Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions, as determined by PCR-denaturing gradient gel electrophoresis analysis

Applied and Environmental Microbiology

Volumn 76, Issue 12, 2010, Pages 3776-3786

  Zhou, Mi ^a   Hernandez Sanabria, Emma ^a   Luo Guan, Le ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; ANIMAL PERFORMANCE; BEEF CATTLE; DENATURING GRADIENT GEL ELECTROPHORESIS; DIETARY CONDITIONS; GREENHOUSE GAS MITIGATION; HIGH ENERGY; LOW ENERGIES; METHANE PRODUCTION; METHANOGENIC COMMUNITY; METHANOGENIC DIVERSITY; PCR-DGGE; STRAIN LEVELS;

AGRICULTURE; ECOLOGY; ELECTROPHORESIS; GELS; GLOBAL WARMING; GREENHOUSE GASES; HIGH ENERGY PHYSICS; METHANE; METHANOGENS; RNA;

NUTRITION;

METHANE; RNA 16S;

ABUNDANCE; AQUACULTURE INDUSTRY; CATTLE; DIET; ELECTROKINESIS; ENERGY BALANCE; GAS FLOW; GEL; GENETIC ANALYSIS; GREENHOUSE GAS; METABOLISM; METHANE; METHANOGENESIS; MICROBIAL COMMUNITY; POPULATION SIZE;

ANIMAL; ARCHAEBACTERIUM; ARTICLE; BACTERIUM; BIODIVERSITY; CATTLE; CLASSIFICATION; CLUSTER ANALYSIS; DIET; DNA DENATURATION; DNA FINGERPRINTING; GENETICS; METABOLISM; METAGENOME; METHODOLOGY; MICROBIOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; RUMINANT STOMACH; ARCHAEON; BACTERIA; BOVINAE; PROCEDURES;

ANIMALS; ARCHAEA; BACTERIA; BIODIVERSITY; CATTLE; CLUSTER ANALYSIS; DIET; DNA FINGERPRINTING; ELECTROPHORESIS, POLYACRYLAMIDE GEL; METAGENOME; METHANE; NUCLEIC ACID DENATURATION; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RUMEN;

ANIMALIA; BOS; METHANOBREVIBACTER; METHANOBREVIBACTER RUMINANTIUM; METHANOBREVIBACTER SMITHII; METHANOBREVIBACTER SP.;

EID: 77953627328     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00010-10     Document Type: Article

References (38)

