Linking rumen function to animal response by application of metagenomics techniques

Australian Journal of Experimental Agriculture

Volumn 48, Issue 7, 2008, Pages 711-721

  Firkins, J L ^a   Karnati, S K R ^a   Yu, Z ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; CLUSTER ANALYSIS; COMMUNITY STRUCTURE; CONCENTRATION (COMPOSITION); DIET; DIGESTIVE SYSTEM; FOOD SUPPLY; GENOMICS; METABOLITE; NUTRITION; PROTOZOAN; RUMINANT;

ANIMALIA; ARCHAEA; BACTERIA (MICROORGANISMS); BOVIDAE; CLOSTRIDIA; PROTOZOA;

EID: 45849090282     PISSN: 08161089     EISSN: None     Source Type: Journal    
DOI: 10.1071/EA08028     Document Type: Conference Paper

References (68)

1. Allen MS (2000) Effects of diet on short-term regulation of feed intake by lactating dairy cattle. Journal of Dairy Science 83, 1598-1624.
2. Beauchemin KA, Kreuzer M, O'Mara FO, McAllister TA (2008) Nutritional management for enteric methane abatement: a review. Australian Journal of Experimental Agriculture 48, 21-27. doi: 10.1071/EA07199
3. Beloqui A, Pita M, Polaina J, Martínez-Arias A, Golyshina OV et al. (2006) Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen. Journal of Biological Chemistry 281, 22933-22942. doi: 10.1074/jbc.M600577200
4. Blum DL, Kataeva A, Li XL, Ljungdahl LG (2000) Feruloyl esterase activity of the Clostridium thermocellum cellulosome can be attributed to previously unknown domains of Xyny and Xynz. Journal of Bacteriology 182, 1346-1351. doi: 10.1128/JB.182.5.1346-1351.2000
5. Calsamiglia S, Busquet M, Cordozo PW, Castillejos L, Ferret A (2007) Invited Review: essential oils as modifiers of rumen microbial fermentation. Journal of Dairy Science 90, 2580-2595. doi: 10.3168/jds.2006-644
6. Cho KM, Hong SY, Lee SM, Kim YH, Kahng GG, Kim H, Yun HD (2006) A cel44C-man26A gene of endophytic Paenibacillus polymyxa GS01 has multi-glycosyl hydrolases in two catalytic domains. Applied Microbiology and Biotechnology 73, 618-630. doi: 10.1007/s00253-006-0523-2
7. Demain AL, Newcomb M, Wu JH (2005) Cellulase, clostridia, and ethanol. Microbiology and Molecular Biology Reviews 69, 124-154. doi: 10.1128/MMBR.69.1.124-154.2005
8. Denman SE, McSweeney CS (2006) Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiology Ecology 58, 572-582. doi: 10.1111/j.1574-6941.2006.00190.x
9. Desvaux M (2006) Unravelling carbon metabolism in anaerobic cellulolytic bacteria. Biotechnology Progress 22, 1229-1238. doi: 10.1021/bp060016e
10. Devillard E, McIntosh FM, Newbold CJ, Wallace RJ (2006) Rumen ciliate protozoa contain high concentrations of conjugated linoleic acids and vaccenic acid, yet do not hydrogenate linoleic acid or desaturate stearic acid. British Journal of Nutrition 96, 697-704.
11. Edwards JE, McEwan NR, Travis AJ, Wallace RJ (2004) 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie Van Leeuwenhoek 86, 263-281. doi: 10.1023/B:ANTO.0000047942.69033.24
12. Eugène M, Archimède H, Sauvant D (2004) Quantitative meta-analysis on the effects of defaunation of the rumen on growth, intake and digestion in ruminants. Livestock Production Science 85, 81-97. doi: 10.1016/S0301-6226(03)00117-9
13. Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Reyes-Duarte D et al. (2005) Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora. Environmental Microbiology 7, 1996-2010. doi: 10.1111/j.1462-2920.2005.00920.x
14. Ferrer M, Beloqui A, Golyshina OV, Plou FJ, Neef A et al. (2007) Biochemical and structural features of a novel cyclodextrinase from cow rumen metagenome. Biotechnology Journal 2, 207-213. doi: 10.1002/biot.200600183
15. Firkins JL (1997) Effects of feeding nonforage fiber sources on site of fiber digestion. Journal of Dairy Science 80, 1426-1437.
