Postprandial changes of fiber-degrading microbes in the rumen of sheep fed diets varying in type of forage as monitored by real-time pcr and automated ribosomal intergenic spacer analysis

Journal of Animal Science

Volumn 90, Issue 12, 2012, Pages 4487-4494

  Saro, C ^a   Ranilla, M J ^a   Carro, D ^a  

^a UNIVERSITY OF LEÓN   (Spain)

Author keywords

Cellulolytic bacteria; Fungi; Protozoa; Real time PCR; Sheep

Indexed keywords

RIBOSOMAL SPACER DNA;

ALFALFA; ANIMAL; ANIMAL DISEASE; ANIMAL FOOD; ARTICLE; AUTOMATION; BACTERIUM; CHEMISTRY; CLASSIFICATION; CROSSOVER PROCEDURE; DIET; DIETARY FIBER; GENETICS; METABOLISM; MICROBIOLOGY; PHYSIOLOGY; POACEAE; REAL TIME POLYMERASE CHAIN REACTION; RUMINANT STOMACH; SHEEP;

ANIMAL FEED; ANIMAL NUTRITIONAL PHYSIOLOGICAL PHENOMENA; ANIMALS; AUTOMATION; BACTERIA; CROSS-OVER STUDIES; DIET; DIETARY FIBER; DNA, RIBOSOMAL SPACER; MEDICAGO SATIVA; POACEAE; REAL-TIME POLYMERASE CHAIN REACTION; RUMEN; SHEEP;

EID: 84882579690     PISSN: 00218812     EISSN: 15253163     Source Type: Journal    
DOI: 10.2527/jas.2012-5265     Document Type: Article

References (39)

