrads, G ^a  

^a UNIVERSITY HOSPITAL RWTH AACHEN   (Germany)

^b RWTH AACHEN UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 84864000762     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2012.00340.x     Document Type: Article

References (39)

1. Aas, J.A., Paster, B.J., Stokes, L.N., Olsen, I., and Dewhirst, F.E. (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43: 5721-5732.
2. Abdo, Z., Schuette, U.M., Bent, S.J., Williams, C.J., Forney, L.J., and Joyce, P. (2006) Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ Microbiol 8: 929-938.
3. Blackwood, C.B., Hudleston, D., Zak, D.R., and Buyer, J.S. (2007) Interpreting ecological diversity indices applied to terminal restriction fragment length polymorphism data: insights from simulated microbial communities. Appl Environ Microbiol 73: 5276-5283.
4. Bolstad, A.I., Jensen, H.B., and Bakken, V. (1996) Taxonomy, biology, and periodontal aspects of Fusobacterium nucleatum. Clin Microbiol Rev 9: 55-71.
5. Brands, B., Vianna, M.E., Seyfarth, I., Conrads, G., and Horz, H.P. (2010) Complementary retrieval of 16S rRNA gene sequences using broad-range primers with inosine at the 3′-terminus: implications for the study of microbial diversity. FEMS Microbiol Ecol 71: 157-167.
6. Brogden, K.A., Guthmiller, J.M., and Taylor, C.E. (2005) Human polymicrobial infections. Lancet 365: 253-255.
7. Camarinha-Silva, A., Wos-Oxley, M.L., Jauregui, R., Becker, K., and Pieper, D.H. (2012) Validating T-RFLP as a sensitive and high-throughput approach to assess bacterial diversity patterns in human anterior nares. FEMS Microbiol Ecol 79: 98-108.
8. Culman, S.W., Gauch, H.G., Blackwood, C.B., and Thies, J.E. (2008) Analysis of T-RFLP data using analysis of variance and ordination methods: a comparative study. J Microbiol Methods 75: 55-63.
9. Culman, S.W., Bukowski, R., Gauch, H.G., Cadillo-Quiroz, H., and Buckley, D.H. (2009) T-REX: software for the processing and analysis of T-RFLP data. BMC Bioinformatics 10: 171.
10. Dewhirst, F.E., Chen, T., Izard, J., Paster, B.J., Tanner, A.C., Yu, W.H., etal. (2010) The human oral microbiome. J Bacteriol 192: 5002-5017.
11. Dunbar, J., Ticknor, L.O., and Kuske, C.R. (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67: 190-197.
12. Feres, M., Haffajee, A.D., Allard, K., Som, S., and Socransky, S.S. (2001) Change in subgingival microbial profiles in adult periodontitis subjects receiving either systemically-administered amoxicillin or metronidazole. J Clin Periodontol 28: 597-609.
13. Fleiss, J.L., Park, M.H., Chilton, N.W., Alman, J.E., Feldman, R.S., and Chauncey, H.H. (1987) Representativeness of the 'Ramfjord teeth' for epidemiologic studies of gingivitis and periodontitis. Community Dent Oral Epidemiol 15: 221-224.
14. Gallagher, S.A., and Hackett, P.H. (2004) High-altitude illness. Emerg Med Clin North Am 22: 329-355.
15. Hartmann, M., and Widmer, F. (2006) Community structure analyses are more sensitive to differences in soil bacterial communities than anonymous diversity indices. Appl Environ Microbiol 72: 7804-7812.
16. Hartmann, M., and Widmer, F. (2008) Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling. FEMS Microbiol Ecol 63: 249-260.
17. Imray, C., Wright, A., Subudhi, A., and Roach, R. (2010) Acute mountain sickness: pathophysiology, prevention, and treatment. Prog Cardiovasc Dis 52: 467-484.
18. Jenkinson, H.F., and Lamont, R.J. (2005) Oral microbial communities in sickness and in health. Trends Microbiol 13: 589-595.
