Diet-Dependent Shifts in the Bacterial Population of the Rumen Revealed with Real-Time PCR

Applied and Environmental Microbiology

Volumn 67, Issue 6, 2001, Pages 2766-2774

  Tajima, K ^a   Aminov, R I ^b,c   Nagamine, T ^a   Matsui, H ^a   Nakamura, M ^a   Benno, Y ^a,c  

^a STAFF Institute   (Japan)

^b RIKEN BIORESOURCE CENTER   (Japan)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER DNA; RIBOSOME DNA; RNA 16S;

ANIMAL; ANIMAL DISEASE; ANIMAL FOOD; ARTICLE; BACTERIUM; CATTLE; CLASSIFICATION; DIET; DNA SEQUENCE; ECOSYSTEM; FEMALE; GENETICS; HAY FEVER; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; POLYMERASE CHAIN REACTION; RUMINANT STOMACH;

ANIMAL FEED; ANIMALS; BACTERIA; CATTLE; DIET; DNA PRIMERS; DNA, RIBOSOMAL; ECOSYSTEM; FEMALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; RHINITIS, ALLERGIC, SEASONAL; RNA, RIBOSOMAL, 16S; RUMEN; SEQUENCE ANALYSIS, DNA;

EID: 0035374841     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.6.2766-2774.2001     Document Type: Article

References (39)