16. Firkins JL, Yu Z (2006) Characterisation and quantification of the microbial populations in the rumen. In 'Ruminant physiology, digestion, metabolism and impact of nutrition on gene expression, immunology and stress'. (Eds K Sejrsen, T Hvelplund, MO Nielsen) pp. 19-54. (Wageningen Academic Publishers: Wageningen, The Netherlands)
17. Firkins JL, Hristov AN, Hall MB, Varga GA, St-Pierre NR (2006) Integration of ruminal metabolism in dairy cattle. Journal of Dairy Science 89, E31-E51. [E. Suppl]
18. Firkins JL, Yu Z, Morrison M (2007) Ruminal nitrogen metabolism: perspectives for integration of microbiology and nutrition for dairy. Journal of Dairy Science 90, E1-E16. [E. Suppl]
19. Firkins JL, Oldick BS, Pantoja J, Gilligan LE, Carver L (2008) Efficacy of liquid feeds varying in concentration and composition of fat, non-protein nitrogen, and non-fiber carbohydrates for lactating dairy cows. Journal of Dairy Science 91, in press.
20. Gabor EM, Alkema WB, Janssen DB (2004) Quantifying the accessibility of the metagenome by random expression cloning techniques. Microbiology 6, 879-886.
21. Gilbert HJ (2007) Cellulosomes: Microbial nanomachines that display plasticity in quaternary structure. Molecular Microbiology 63, 1568-1576. doi: 10.1111/j.1365-2958.2007.05640.x
22. Gozho GN, Krause DO, Plaizier JC (2007) Ruminal lipopolysaccharide concentration and inflammatory response during grain-induced subacute ruminal acidosis in dairy cows. Journal of Dairy Science 90, 856-866.
23. Guan H, Wittenberg KM, Ominski KH, Krause DO (2006) Efficacy of ionophores in cattle diets for mitigation of enteric methane. Journal of Animal Science 84, 1896-1906. doi: 10.2527/jas.2005-652
24. Hegarty RS (1999) Reducing rumen methane emissions through elimination of rumen protozoa. Australian Journal of Agricultural Research 50, 1321-1327. doi: 10.1071/AR99008
25. Hristov AN, Jouany J-P (2005) Factors affecting the efficiency of nitrogen utilization in the rumen. In 'Nitrogen and phosphorus nutrition of cattle and environment'. (Eds AN Hristov, E Pfeffer) pp. 117-166. (CAB International: Wallingford, UK)
26. Huws SA, Edwards JE, Kim EJ, Scollan ND (2007) Specificity and sensitivity of eubacterial primers utilized for molecular profiling of bacteria within complex microbial ecosystems. Journal of Microbiological Methods 70, 565-569. doi: 10.1016/j.mimet.2007.06.013
27. Karnati SKR (2006) Application of molecular techniques to assess changes in ruminal microbial populations and protozoal generation time in cows and continuous culture. Available at http://www.ohiolink.edu/etd/view.cgi?acc%5Fnum= osu1164662405 [Verified 9 April 2008]
28. Karnati SKR, Sylvester JT, Noftsger SM, Yu Z, St-Pierre NR, Firkins JL (2007) Assessment of ruminal bacterial populations and protozoal generation time in cows fed different methionine sources. Journal of Dairy Science 90, 798-809.
29. Klieve AV, Hennessey D, Ouwerkerk D, Forster RJ, Mackie RI, Attwood GT (2003) Establishing populations of Megasphaera elsdenii YE34 and Butyrivibrio fibrisolvens YE44 in the rumen of cattle fed high grain diets. Journal of Applied Microbiology 95, 621-630. doi: 10.1046/j.1365-2672.2003.02024.x
30. Klieve AV, O'Leary MN, McMillen L, Ouwerkerk D (2007) Ruminococcus bromii, identification and isolation as a dominant community member in the rumen of cattle fed a barley diet. Journal of Applied Microbiology 103, 2065-2073. doi: 10.1111/j.1365-2672.2007.03492.x
31. Kocherginskaya S, Aminov RI, White BA (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. doi: 10.1006/anae.2001.0378
32. Koenig KM, Ivan M, Teferedegne BT, Morgavi DP, Rode LM, Ibrahim IM, Newbold CJ (2007) Effect of dietary Enterolobium cyclocarpum on microbial protein flow and nutrient digestibility in sheep maintained fauna-free, with total mixed fauna or with Entodinium caudatum monofauna. British Journal of Nutrition 98, 504-516. doi: 10.1017/S0007114507723930
