Improved accuracy in terminal restriction fragment length polymorphism phylogenetic analysis using a novel internal size standard definition

Oral Microbiology and Immunology

Volumn 22, Issue 6, 2007, Pages 419-428

  Takeshita, T ^a   Nakano, Y ^a   Yamashita, Y ^a  

^a KYUSHU UNIVERSITY   (Japan)

Author keywords

16S recombinant RNA gene; Oral microflora; Terminal restriction fragment length polymorphism

Indexed keywords

6 CARBOXYFLUORESCEIN;

ARTICLE; BACTERIUM DETECTION; BACTERIUM ISOLATION; DIAGNOSTIC ACCURACY; MICROFLORA; MOLECULAR CLONING; MOLECULAR WEIGHT; MOUTH FLORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PERCEPTION; PHYLOGENY; PHYLUM; PORPHYROMONAS GINGIVALIS; RESTRICTION FRAGMENT; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RNA GENE; SALIVA ANALYSIS; STANDARD;

ACTINOMYCETACEAE; DNA, BACTERIAL; FLUORESCEINS; FLUORESCENT DYES; FUSOBACTERIUM NUCLEATUM; GENE LIBRARY; GRAM-NEGATIVE BACTERIA; GRAM-POSITIVE BACTERIA; HUMANS; MOLECULAR WEIGHT; NEISSERIA MUCOSA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PORPHYROMONAS ENDODONTALIS; PORPHYROMONAS GINGIVALIS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; STREPTOCOCCUS MUTANS; TREPONEMA DENTICOLA; VEILLONELLA;

EID: 35448932508     PISSN: 09020055     EISSN: 1399302X     Source Type: Journal    
DOI: 10.1111/j.1399-302X.2007.00384.x     Document Type: Article

References (26)

1. 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 5732.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990 : 215 : 403 410.
3. Becker MR, Paster BJ, Leys EJ et al. Molecular analysis of bacterial species associated with childhood caries. J Clin Microbiol 2002 : 40 : 1001 1009.
4. Dunbar J, Ticknor LO, Kuske CR. Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 2001 : 67 : 190 197.
5. Engebretson JJ, Moyer CL. Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism. Appl Environ Microbiol 2003 : 69 : 4823 4829.
6. Fukamachi H, Nakano Y, Okano S, Shibata Y, Abiko Y, Yamashita Y. High production of methyl mercaptan by l-methionine-α-deamino-γ- mercaptomethane lyase from Treponema denticola. Biochem Biophys Res Commun 2005 : 331 : 127 131.
7. Guerrero R. Bergey's manuals and the classification of prokaryotes. Int Microbiol 2001 : 4 : 103 109.
8. Harmsen D, Singer C, Rothganger J et al. Diagnostics of Neisseriaceae and Moraxellaceae by ribosomal DNA sequencing: ribosomal differentiation of medical microorganisms. J Clin Microbiol 2001 : 39 : 936 942.
9. Kaplan CW, Astaire JC, Sanders ME, Reddy BS, Kitts CL. 16S ribosomal DNA terminal restriction fragment pattern analysis of bacterial communities in feces of rats fed Lactobacillus acidophilus NCFM. Appl Environ Microbiol 2001 : 67 : 1935 1939.
10. Kaplan CW, Kitts CL. Variation between observed and true Terminal Restriction Fragment length is dependent on true TRF length and purine content. J Microbiol Methods 2003 : 54 : 121 125.
11. Kazor CE, Mitchell PM, Lee AM et al. Diversity of bacterial populations on the tongue dorsa of patients with halitosis and healthy patients. J Clin Microbiol 2003 : 41 : 558 563.
12. Kent AD, Smith DJ, Benson BJ, Triplett EW. Web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Appl Environ Microbiol 2003 : 69 : 6768 6776.
13. Liu WT, Marsh TL, Cheng H, Forney LJ. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 1997 : 63 : 4516 4522.
14. Luckey JA, Smith LM. A model for the mobility of single-stranded DNA in capillary gel electrophoresis. Electrophoresis 1993 : 14 : 492 501.
15. Maidak BL, Cole JR, Lilburn TG et al. The RDP-II (Ribosomal Database Project). Nucleic Acids Res 2001 : 29 : 173 174.
16. Marsh TL. Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol 1999 : 2 : 323 327.
17. Marsh TL. Culture-independent microbial community analysis with terminal restriction fragment length polymorphism. Methods Enzymol 2005 : 397 : 308 329.
18. Marsh TL, Saxman P, Cole J, Tiedje J. Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl Environ Microbiol 2000 : 66 : 3616 3620.
19. Matsumoto M, Sakamoto M, Hayashi H, Benno Y. Novel phylogenetic assignment database for terminal-restriction fragment length polymorphism analysis of human colonic microbiota. J Microbiol Methods 2005 : 61 : 305 319.
20. Nakano Y, Takeshita T, Yamashita Y. TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight. Bioinformatics 2006 : 22 : 1788 1789.
21. Nyman JL, Marsh TL, Ginder-Vogel MA, Gentile M, Fendorf S, Criddle C. Heterogeneous response to biostimulation for U(VI) reduction in replicated sediment microcosms. Biodegradation 2006 : 17 : 303 316.
22. Oho T, Yamashita Y, Shimazaki Y, Kushiyama M, Koga T. Simple and rapid detection of Streptococcus mutans and Streptococcus sobrinus in human saliva by polymerase chain reaction. Oral Microbiol Immunol 2000 : 15 : 258 262.
23. Paster BJ, Boches SK, Galvin JL et al. Bacterial diversity in human subgingival plaque. J Bacteriol 2001 : 183 : 3770 3783.
24. Persson S, Edlund MB, Claesson R, Carlsson J. The formation of hydrogen sulfide and methyl mercaptan by oral bacteria. Oral Microbiol Immunol 1990 : 5 : 195 201.
25. Sakamoto M, Rocas IN, Siqueira JF Jr., Benno Y. Molecular analysis of bacteria in asymptomatic and symptomatic endodontic infections. Oral Microbiol Immunol 2006 : 21 : 112 122.
26. Sakamoto M, Takeuchi Y, Umeda M, Ishikawa I, Benno Y. Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis. J Med Microbiol 2003 : 52 : 79 89.