1. Attwood, G. T., R. A. Lockington, G. P. Xue, and J. D. Brooker. 1988. Use of a unique gene sequence as a probe to enumerate a strain of Bacteroides ruminicola introduced into the rumen. Appl. Environ. Microbiol. 54:534-539.
2. Birnboim, H. C., and J. Doly. 1979. A rapid alkaline extraction procedure for recombinant plasmid DNA. Nucleic Acids Res. 7:1513-1523.
3. Briesacher, S. L., T. May, K. N. Grigsby, M. S. Kerley, R. V. Anthony, and J. A. Paterson. 1992. Use of DNA probes to monitor nutritional effects on ruminal prokaryotes and Fibrobacter succinogenes S85. J. Anim. Sci. 70:289-295.
4. Bryant, M. P. 1959. Bacterial species of the rumen. Bacteriol. Rev. 23:125-153.
5. Caldwell, D. R., and M. P. Bryant. 1966. Medium without rumen fluid for nonselective enumeration and isolation of rumen bacteria. Appl. Microbiol. 14:794-801.
6. Ezaki, T., and S. Suzuki. 1982. Achromopeptidase for lysis of anaerobic gram-positive cocci. J. Clin. Microbiol. 16:844-846.
7. Ezaki, T., Y. Hashimoto, N. Takeuchi, H. Yamamoto, S.-L. Liu, H. Miura, K. Matsui, and E. Yabuuchi. 1988. Simple genetic methods to identify viridans group streptococci by colorimetric dot hybridization and fluorometric hybridization in microdilution wells. J. Clin. Microbiol. 26:1708-1713.
8. Farrow, J. A. E., J. Kruze, B. A. Phillips, A. J. Bramley, and M. D. Collins. 1984. Taxonomic studies on Streptococcus bovis and Streptococcus equinus: description of Streptococcus alactolyticus sp. nov. and Streptococcus saccharolyticus sp. nov. Syst. Appl. Microbiol. 5:467-482.
9. Flint, H. J. 1997. The rumen microbial ecosystem - some recent developments. Trends Microbiol. 5:483-488.
10. Forster, R. J., J. Gong, and R. M. Teather. 1997. Group-specific 16S rRNA hybridization probes for determinative and community structure studies of Butyrivibrio fibrisolvens in the rumen. Appl. Environ. Microbiol. 63:1256-1260.
11. Gill, H. S., Q. Shu, and R. A. Leng. 2000. Immunization with Streptococcus bovis protects against lactic acidosis in sheep. Vaccine 18:2541-2548.
12. Hungate, R. E. 1966. The rumen and its microbes. Academic Press, New York, N.Y.
13. Kobayashi, Y., R. J. Foster, and R. M. Teather. 2000. Development of a competitive polymerase chain reaction assay for the ruminal bacterium Butyrivibrio fibrisolvens OB156 and its use for tracking an OB156-derived recombinant. FEMS Microbiol. Lett. 188:185-190.
14. Krause, D. O., B. P. Dalrymple, W. J. Smith, R. I. Mackie, and C. S. McSweeney. 1999. 16S rDNA sequencing of Ruminococcus albus and Ruminococcus flavefaciens: design of a signature probe and its application in adult sheep. Microbiology 145:1797-1807.
15. Krause, D. O., W. J. Smith, F. M. Ryan, R. I. Mackie, and C. S. McSweeney. 1999. Use of 16S-rRNA based techniques to investigate the ecological succession of microbial populations in the immature lamb rumen: tracking of a specific strain of inoculated Ruminococcus and interactions with other microbial populations in vivo. Microb. Ecol. 38:365-376.
16. Kudo, H., K. J. Cheng, and J. W. Costerton. 1987. Interactions between Treponema bryantii and cellulolytic bacteria in the in vitro degradation of straw cellulose. Can. J. Microbiol. 33:244-248.
17. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115-175. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley and Sons, New York, N.Y.
18. Madden, T. L., R. L. Tatusov, and J. Zhang. 1996. Application of network BLAST server. Methods Enzymol. 266:131-141.
19. Nocey, J. E. 1995. Bovine acidosis: implications on laminitis. J. Dairy Sci. 80:1005-1028.
20. Ogata, K., R. I. Aminov, T. Nagamine, M. Sugiura, K. Tajima, M. Mitsumori, T. Sekizaki, H. Kudo, H. Minato, and Y. Benno. 1997. Construction of a Fibrobacter succinogenes genomic map and demonstration of diversity at the genomic level. Curr. Microbiol. 35:22-27.
21. Ogimoto, K., and S. Imai. 1981. Atlas of rumen microbiology. Japan Scientific Society Press, Tokyo, Japan.
22. Owens, F. N., D. S. Secrist, W. J. Hil, and D. R. Gill. 1998. Acidosis in cattle: a review. J. Anim. Sci. 76:275-286.
23. Prins, R. A., A. Lankhorst, P. van der Meer, and C. J. Van Nevel. 1975. Some characteristics of Anaerovibrio lipolytica, a rumen lipolytic organism. Antonie Leeuwenhoek 41:1-11.
24. Ramsak, A., M. Peterka, K. Tajima, J. C. Martin, J. Wood, M. E. Johnston, R. I. Aminov, H. J. Flint, and G. Avgustin. 2000. Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol. Ecol. 33:69-79.
25. Reilly, K., and G. T. Attwood. 1998. Detection of Clostridium proteoclasticum and closely related strains in the rumen by competitive PCR. Appl. Environ. Microbiol. 64:907-913.
26. Saito, N., and M. Nei. 1987. The neighbor-joining method: a new method for constructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
27. Shu, Q., H. S. Gill, R. A. Leng, and J. B. Rowe. 2000. Immunization with a Streptococcus bovis vaccine administered by different routes against lactic acidosis in sheep. Vet. J. 159:262-269.
28. Stackebrandt, E., and B. M. Goebel. 1994. Taxonomic notice: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44:846-849.
29. Stahl, D. A., B. Flesher, H. R. Mansfield, and L. Montgomery. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54:1079-1084.
30. Stanton, T. B., and E. Canale-Parola. 1980. Treponema bryantii sp. nov., a rumen spirochete that interacts with cellulolytic bacteria. Arch. Microbiol. 127:145-156.
31. Stewart, C. S., and M. P. Bryant. 1988. The rumen bacteria, p. 21-76. In P.N. Hobson (ed.), The rumen microbial ecosystem. Elsevier Applied Science, London, United Kingdom.
32. Tajima, K., R. I. Aminov, T. Nagamine, K. Ogata, M. Nakamura, H. Matsui, and Y. Benno. 1999. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29:159-169.
33. Tajima, K., S. Arai, K. Ogata, T. Nagamine, H. Matsui, M. Nakamura, R. I. Aminov, and Y. Benno. 2000. Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 6:273-284.
34. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
35. von Wintzingerode, V., U. B. Gobel, and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21:213-229.
36. Weimer, P. J., G. C. Waghorn, C. L. Odt, and D. R. Mertens. 1999. Effect of diet on populations of three species of ruminal cellulolytic bacteria in lactating dairy cows. J. Dairy Sci. 82:122-134.
37. Whitehead, T. R., and M. A. Cotta. 2000. Development of molecular methods for identification of Streptococcus bovis from human and ruminal origins. FEMS Microbiol. Lett. 182:237-240.
38. Whitford, M. F., R. J. Foster, C. E. Beard, J. Gong, and R. M. Teather. 1998. Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4:153-163.
39. Yanagita, K., Y. Kamagata, M. Kawaharasaki, T. Suzuki, Y. Nakamura, and H. Minato. 2000. Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization.