Quantitative PCR with 16S rRNA-Gene-Targeted Species-Specific Primers for Analysis of Human Intestinal Bifidobacteria

Applied and Environmental Microbiology

Volumn 70, Issue 1, 2004, Pages 167-173

  Matsuki, Takahiro ^a   Watanabe, Koichi ^a   Fujimoto, Junji ^a   Kado, Yukiko ^a   Takada, Toshihiko ^a   Matsumoto, Kazumasa ^a   Tanaka, Ryuichiro ^a  

^a YAKULT CENTRAL INSTITUTE FOR MICROBIOLOGICAL RESEARCH   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOASSAY; DNA; GENES; RNA;

CELL COUNTS;

BACTERIOLOGY;

RIBOSOME RNA;

ADULT; ARTICLE; BIFIDOBACTERIUM; BIFIDOBACTERIUM ADOLESCENTIS; BIFIDOBACTERIUM CATENULATUM; BIFIDOBACTERIUM LONGUM; CELL COUNT; CHEMICAL COMPOSITION; CONCENTRATION RESPONSE; DILUTION; DNA EXTRACTION; FECES ANALYSIS; FEMALE; GENE TARGETING; HUMAN; HUMAN EXPERIMENT; INTESTINE FLORA; MALE; NONHUMAN; NORMAL HUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; QUANTITATIVE DIAGNOSIS; RNA GENE; SPECIES DIFFERENCE; SPECIES IDENTIFICATION;

ADULT; BASE SEQUENCE; BIFIDOBACTERIUM; COLONY COUNT, MICROBIAL; DNA PRIMERS; DNA, RIBOSOMAL; FEMALE; GENES, RRNA; HUMANS; INTESTINES; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

BIFIDOBACTERIUM; BIFIDOBACTERIUM ADOLESCENTIS; BIFIDOBACTERIUM CATENULATUM; BIFIDOBACTERIUM LONGUM; NEGIBACTERIA;

EID: 0345869650     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.70.1.167-173.2004     Document Type: Article

References (38)

1. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Benno, Y., K. Sawada, and T. Mitsuoka. 1984. The intestinal microflora of infants: composition of fecal flora in breast-fed and bottle-fed infants. Microbiol. Immunol. 28:975-986.
3. Biavati, B., P. Castagnoli, F. Crociani, and L. D. Trovatelli. 1984. Species of the Bifidobacterium in the feces of infants. Microbiologica 7:341-345.
4. Biavati, B., P. Castagnoli, and L. D. Trovatelli. 1986. Species of the genus Bifidobacterium in the feces of human adults. Microbiologica 9:39-45.
5. Finegold, S. M., V. S. Sutter, and G. E. Mathisen. 1983. Normal indigenous intestinal flora, p. 3-31. In D. J. Hentges (ed.), Human intestinal microflora in health and disease. Academic Press, New York, N.Y.
6. Franks, A. H., H. J. Harmsen, G. C. Raangs, G. J. Jansen, F. Schut, and G. W. Welling. 1998. Variations of bacterial populations in human feces measured by fluorescence in situ hybridization with group-specific 16S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 64:3336-3345.
7. Fuller, R. 1989. Probiotics in man and animals. J. Appl. Bacteriol. 66:365-378.
8. Gibson, G. R., and M. B. Roberfroid. 1995. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J. Nutr. 125:1401-1412.
9. Harmsen, H. J., G. R. Gibson, P. Elfferich, G. C. Raangs, A. C. Wildeboer-Veloo, A. Argaiz, M. B. Roberfroid, and G. W. Welling. 2000. 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. 183:125-129.
10. Harmsen, H. J., G. C. Raangs, T. He, J. E. Degener, and G. W. Welling. 2002. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Appl. Environ. Microbiol. 68:2982-2990.
11. Kageyama, A., M. Sakamoto, and Y. Benno. 2000. Rapid identification and quantification of Collinsella aerofaciens using PCR. FEMS Microbiol. Lett. 183:43-47.
12. Kaufmann, P., A. Pfefferkorn, M. Teuber, and L. Meile. 1997. Identification and quantification of Bifidobacterium species isolated from food with genus-specific 16S rRNA-targeted probes by colony hybridization and PCR. Appl. Environ. Microbiol. 63:1268-1273.
13. Kitajima, H., Y. Sumida, R. Tanaka, N. Yuki, H. Takayama, and M. Fujimura. 1997. Early administration of Bifidobacterium breve to preterm infants: randomised controlled trial. Arch. Dis. Child Fetal Neonatal 76:F101-F107.
14. Langendijk, P. S., F. Schut, G. J. Jansen, G. C. Raangs, G. R. Kamphuis, M. H. Wilkinson, and G. W. Welling. 1995. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl. Environ. Microbiol. 61:3069-3075.
15. Lee, Y.-K., K. Nomoto, S. Salminen, and S. L. Gorbach. 1999. Handbook of probiotics. Wiley Interscience, New York, N.Y.
16. Lyons, S. R., A. L. Griffen, and E. J. Leys. 2000. Quantitative real-time PCR for Porphyromonas gingivalis and total bacteria. J. Clin. Microbiol. 38:2362-2365.
17. Matsuki, T., K. Watanabe, J. Fujimoto, Y. Miyamoto, T. Takada, K. Matsumoto, H. Oyaizu, and R. Tanaka. 2002. Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl. Environ. Microbiol. 68:5445-5451.
18. Matsuki, T., K. Watanabe, R. Tanaka, M. Fukuda, and H. Oyaizu. 1999. Distribution of bifidobacterial species in human intestinal microflora examined with 16S rRNA-gene-targeted species-specific primers. Appl. Environ. Microbiol. 65:4506-4512.
19. Matsuki, T., K. Watanabe, R. Tanaka, and H. Oyaizu. 1998. Rapid identification of human intestinal bifidobacteria by 16S rRNA-targeted species-and group-specific primers. FEMS Microbiol. Lett. 167:113-121.
20. McCartney, A. L., W. Wenzhi, and G. W. Tannock. 1996. Molecular analysis of the composition of the bifidobacterial and lactobacillus microflora of humans. Appl. Environ. Microbiol. 62:4608-4613.
21. Mitsuoka, T., K. Hayakawa, and N. Kimura. 1974. Die faekalflora bei menschen. II. Mitteilung: die zusammensetzung der bifidobakerien flora der verschiedenen altersgruppen. Zentbl. Bakteriol. Parasitenkd. Infektionskr. Abt. 1 Orig. Reihe A 226:469-478.
22. Miyake, T., K. Watanabe, T. Watanabe, and H. Oyaizu. 1998. Phylogenetic analysis of the genus Bifidobacterium and related genera based on 16S rDNA sequences. Microbiol. Immunol. 42:661-667.
23. Moore, W. E. C., and L. V. Holdeman. 1974. Human fecal flora: the normal flora of 20 Japanese-Hawaiians. Appl. Microbiol. 27:961-979.
24. Mutai, M., and R. Tanaka. 1987. Ecology of Bifidobacterium in the human intestinal flora. Bifidobacteria Microflora 6:33-41.
25. Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.
26. a. Requena, T., J. Burton, T. Matsuki, K. Munro, M. A. Simon, R. Tanaka, K. Watanabe, and G. W. Tannock. 2002. Identification, detection, and enumeration of Bifidobacterium species by PCR targeting the transaldolase gene. Appl. Environ. Microbiol. 68:2420-2427.
27. Sakamoto, M., Y. Takeuchi, M. Umeda, I. Ishikawa, and Y. Benno. 2001. Rapid detection and quantification of five periodontopathic bacteria by real-time PCR. Microbiol. Immunol. 45:39-44.
28. Sakata, S., M. Kitahara, M. Sakamoto, H. Hayashi, M. Fukuyama, and Y. Benno. 2002. Unification of Bifidobacterium infantis and Bifidobacterium suis as Bifidobaterium longum. Int. J. Syst. Evol. Microbiol. 52:1945-1951.
29. Satokari, R. M., E. E. Vaughan, A. D. Akkermans, M. Saarela, and W. W. de Vos. 2001. Bifidobacterial diversity in human feces detected by genus-specific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 67:504-513.
30. Scardovi, V. 1984. Genus Bifidobacterium Orla-Jensen, 1924, 472, p. 1418-1434. In N. R. Krieg and J. G. Holt (ed.), Bergey's manual of systematic bacteriology, vol. 1. The Williams & Wilkins Co., Baltimore, Md.
31. Song, Y., N. Kato, C. Liu, Y. Matsumiya, H. Kato, and K. Watanabe. 2000. Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group- and species-specific primers derived from the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA. FEMS Microbiol. Lett. 187:167-173.
32. Sonoike, K., M. Maeda, and M. Mutai. 1986. Selective agar medium for counting viable cells of bifidobacteria in fermented milk. J. Food Hygienic Soc. Jpn. 27:238-244.
33. Suau, A., R. Bonnet, M. Sutren, J. J. Godon, G. R. Gibson, M. D. Collins, and J. Dore. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65:4799-4807.
34. Tajima, K., R. I. Aminov, T. Nagamine, H. Matsui, M. Nakamura, and Y. Benno. 2001. Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl. Environ. Microbiol. 67:2766-2774.
35. Wang, R. F., W. W. Cao, and C. E. Cerniglia. 1996. PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl. Environ. Microbiol. 62:1242-1247.
36. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
37. Yamamoto, T., M. Morotomi, and R. Tanaka. 1992. Species-specific oligonucleotide probes for five Bifidobacterium species detected in human intestinal microflora. Appl. Environ. Microbiol. 58:4076-4079.
38. Zoetendal, E. G., A. D. Akkermans, and W. M. De Vos. 1998. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl. Environ. Microbiol. 64:3854-3859.