Prediction of Plausible Bacterial Composition Based on Terminal Restriction Fragment Length Polymorphisms using a Monte Carlo Method

Microbial Ecology

Volumn 60, Issue 2, 2010, Pages 364-372

  Nakano, Yoshio ^a,b   Takeshita, Toru ^a   Yasui, Masaki ^a   Yamashita, Yoshihisa ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b NIHON UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

ALGORITHM; ARTICLE; BACTERIUM; CLASSIFICATION; DNA SEQUENCE; GENETICS; HUMAN; METAGENOME; METHODOLOGY; MICROBIOLOGY; MOLECULAR CLONING; MONTE CARLO METHOD; PRINCIPAL COMPONENT ANALYSIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SALIVA; TIME;

ALGORITHMS; BACTERIA; CLONING, MOLECULAR; DNA, BACTERIAL; HUMANS; METAGENOME; MONTE CARLO METHOD; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PRINCIPAL COMPONENT ANALYSIS; RNA, RIBOSOMAL, 16S; SALIVA; SEQUENCE ANALYSIS, DNA; TIME FACTORS;

BACTERIA (MICROORGANISMS);

EID: 77956877422     PISSN: 00953628     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00248-010-9703-9     Document Type: Article

References (15)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35(Database issue): D169-D172.
3. DeLong EF, Pace NR (2001) Environmental diversity of bacteria and archaea. Syst Biol 50: 470-478.
4. Kumar PS, Griffen AL, Moeschberger ML, Leys EJ (2005) Identification of candidate periodontal pathogens and beneficial species by quantitative 16S clonal analysis. J Clin Microbiol 43: 3944-3955.
5. Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16s rRNA. Appl Environ Microbiol 63: 4516-4522.
6. Marsh TL (2005) Culture-independent microbial community analysis with terminal restriction fragment length polymorphism. Methods Enzymol 397: 308-329.
7. Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59: 695-700.
8. Nakano Y, Takeshita T, Yamashita Y (2006) TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight. Bioinformatics 22: 1788-1789.
9. Nakano Y, Takeshita T, Kamio N, Shiota S, Shibata Y, Yasui M, Yamashita Y (2008) Development and application of a T-RFLP data analysis method using correlation coefficient matrices. J Microbiol Methods 75: 501-505.
10. R Development Core Team (2006) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
11. Rosenberg M (1996) Clinical assessment of bad breath: current concepts. J Am Dent Assoc 127: 475-482.
12. Shibata Y, Ozaki K, Seki M, Kawato T, Tanaka H, Nakano Y, Yamashita Y (2003) Analysis of loci required for determination of serotype antigenicity in Streptococcus mutans and its clinical utilization. J Clin Microbiol 41: 4107-4112.
13. Siqueira JF, Rôças IN, Souto R, Uzeda M, Colombo AP (2000) Checkerboard DNA-DNA hybridization analysis of endodontic infections. Oral Surg Oral Med Oral Pathol Oral Radiol Endo 89: 744-748.
14. Takeshita T, Nakano Y, Yamashita Y (2007) Improved accuracy in terminal restriction fragment length polymorphism phylogenetic analysis using a novel internal size standard definition. Oral Microbiol Immunol 22: 419-428.
15. Takeshita T, Nakano Y, Kumagai T, Yasui M, Kamio N, Shibata Y, Shiota S, Yamashita Y (2009) The ecological proportion of indigenous bacterial populations in saliva is correlated with oral health status. ISME J 3: 65-78.