Development of phylogenetic oligonucleotide probes for screening foodborne bacteria

Journal of Health Science

Volumn 51, Issue 4, 2005, Pages 469-476

  Ikeda, Masafumi ^a   Yamaguchi, Nobuyasu ^a   Tani, Katsuji ^a   Nasu, Masao ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

16s rrna; DNA microarray; Foodborne bacteria; Oligonucleotide probe; Phylogenetic analysis

Indexed keywords

DNA 16S; FLUORESCENT DYE; OLIGONUCLEOTIDE; RNA; RNA 16S;

ARTICLE; BACILLUS CEREUS; BACTERIAL STRAIN; DNA MICROARRAY; ESCHERICHIA COLI; FLUORESCENCE IN SITU HYBRIDIZATION; FOOD; FOOD ANALYSIS; NONHUMAN; OLIGONUCLEOTIDE PROBE; PHYLOGENY; RNA EXTRACTION; SALMONELLA ENTERICA; SHIGELLA; YERSINIA ENTEROCOLITICA;

BACILLUS CEREUS; BACILLUS CEREUS GROUP; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR ENTERITIDIS; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM; SHIGELLA; YERSINIA ENTEROCOLITICA;

EID: 24744442341     PISSN: 13449702     EISSN: None     Source Type: Journal    
DOI: 10.1248/jhs.51.469     Document Type: Article

References (16)

1. WHO (2002) Food Safety and foodborne illness, http://www.who.int/ mediacentre/factsheets/fs237/ en/.
2. Ministry of Health, Labour, Welfare (Japan) (2002) Food Poisoning Report, http://www.mhlw.go.jp.
3. Wang, R. F., Cao, W. W. and Cernigila, C. E. (1997) A universal protocol for PCR detection of 13 species of foodborne pathogens in foods. J. Appl. Microbiol., 83, 727-736.
4. Chizhikov, V., Rasooly, A., Chumakov, K. and Levy, D. D. (2001) Microarray analysis of microbial virulence factors. Appl. Environ. Microbiol., 67, 3258-3263.
5. Amann, R. I. (1995) Fluorescently labeled, rRNA targeted oligonucleotide probes in the study of microbial ecology. Mol. Ecol., 4, 543-553.
6. Woese, C. R. (1987) Bacterial Evolution. Micribiol. Rev., 51, 221-271.
7. Small, J., Call, D. R., Brockman, F. J., Strarub, T. M. and Chandler, D. P. (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol., 67, 4708-4716.
8. Guschin, D. Y., Mobarry, B. K., Proudnikov, D., Stahl, D. A., Rittmann, B. E. and Mirzabekov, A. D. (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol., 63, 2397-2402.
9. Bavykin, S. G., Akowski, J. P., Zakhariev, V. M., Barsky, V. E., Perov, A. N. and Mirzabekov, A. D. (2001) Portable system for microbial sample preparation and oligonucleotide microarray analysis. Appl. Environ. Microbiol., 67, 922-928.
10. Valinsky, L., Vedova, G. D., Scupham, A. J., Alvey, S., Figueroa, A., Yin, B., Hartin, R. J., Chrobak, M., Crowley, D. E., Jiang, T. and Borneman, J. (2002) Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol., 68, 3243-3250.
11. E.B.I. (2004) EBI server for multiple sequence alignment on the web, http://www.ebi.ac.uk/clustalw.
12. Stahl, D. A. and Amann, R. I. (1991) Development and application of nucleic acid probes. In Nucleic acid techniques in bacterial systematics (Stackebrandt, E. and Goodfellow, M., Eds.), John Willey & Sons, Chichster, England, pp. 205-248.
13. Pearson, W. R. and Lipman, D. J. (1988) Improved tools for bacterial sequence comparison. Proc. Natl. Acad. Sci. U.S.A., 85, 2444-2448.
14. Choi, J. H., Jung, H. Y., Kims, H. S. and Cho, H. G. (2000) PhyloDraw: a phylogenetic tree drawing system. Bioinformatics, 16, 1056-1058.
15. Urakawa, H., Noble, P. A., Fantroussi, S. E., Kelly, J. J. and Stahl, D. A. (2002) Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analysis. Appl. Environ. Microbiol., 68, 235-244.
16. Peplies, J., Glöckner, F. O. and Amann, R. (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol., 69, 1397-1407.