33. Konstantinidis K, Tiedje JM (2007) Prokaryotic taxonomy and phylogeny in the genomic era: Advancements and challenges ahead. Current Opinion in Microbiology 10, 504-509. doi: 10.1016/j.mib.2007.08.006
34. Krause DO, Bunch RJ, Conlan LL, Kennedy PM, Smith WJ, Mackie RI, McSweeney CS (2001) Repeated ruminal dosing of Ruminococcus spp. does not result in persistence, but changes in other microbial populations occur that can be measured with quantitative 16S-rRNA-based probes. Microbiology 147, 1719-1729.
35. Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS (2003) Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiology Reviews 27, 663-693. doi: 10.1016/S0168-6445(03)00072-X
36. Larue R, Yu Z, Parisi VA, Egan AR, Morrison M (2005) Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environmental Microbiology 7, 530-543. doi: 10.1111/j.1462-2920. 2005.00721.x
37. Leggewie C, Henning H, Schmeisser C, Streit WR, Jaeger KE (2006) A novel transposon for functional expression of DNA libraries. Journal of Biotechnology 123, 281-287. doi: 10.1016/j.jbiotec.2005.12.010
38. Love JL, Scholes P, Gilpin B, Savill M, Lin S, Samuel L (2006) Evaluation of uncertainty in quantitative real-time PCR. Journal of Microbiological Methods 67, 349-356. doi: 10.1016/j.mimet.2006.04.005
39. Maia MRG, Chaudhary LC, Figueres L, Wallace RJ (2007) Metabolism of polyunsaturated fatty acids and their toxicity to the microflora of the rumen. Antonie Van Leeuwenhoek 91, 303-314. doi: 10.1007/s10482-006-9118- 2
40. McAllister TA, Newbold CJ (2008) Redirecting rumen fermentation to reduce methanogenesis. Australian Journal of Experimental Agriculture 48, 7-13. doi: 10.1071/EA07218
41. Mouriño F, Akkarawongsa R, Weimer PJ (2001) Initial pH as a determinant of cellulose digestion rate by mixed ruminal microorganisms in vitro. Journal of Dairy Science 84, 848-859.
42. Nagaraja TG, Titgemeyer EC (2007) Ruminal acidosis in beef cattle: the current microbiological and nutritional outlook. Journal of Dairy Science 90, E17-E38. [E. Suppl]
43. Ohene-Adjei S, Teather RM, Ivan M, Forster RJ (2007) Postinoculation protozoan establishment and association patterns of methanogenic archaea in the ovine rumen. Applied and Environmental Microbiology 73, 4609-4618. doi: 10.1128/AEM.02687-06
44. Paillard D, McKain N, Chaudhary LC, Walker ND, Pizette F et al. (2007) Relation between phylogenetic position, lipid metabolism and butyrate production by different Butyrivibrio-like bacteria fromthe rumen. Antonie Van Leeuwenhoek 91, 417-422. doi: 10.1007/s10482-006-9121- 7
45. Palackal N, Lyon CS, Zaidi S, Luginbül P, Dupree P et al. (2007) A multifunctional hybrid glycosyl hydrolase discovered in an uncultured microbial consortium from ruminant gut. Applied Microbiology and Biotechnology 74, 113-124. doi: 10.1007/s00253-006-0645-6
46. Pinares-Patiño CS, Clark H (2008) Reliability of the sulfur hexafluoride tracer techniques for methane emission measurement from individual animals: an overview. Australian Journal of Experimental Agriculture 48, 223-229. doi: 10.1071/EA07297
47. Potter EL, Dehority BA (1973) Effects of changes in feed level, starvation, and level of feed after starvation upon the concentration of rumen protozoa in the ovine. Applied Microbiology 26, 692-698.
48. Russell JB, Mantovani HC (2002) The bacteriocins of ruminal bacteria and their potential as an alternative to antibiotics. Journal of Molecular Microbiology and Biotechnology 4, 347-355.
49. Schloss PD, Handelsman J (2005) Metagenomics for studying unculturable microorganisms: cutting the gordian knot. Genome Biology 6, 229. doi: 10.1186/gb-2005-6-8-229
50. Selinger LB, Forsberg CW, Cheng K-J (1996) The rumen: a unique source of enzymes for enhancing livestock production. Anaerobe 2, 263-284. doi: 10.1006/anae.1996.0036