1. Bryant, M. P., and I. M. Robinson. 1961. An improved nonselective culture medium for ruminal bacteria and its use in determining diurnal variation in numbers of bacteria in the rumen. J. Dairy Sci. 44:1446-1456.
2. Chen, X. L., J. K. Wang, Y. M. Wu, and J. X. Liu. 2008. Effects of chemical treatments of rice straw on rumen fermentation characteristics, fi brolytic enzyme activities and populations of liquid- and solid-associated ruminal microbes in vitro. Anim. Feed Sci. Technol. 141:1-14.
3. Danovaro, R., G. M. Luna, A. Dell'Anno, and B. Pietrangeli. 2006. Comparison of two fi ngerprinting techniques, terminal restriction fragment length polymorphism and automated ribosomal inter-genic spacer analysis, for determination of bacterial diversity in aquatic environments. Appl. Environ. Microbiol. 72:5982-5989.
4. Dehority, B. A., and C. G. Orpin. 1997. Development of and natural fl uctuations in rumen microbial populations. Pages 196-245 in The Rumen Microbial Ecosystems. P. N. Hobson and C. S. Stewart, eds. 2nd ed. Blackie Academic & Professional, London, UK.
5. Denman, S. E., and C. S. McSweeney. 2006. Development of a real-Saro et al. time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiol. Ecol. 58:572-582.
6. Edwards, J. E., A. H. Kingston-Smith, H. R. Jimenez, S. A. Huws, K. P. Skøt, G. W. Griffith, N. R. McEwan, and M. K. Theodorou. 2008. Dynamics of initial colonization of nonconserved perennial rye-grass by anaerobic fungi in the bovine rumen. FEMS Microbiol. Ecol. 66:537-545.
7. Giraldo, L. A., M. L. Tejido, M. J. Ranilla, and M. D. Carro. 2008. Effects of exogenous fi brolytic enzymes on in vitro ruminal fermentation of substrates with different forage:concentrate ratios. Anim. Feed Sci. Technol. 141:306-325.
8. Julien, C., J. P. Marden, C. Bonnefont, R. Moncoulon, E. Auclair, V. Monteils, and C. Bayourthe. 2010. Effects of varying proportions of concentrates on ruminal-reducing power and bacterial community structure in dry dairy cows fed hay-based diets. Animal 4:1641-1646.
9. Kocherginskaya, S. A., R. I. Aminov, and B. A. White. 2001. Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches. Anaerobe 7:119-134.
10. Koike, S., and Y. Kobayashi. 2001. Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter suc-cinogenes, Ruminococcus albus and Ruminococcus fl avefaciens. FEMS Microbiol. Lett. 204:361-366.
11. Koike, S., J. Pan, Y. Kobayashi, and K. Tanaka. 2003. Kinetics of in sacco fi ber-attachment of representative ruminal cellulolytic bacteria monitored by competitive PCR. J. Dairy Sci. 86:1429-1435.
12. Komarek, R. J. 1981. Rumen and abomasal cannulation of sheep with specially designed cannulas and a cannula insertion instrument. J. Anim. Sci. 52:790-795.
13. Larue R., Z. Yu, A. A. Parisi, A. R. Egan, and M. Morrison. 2005. Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ. Microbiol. 7:530-543.
14. Leedle, J. A., M. P. Bryant, and R. B. Hespell. 1982. Diurnal variations in bacterial numbers and fl uid parameters in ruminal contents of animals fed low- or high-forage diets. Appl. Environ. Microbiol. 44:402-412.
15. Li, M., G. B. Penner, E. Hernandez-Sanabria, M. Oba, and L. L. Guan. 2009.Effects of sampling location and time, and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen. J. Appl. Microbiol. 107:1924-1934.
16. Martin, C., E. Devillard, and B. Michalet-Doreau. 1999. Infl uence of sampling site on concentrations and carbohydrate-degrading enzyme activities of protozoa and bacteria in the rumen. J. Anim. Sci. 77:979-987.
17. Martin, C., and B. Michalet-Doreau. 1995. Variations in mass and enzyme activity of rumen microorganisms: Effect of barley and buffer supplements. J. Food Agric. Sci. 67:407-413.
18. Martin, C., B. Michalet-Doreau, G. Fonty, and A. Williams. 1993. Postprandial variations in the activity of polysaccharide-degrading enzymes of fl uid- and particle-associated ruminal microbial populations. Curr. Microbiol. 27:223-228.
19. Martin, C., L. Millet, G. Fonty, and B. Michalet-Doreau. 2001. Cereal supplementation modifi ed the fi brolytic activity but not the structure of the cellulolytic bacterial community associated with rumen solid digesta. Reprod. Nutr. Dev. 41:413-424.
20. Martínez, M. E., M. J. Ranilla, M. L. Tejido, S. Ramos, and M. D. Carro. 2010.Comparison of fermentation of diets of variable composition and microbial populations in the rumen of sheep and Rusitec fermenters. I. Digestibility, fermentation parameters, and microbialgrowth. J. Dairy Sci. 93:3684-3698.
21. Michalet-Doreau, B., I. Fernandez, and G. Fonty. 2002. A comparison of enzymatic and molecular approaches to characterize the cellu-lolytic microbial ecosystems of the rumen and the cecum. J. Anim. Sci. 80:790-796.
22. Michalet-Doreau, B., I. Fernandez, C. Peryon, L. Millet, and G. Fonty. 2001. Fibrolytic activities and cellulolytic bacterial community structure in the solid and liquid phases of rumen contents. Reprod. Nutr. Dev. 41:187-194.
23. Mosoni, P., F. Chaucheyras-Durand, C. Béra-Maillet, and E. Forano. 2007. Quantifi cation by real-time PCR of cellulolytic bacteria in the rumen of sheep after supplementation of a forage diet with readily fermentable carbohydrates: Effect of a yeast additive. J. Appl. Microbiol. 103:2676-2685.
24. Mosoni, P., C. Martin, E. Forano, and D. P. Morgavi. 2011. Long-term defaunation increases the abundance of cellulolytic ruminococci and methanogens but does not affect the bacterial and methanogen diversity in the rumen of sheep. J. Anim. Sci. 89:783-791.
25. NRC. 2007. Nutrient Requirements of Small Ruminants: Sheep, Goats, Cervids, and New World Camelids. Natl. Acad. Press, Washington, DC.
26. Petri, R. M., R. J. Forster, W. Yang, J. J. McKinnon, and T. A. McAllister. 2012. Characterization of rumen bacterial diversity and fermentation parameters in concentrate fed cattle with and without forage. J. Appl. Microbiol. (In press).
27. Pfaffl, M. W. 2001. A new mathematical model for relative quantifi cation in real time RT-PCR. Nucleic Acids Res. 29:e45.
28. Ramos, S., M. L. Tejido, M. J. Ranilla, M. E. Martínez, C. Saro, and M. D. Carro. 2009. Infl uence of detachment procedure and diet on recovery of solid-associated bacteria from sheep ruminal digesta and representativeness of bacterial isolates as assessed by automated ribosomal intergenic spacer analysis-polymerase chain reaction. J. Dairy Sci. 92:5659-5668.
29. Santra, A., S. A. Karim, A. S. Mishra, O. H. Chaturvedi, and R. Prasad. 1998. Rumen ciliate protozoa and fi bre utilization in sheep and goats. 30:13-18.
30. Shannon, C. E., and W. Weaver. 1949. The mathematical theory. Small Rumin. Res of communication. University of Illinois Press. Urbana, IL.
31. Sharma, R., S. J. John, D. M. Damgaard, and T.A. McAllister. 2003. Extraction of PCR quality plant and microbial DNA from total rumen contents. BioTechniques 34:92-97.
32. Stewart, C. S. 1977. Factors affecting the cellulolytic activity of rumen contents. Appl. Environ. Microbiol. 33:497-502.
33. Sylvester, J. T., S. K. R. Karnati, Z. Yu, M. Morrison, and J. L. Firkins. 2004.Development of an assay to quantify rumen ciliate protozoalbiomass in cows using real-time PCR. J. Nutr. 134:3378-3384.
34. Sylvester, J. T., S. K. R. Karnati, Z. Yu, C. J. Newbold, and J. L. Firkins. 2005. Evaluation of a real-time PCR assay quantifying the ruminal pool size and duodenal fl ow of protozoal nitrogen. J. Dairy Sci. 88:2083-2095.
35. Weimer, P. J., D. M. Stevenson, and D. R. Mertens. 2010. Shifts in bacterial community composition in the rumen of lactating dairy cows under milk fat-depressing conditions. J. Dairy Sci. 93:265-278.
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. Welkie, D. G., D. M. Stevenson, and P. J. Weimer. 2010. ARISA analysis of ruminal bacterial community dynamics in lactating dairy cows during the feeding cycle. Anaerobe 16:94-100.
38. Wora-anu, S., M. Wanapat, C. Wachirapakorn, and N. Nontaso. 2007. Effect of roughage sources on cellulolytic bacteria and rumen ecology of beef cattle. Asian-Aust. J. Anim. Sci. 20:1705-1712.
39. Yu, Z., and M. Morrison. 2004. Improved extraction of PCR-quality community DNA from digesta and fecal samples. BioTechniques 36:808-812.