19. Kolenbrander, P.E., Andersen, R.N., Blehert, D.S., Egland, P.G., Foster, J.S., and Palmer, R.J., Jr. (2002) Communication among oral bacteria. Microbiol Mol Biol Rev 66: 486-505.
20. Lazarevic, V., Whiteson, K., Hernandez, D., Francois, P., and Schrenzel, J. (2010) Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics 11: 523.
21. Ledder, R.G., Gilbert, P., Huws, S.A., Aarons, L., Ashley, M.P., Hull, P.S., and McBain, A.J. (2007) Molecular analysis of the subgingival microbiota in health and disease. Appl Environ Microbiol 73: 516-523.
22. MacInnis, M.J., Wang, P., Koehle, M.S., and Rupert, J.L. (2011) The genetics of altitude tolerance: the evidence for inherited susceptibility to acute mountain sickness. J Occup Environ Med 53: 159-168.
23. Marsh, P.D. (2003) Are dental diseases examples of ecological catastrophes? Microbiology 149: 279-294.
24. Nadkarni, M.A., Martin, F.E., Jacques, N.A., and Hunter, N. (2002) Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology 148: 257-266.
25. Neefs, J.M., Van de Peer, Y., De Rijk, P., Goris, A., and De Wachter, R. (1991) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 19 (Suppl.): 1987-2015.
26. Osborn, A.M., Moore, E.R., and Timmis, K.N. (2000) An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ Microbiol 2: 39-50.
27. Osborne, C.A., Rees, G.N., Bernstein, Y., and Janssen, P.H. (2006) New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl Environ Microbiol 72: 1270-1278.
28. Pennisi, E. (2005) A mouthful of microbes. Science 307: 1899-1901.
29. Pihlstrom, B.L., Michalowicz, B.S., and Johnson, N.W. (2005) Periodontal diseases. Lancet 366: 1809-1820.
30. Rams, T.E., Oler, J., Listgarten, M.A., and Slots, J. (1993) Utility of Ramfjord index teeth to assess periodontal disease progression in longitudinal studies. J Clin Periodontol 20: 147-150.
31. Sakamoto, M., Takeuchi, Y., Umeda, M., Ishikawa, I., and Benno, Y. (2003) Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis. J Med Microbiol 52: 79-89.
32. Sakamoto, M., Huang, Y., Ohnishi, M., Umeda, M., Ishikawa, I., and Benno, Y. (2004) Changes in oral microbial profiles after periodontal treatment as determined by molecular analysis of 16S rRNA genes. J Med Microbiol 53: 563-571.
33. Shannon, C.E. (1997) The mathematical theory of communication. 1963. MD Comput 14: 306-317.
34. Shyu, C., Soule, T., Bent, S.J., Foster, J.A., and Forney, L.J. (2007) MiCA: a web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microb Ecol 53: 562-570.
35. Takeshita, T., Nakano, Y., Kumagai, T., Yasui, M., Kamio, N., Shibata, Y., etal. (2009) The ecological proportion of indigenous bacterial populations in saliva is correlated with oral health status. ISME J 3: 65-78.
36. Takeshita, T., Suzuki, N., Nakano, Y., Shimazaki, Y., Yoneda, M., Hirofuji, T., and Yamashita, Y. (2010) Relationship between oral malodor and the global composition of indigenous bacterial populations in saliva. Appl Environ Microbiol 76: 2806-2814.
37. Turnbaugh, P.J., Ley, R.E., Hamady, M., Fraser-Liggett, C.M., Knight, R., and Gordon, J.I. (2007) The human microbiome project. Nature 449: 804-810.
38. Zaura, E., Keijser, B.J., Huse, S.M., and Crielaard, W. (2009) Defining the healthy 'core microbiome' of oral microbial communities. BMC Microbiol 9: 259.
39. Zhang, R., Thiyagarajan, V., and Qian, P.Y. (2008) Evaluation of terminal-restriction fragment length polymorphism analysis in contrasting marine environments. FEMS Microbiol Ecol 65: 169-178.