51. Shinkai T, Kobayashi T (2007) Localization of ruminal cellulolytic bacteria on plant fibrous materials as determined by fluorescence in situ hybridization and real-time PCR. Applied and Environmental Microbiology 73, 1646-1652. doi: 10.1128/AEM.01896-06
52. Stewart CS, Flint HJ, Bryant MP (1997) The rumen bacteria. In 'The rumen microbial ecosystem'. (Eds PN Hobson, CS Stewart) pp. 10-72. (Blackie Academic & Professional: New York)
53. Sylvester JT, Karnati SKR, Yu Z, Morrison M, Firkins JL (2004) Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. Journal of Nutrition 134, 3378-3384.
54. Sylvester JT, Karnati SKR, Yu Z, Newbold CJ, Firkins JL (2005) Evaluation of a real-time PCR assay for measuring the ruminal pool and duodenal flow of protozoal nitrogen. Journal of Dairy Science 88, 2083-2095.
55. Sylvester JT (2005) Development and evaluation of new techniques to quantify ruminal pool size and duodenal flow of protozoal nitrogen. PhD Dissertation. The Ohio State University, Columbus, OH.
56. Tajima K, Arai S, Ogata K, Nagamine T, Matsui H, Nakamura M, Aminov RI, Benno Y (2000) Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 6, 273-284. doi: 10.1006/anae.2000.0353
57. Takenaka A, D'Silva CG, Kudo H, Itabashi H, Cheng K-J (1999) Molecular cloning, expression, and characterization of an endo-beta-1,4-glucanase cDNA from Epidinium caudatum. Journal of General and Applied Microbiology 45, 57-61. doi: 10.2323/jgam.45.57
58. Tringe SG, Rubin EM (2005) Metagenomics: DNA sequencing of environmental samples. Nature Reviews. Genetics 6, 805-814. doi: 10.1038/nrg1709
59. Walker ND, Newbold CJ, Wallace RJ (2005) Nitrogen metabolism in the rumen. In 'Nitrogen and phosphorus nutrition of cattle'. (Eds E Pfeffer, A Hristov) pp. 71-115. (CABI Publishing: Cambridge, MA)
60. Willems A, Amat-Marco M, Collins MD (1996) Phylogenetic analysis of Butyrivibrio strains reveals three distinct groups of species within the Clostridium subphylum of the Gram-positive bacteria. International Journal of Systematic Bacteriology 46, 195-199.
61. Wright A-DG, Auckland CH, Lynn DH (2007) Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Applied and Environmental Microbiology 73, 4206-4210. doi: 10.1128/AEM.00103-07
62. Yáñez-Ruiz DR, Scollan ND, Merry RJ, Newbold CJ (2006) Contribution of rumen protozoa to duodenal flow of nitrogen, conjugated linoleic acid and vaccenic acid in steers fed silages differing in their water-soluble carbohydrate content. British Journal of Nutrition 96, 861-869. doi: 10.1017/BJN20061927
63. Yáñez-Ruiz DR, Williams S, Newbold CJ (2007) The effect of absence of protozoa on rumen biohydrogenation and the fatty acid composition of lamb muscle. British Journal of Nutrition 97, 938-948. doi: 10.1017/S0007114507675187
64. Yu Z, Morrison M (2004) Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 70, 4800-4806. doi: 10.1128/AEM.70.8.4800-4806.2004
65. Yu Z, Yu M, Morrison M (2006) Improved serial analysis of V1 ribosomal sequence tags (SARST-V1) provides a rapid, comprehensive, sequence-based characterization of bacterial diversity and community composition. Applied and Environmental Microbiology 8, 603-611. doi: 10.1111/j.1462-2920. 2005.00933.x
66. Yu Z, García-González R, Schanbacher FL, Morrison M (2008) Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by Archaea-specific PCR and denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 74, 889-893. doi: 10.1128/AEM.00684-07
67. Yun J, Ryu S (2005) Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microbial Cell Factories 4, 8. doi: 10.1186/1475-2859-4-8
68. Zhu YX, Wang JQ, Ma RL, Huang L, Dong ZY (2007) Construction and analysis of rumen bacterial artificial chromosome library froma dairy cow rumen microflora. Acta Microbiologica Sinica 47, 213-216. [In Chinese]