1. Archer, J. A., E. C. Richardson, R. M. Herd, and P. F. Arthur. 1999. Potential for selection to improve efficiency of feed use in beef cattle: a review. Aust. J. Agric. Res. 50:147-161.
2. Bano, N., S. Ruffin, B. Ransom, and J. T. Hollibaugh. 2004. Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages. Appl. Environ. Microbiol. 70:781-789.
3. Berk, H., and R. K. Thauer. 1997. Function of coenzyme F420-dependent NADP reductase in methanogenic archaea containing an NADP-dependent alcohol dehydrogenase. Arch. Microbiol. 168:396-402.
4. Environment Canada. 2004. Canada's greenhouse gas inventory, 1990-2001. Environment Canada, Ottawa, Ontario, Canada. http://www.ec.gc.ca/ Publicationshttp://default.asp?lang-En&xml-FBDDD1E2-0183-4FD8-9B7E- 247D92BD7348.
5. Finlay, B. J., G. Esteban, K. J. Clarke, A. G. Williams, T. M. Embley, and R. P. Hirt. 1994. Some rumen ciliates have endosymbiotic methanogens. FEMS Microbiol. Lett. 117:157-161.
6. 2 for methane formation and ATP synthesis. J. Bacteriol. 188:642-658.
7. Guan, L. L., J. D. Nkrumah, J. A. Basarab, and S. S. Moore. 2008. Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency. FEMS Microbiol. Lett. 288:85-91.
8. Hegarty, R. S., J. P. Goopy, R. M. Herd, and B. McCorkell. 2007. Cattle selected for lower residual feed intake have reduced daily methane production. J. Anim. Sci. 85:1479-1486.
9. Hook, S. E., K. S. Northwood, A. D. Wright, and B. W. McBride. 2009. Long-term monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow. Appl. Environ. Microbiol. 75:374-380.
10. Intergovernmental Panel on Climate Change. 2001. Climate change 2001: a scientific basis. University Press, Cambridge, United Kingdom.
11. Irbis, C., and K. Ushida. 2004. Detection of methanogens and proteobacteria from a single cell of rumen ciliate protozoa. J. Gen. Appl. Microbiol. 50:203-212.
12. Janssen, P. H., and M. Kirs. 2008. Structure of the archaeal community of the rumen. Appl. Environ. Microbiol. 74:3619-3625.
13. Jarvis, G. N., C. Strompl, D. M. Burgess, L. C. Skillman, E. R. Moore, and K. N. Joblin. 2000. Isolation and identification of ruminai methanogens from grazing cattle. Curr. Microbiol. 40:327-332.
14. Johnson, K. A., and D. E. Johnson. 1995. Methane emissions from cattle. J. Anim. Sci. 73:2483-2492.
15. Ley, R. E., P. J. Turnbaugh, S. Klein, and J. I. Gordon. 2006. Microbial ecology: human gut microbes associated with obesity. Nature 444:1022-1023.
16. Lozupone, C., M. Hamady, and R. Knight. 2006. UniFrac - an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinform. 7:371. (Pubitemid 44390007)
17. Miller, T. L., and C. Lin. 2002. Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov. Int. J. Syst. Evol. Microbiol. 52:819-822.
18. Miller, T. L., M. J. Wolin, H. X. Zhao, and M. P. Bryant. 1986. Characteristics of methanogens isolated from bovine rumen. Appl. Environ. Microbiol. 51:201-202.
19. Nkrumah, J. D., E. K. Okine, G. W. Mathison, K. Schmid, C. Li, J. A. Basarab, M. A. Price, Z. Wang, and S. S. Moore. 2006. Relationships of feedlot feed efficiency, performance, and feeding behavior with metabolic rate, methane production, and energy partitioning in beef cattle. J. Anim. Sci. 84:145-153.
20. Samuel, B. S., E. E. Hansen, J. K. Manchester, P. M. Coutinho, B. Henrissat, R. Fulton, P. Latreille, K. Kim, R. K. Wilson, and J. I. Gordon. 2007. Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc. Natl. Acad. Sci. U. S. A. 104:10643-10648.
21. Sharp, R., C. J. Ziemer, M. D. Stern, and D. A. Stahl. 1998. Taxon-specific association between protozoal and methanogen populations in the rumen and a model rumen system. FEMS Microbiol. Ecol. 26:71-78.
22. Skillman, L. C., P. N. Evans, G. E. Naylor, B. Morvan, G. N. Jarvis, and K. N. Joblin. 2004. 16S ribosomal DNA-directed PCR primers for ruminai methanogens and identification of methanogens colonising young lambs. Anaerobe 10:277-285.
23. Skillman, L. C., P. N. Evans, C. Strompl, and K. N. Joblin. 2006.16S rDNA directed PCR primers and detection of methanogens in the bovine rumen. Lett. Appl. Microbiol. 42:222-228.
24. Stewart, C. S., H. J. Flint, and M. P. Bryant. 1997. The rumen bacteria, p. 10-72. In P. N. Hobson and C. S. Stewart (ed.), The rumen microbial system, 2nd ed. Blackie Academic and Professional, New York, NY.
25. Stumm, C. K., H. J. Gijzen, and G. D. Vogels. 1982. Association of methanogenic bacteria with ovine rumen ciliates. Br. J. Nutr. 47:95-99.
26. Sundset, M. A., J. E. Edwards, Y. F. Cheng, R. S. Senosiain, M. N. Fraile, K. S. Northwood, K. E. Praesteng, T. Glad, S. D. Mathiesen, and A. D. Wright. 2009. Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture. Microb. Ecol. 57:335-348.
27. Tajima, K., T. Nagamine, H. Matsui, M. Nakamura, and R. I. Aminov. 2001. Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol. Lett. 200:67-72.
28. Tokura, M., I. Chagan, K. Ushida, and Y. Kojima. 1999. Phylogenetic study of methanogens associated with rumen ciliates. Curr. Microbiol. 39:123-128.
29. Turnbaugh, P. J., F. Backhed, L. Fulton, and J. I. Gordon. 2008. Dietinduced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:213-223.
30. Watanabe, T., S. Asakawa, A. Nakamura, K. Nagaoka, and M. Kimura. 2004. DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil. FEMS Microbiol. Lett. 232:153-163.
31. Whitford, M. F., R. M. Teather, and R. J. Forster. 2001. Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol. 1:5.
32. Wolin, M. J., T. L. Miller, and C. S. Stewart. 1997. Microbe-microbe interactions, p. 467-491. In P. N. Hobson and C. S. Steward (ed.), The rumen microbial ecosystem. Blackie Academic and Professional, New York, NY.
33. Wright, A. D., C. H. Auckland, and D. H. Lynn. 2007. Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Appl. Environ. Microbiol. 73:4206-4210.
34. Wright, A. D., X. Ma, and N. E. Obispo. 2008. Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela. Microb. Ecol. 56:390-394.
35. Wright, A. D., and C. Pimm. 2003. Improved strategy for presumptive identification of methanogens using 16S riboprinting. J. Microbiol. Methods 55:337-349.
36. Yu, Z., R. Garcia-Gonzalez, F. L. Schanbacher, and M. Morrison. 2008. Evaluation of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by Archaea-specific PCR and denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 74:889-893.
37. Zhou, M., E. Hernandez-Sanabria, and L. L. Guan. 2009. Assessment of the microbial ecology of ruminai methanogens in cattle with different feed efficiencies. Appl. Environ. Microbiol. 75:6524-6533.
38. Zinder, S. H. 1993. Physiological ecology of methanogens, p. 128-206. In J. G. Ferry (ed.), Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman & Hall, New York, NY.