Development and Use of Rumen Molecular Techniques for Predicting and Enhancing Livestock Productivity

Closed for proposals

Project Type

Coordinated Research Project

Project Code

D31024

CRP

304

Approved Date

24 October 2003

Status

4 - Closed

Start Date

15 November 2003

Expected End Date

11 October 2010

Completed Date

11 October 2010

Participating Countries

Australia
Brazil
China
Colombia
Cuba
Ethiopia
Germany
India
Japan
New Zealand
Switzerland
Thailand
Turkey
United Kingdom of Great Britain and Northern Ireland
United States of America

Description

The world's livestock sector is amidst a massive transformation, fuelled by high demand for meat and milk, which is likely to double over the next two decades in developing countries. The major driving force behind this soaring demand for livestock products is a combination of population growth, urbanization and income growth, especially in developing countries. The challenge is to enhance animal productivity without any adverse effects on environment.
A large proportion of the global ruminant population is located in tropical environments, where animals feed predominantly on low quality highly fibrous forages. Recent studies in respiration chambers have confirmed that methane emissions from ruminants fed on fibrous diets are higher than outputs from better quality temperate forages. The excretion of methane from the rumen can represent a loss of up to 15% of the digestible energy depending on the type of diet. Therefore, reducing methane production could benefit the ruminant energetically provided the efficiency of ruminal metabolism is not compromised. The challenge therefore is to devise strategies, which reduce methane emissions from ruminants and improve production efficiency.
Current approaches to the evaluation of digestibility and nutritive value of feed resources using conventional in vitro feed evaluation and animal studies have resulted in a large body of information about nutrient composition, digestion kinetics and digestibility. However, these techniques are unable to describe the microbial mechanisms involved in ruminal digestion, and are unlikely to result in the development of rational feeding strategies.
Conventional culture-based methods of enumerating rumen bacteria are being rapidly replaced by the development of nucleic acid based techniques which can be used to characterise complex microbial communities. The foundation of these techniques is SSU rDNA (eg. 16S rRNA sequences) sequence analysis which has provided a phylogenetically based classification scheme for enumeration and identification of microbial community members. The molecular based ecology techniques are also likely to provide better insight into the interactions between methanogens and the other rumen microorganisms. All this information should assist in the development of strategies for improving production by reducing methanogenesis.
The Overall Objective of this CRP is to improve ruminant performance through a reduction in methane production. It is aimed to: i) reduce the level of methane production by up to 50% in animals fed roughage diets, ii) increase microbial protein and energy supply through reduced methane production using approaches such as inhibitors of methanogens, dietary approaches (e.g. use of polyunsaturated fatty acids or ingredients containing these acids), supplementation strategies, etc, iii) build in-country capacity to develop and use molecular techniques for studying rumen function, iv) develop molecular probes for quantifying populations of methanogens, fibre degrading bacteria, fungi and protozoa, v) correlate methane production to methanogen numbers, vi) determine effects of reduced methanogen numbers on fibre degrading bacteria, fungi and protozoa. Through these investigations, feeding strategies and or supplements that reduce methane production and improve productivity in ruminants on tropical diets will be developed, and better insight into the mechanism of feed digestion particularly interactions between various groups of rumen microorganisms will be available. This would lead to development of guidelines for reduction in methane emission and enhancement of animal productivity, for use at a wider scale.

Objectives

To improve ruminant performance through a reduction in methane production

Specific objectives

Build in-country capacity to develop and use molecular techniques for studying rumen function.

Correlate methane production to methanogen numbers.

Determine effects of reduced methanogen numbers on fibre degrading bacteria, fungi and protozoa.

Develop and use molecular probes for quantifying populations of methanogens, fibre degrading bacteria, fungi and protozoa.

Identify naturally occurring plant secondary compounds that inhibit methanogens.

Increase microbial protein and energy supply through reduced methane production using approaches such as inhibitors of methanogens, dietary approaches (e.g. use of polyunsaturated fatty acids or ingredients containing these acids), supplementation strategies, etc.

Reduce the level of methane production by up to 40% in animals fed roughage diets.

Impact

The CRP improved our knowledge and understanding of the ecology of rumen microorganisms, particularly methanogenic archaea and their interaction with predominant rumen microorganisms. Specifically,

• In vitro gas production test was standardized and used for screening antimethanogenic activity of plants containing secondary metabolites.
• Real-time PCR to enumerate rumen microbes in in vitro and in vivo systems, and DGGE for the study of rumen microbial diversity were optimized and implemented.
• Protozoal activity by (14C) Radio Isotope Technique was standardized and used for screening.
• In vivo methane production measurements in small and large ruminants using SF6, tunnel system and open circuit respiration calorimeter were validated and used.
• Increased capacity of NAS - over 30 students were trained to MSc and PhD levels and over 50 project staff, technicians and researchers trained in molecular biology techniques.
• Two (2) books titled "Methods in Gut Microbial Ecology for Ruminants" and "Measuring Methane Production from Ruminants" and over 50 peer-reviewed journal articles were published in peer-review journals. Description of approaches, methodologies and guidelines for methane measurement, methane reduction and enhancement of animal productivity are available to national authorities, farmer organizations and industry for use in implementing these tools on a larger scale.

