Development of multi-color FISH method for analysis of seven Bifidobacterium species in human feces

Journal of Microbiological Methods

Volumn 58, Issue 3, 2004, Pages 413-421

  Takada, Toshihiko ^a   Matsumoto, Kazumasa ^a   Nomoto, Koji ^a  

^a YAKULT CENTRAL INSTITUTE FOR MICROBIOLOGICAL RESEARCH   (Japan)

Author keywords

Bifidobacterium; Human feces; Multi color FISH; Oligonucleotide

Indexed keywords

FLUOROCHROME; RIBOSOME RNA;

ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; BIFIDOBACTERIUM; BIFIDOBACTERIUM ADOLESCENTIS; BIFIDOBACTERIUM BIFIDUM; BIFIDOBACTERIUM BREVE; BIFIDOBACTERIUM LONGUM; FECES ANALYSIS; FLUORESCENCE IN SITU HYBRIDIZATION; NONHUMAN; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; RNA SEQUENCE; SPECIES DIFFERENCE; SPECIES IDENTIFICATION; STAINING;

BIFIDOBACTERIUM; CARBOCYANINES; DNA, BACTERIAL; FECES; FLUORESCEIN-5-ISOTHIOCYANATE; FLUORESCENT DYES; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROSCOPY, FLUORESCENCE; RHODAMINES; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY;

BACTERIA (MICROORGANISMS); BIFIDOBACTERIUM; BIFIDOBACTERIUM ADOLESCENTIS; BIFIDOBACTERIUM ANGULATUM; BIFIDOBACTERIUM BIFIDUM; BIFIDOBACTERIUM BREVE; BIFIDOBACTERIUM CATENULATUM; BIFIDOBACTERIUM DENTIUM; BIFIDOBACTERIUM LONGUM;

EID: 3242750502     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2004.05.006     Document Type: Article

References (22)

1. Amann R.I., Binder B.J., Olson R.J., Chisholm S.W., Devereux R., Stahl D.A. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1990;1919-1925
2. Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:1995;143-169
3. Amann R.I., Snaidr J., Wagner M., Ludwig W., Schleifer K.H. In situ visualization of high genetic diversity in a natural microbial community. J. Bacteriol. 178:1996;3496-3500
4. Biavati B., Mattarelli P. Bifidobacterium ruminantium sp. nov. from the rumens of cattle. Int. J. Syst. Bacteriol. 41:1991;163-168
5. Delong E.F., Wickham G.S., Pace N.R. Phylogenetic stains: ribosomal RNA-based probes for the identification of single microbial cells. Science. 243:1989;1360-1363
6. Franks A.H., Harmsen H.J.M., Raangs G.C., Jansen G.J., Schut F., Welling G.W. Variations of bacterial populations in human feces measured by fluorescent in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64:1998;3336-3345
7. Fuchs B.M., Wallner G., Beisker W., Schwippl I., Ludwig W., Amann R. Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 64:1998;4973-4982
8. Harmsen H.J.M., Gibson G.R., Elfferich P., Raangs G.C., Wildeboer-Veloo A.C.M., Argaiz A., Roberfroid M.B., Welling G.W. Comparison of viable cell counts and fluorescence in situ hybridization using specific rRNA-based probes for the quantification of human fecal bacteria. FEMS Microbiol. Lett. 183:1999;125-129
9. Harmsen H.J., Raangs G.C., He T., Degener J.E., Welling G.W. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl. Environ. Microbiol. 68:2002;2982-2990
10. Jansen G.J., Wildeboer-Veloo A.C.M., Tonk R.H.J., Franks A.H., Welling G.W. Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria. J. Microbiol. Methods. 37:1999;215-221
11. Langendijk P.S., Schut F., Jansen G.J., Raangs G.C., Kamphuis G.R., Wilkinson M.H.F., Welling G.W. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61:1995;3069-3075
12. Maidak B.L., Olsen G.J., Larsen N., Overbeek R., McCaughey M.J., Woese C.R. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:1997;109-110
13. Maruyama A., Sunamura M. Simultaneous direct counting of total and specific microbial cells in seawater, using a deep-sea microbe as target. Appl. Environ. Microbiol. 66:2000;2211-2215
14. Neefs J.M., van de Peer Y., de Rijk P., Chapelle S., de Wachter R. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21:1993;3025-3049
15. Nelson G.M., George S.E. Comparison of media for selection and enumeration of mouse fecal flora populations. J. Microbiol. Methods. 22:1995;293-300
16. Saiki R.K., Gelfand D.H., Stoffel S., Scharf S.J., Higuchi R., Horn G.T., Mullis K.B., Ehrlich H.A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 239:1988;487-491
17. Scardovi V. Genus Bifidobacterium Orla-Jensen, 1924. Krieg N.R., Holt J.G. Bergey's Manual of Systematic Bacteriology. vol. 1:1984;1418-1434 Williams & Wilkins, Baltimore, MD
18. Scardovi V., Trovatelli L.D., Biavati B., Zani G. Bifidobacterium cuniculi, B. choerinum, B. boum, and B. pseudocatenulatum: four new species and their deoxyribonucleic acid homology relationships. Int. J. Syst. Bacteriol. 29:1979;291-311
19. Thompson J.D., Higgens D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, posituon specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680
20. Wang R.F., Cao W.W., Wand Cerniglia C.E. PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl. Environ. Microbiol. 62:1996;1242-1247
21. Woese C.R. Bacterial evolution. Microbiol. Rev. 51:1987;221-271
22. Yamamoto T., Morotomi M., Tanaka R. Species-specific oligonucleotide probes for five Bifidobacterium species detected in human intestinal microflora. Appl. Environ. Microbiol. 58:1992;4076-4079