These techniques which contribute to reducing the impact of ruminants on the environment, are currently being transferred to Member States through Technical Cooperation Projects.

Relevance

The CRP contributed to the project 2.1.2.3: Molecular technologies for improving productivity in smallholder livestock systems. Current approaches to the evaluation of digestibility and nutritive value of feed resources using conventional in vitro feed evaluation and animal studies have resulted in a large body of information about nutrient composition, digestion kinetics and digestibility. However, these techniques are unable to describe the microbial mechanisms involved in ruminal digestion, and are unlikely to result in the development of rational feeding strategies. Gene-based technologies have the potential to improve the nutritive value of ruminant feedstuffs that are fibrous, low in nitrogen and contain anti-nutritive factors.
Until recently our knowledge of rumen microbiology was primarily based on classical culture based techniques (isolation, enumeration and nutritional characterization) which probably only account for 10 to 20% of the rumen microbial population. Conventional culture-based methods of enumerating rumen bacteria are being rapidly replaced by the development of nucleic acid based techniques which can be used to characterise complex microbial communities. The 16S rRNA sequences in DNA extracted from a mixed digesta sample can be amplified by PCR using primers and the diversity and identity of the amplified 16S rDNA can be further analysed by several molecular techniques including: 1) restriction enzyme analysis of amplified polymorphic DNA (RFLP); 2) 16S rDNA based cloning, sequencing and probing; and 3) denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), and single strand conformation polymorphism (SSCP). Therefore RT-PCR and oligonucleotide probes targeting the respective 16S rRNA of the methanogenic archaea, and the major fibrolytic bacteria (Fibrobacter succinogenes, Ruminococcus albus and R. flavefaciens) in the rumen would be a robust approach to quantifying the effect of reduced methanogenesis on important functional microbial groups. The molecular based ecology techniques are also likely to provide better insight into the interactions between methanogens and the other rumen microorganisms. All this information should assist in the development of strategies for improving production by reducing methanogenesis. However, the challenge is how we utilize these technologies to improve ruminant production through a better understanding of microbial function and ecology.

CRP Publications

Type

Research paper

Year

2009

Description

Neeta Agarwal, Chandra Shekhar, Ravindra Kumar, L.C. Chaudhary, D.N. Kamra 2009. Effect of peppermint (Mentha piperita) oil on in vitro methanogenesis and fermentation of feed with buffalo rumen liquor. Animal Feed Science and Technology, 148: 321-327.

Country/Organization

India

Type

Special Issue or TECDOC research & review papers

Year

2011

Description

“Effect of tropical feeds and plants containing secondary metabolites on methane emission by ruminants” by D.N. Kamra, Neeta Agarwal and L.C. Chaudhary

Country/Organization

India

Type

Research paper

Year

2006

Description

Kamra, D.N., Agarwal, N. And Chaudhary, L.C. 2006. Inhibition of ruminal methanogenesis by tropical plants containing secondary compounds. International Congress Series, 1293: 156-163.

Country/Organization

India

Type

Research paper

Year

2009

Description

M. Wanapat, R. Pilajun, P. Kongmun. 2009. Ruminal ecology of swamp buffalo as influenced by dietary sources. Animal Feed Science and Technology, 151: 205-214.

Country/Organization

Thailand

Type

Special Issue or TECDOC research & review papers

Year

2011

Description

“In vitro evaluation, in vivo quantification and microbial diversity studies on using nutritional strategies for reducing enteric methane production” by Adibe Luiz Abdalla, Ives Cláudio da Silva Bueno, Helder Louvandini, Sobhy Mohamed Abdallah Hassan Sallam, Siu Mui Tsai and Antonio Vargas Oliveira Figueira

Country/Organization

Brazil

Type

Research paper

Year

2008

Description

H.D. Hess, M.L. Mera, T.T. Tiemann, C.E. Lascano and M. Kreuzer. 2008. In vitro assessment of the suitability of replacing the low-tannin legume Vigna unguiculata with the tanniniferous legumes Leucaena leucocephala, Flemingia macrophylla or Calliandra calothyrsus in a tropical grass diet. Animal Feed Science and Technology, 147: 105–115.

Country/Organization

Switzerland

Type

Research paper

Year

2008

Description

Zhang C.M., Yi X.W., Yuan Z.P., Liu J.X., Zhu W.Y. 2008. Effects of adding with mixtures of linoleic and linolenic acids on rumen fermentation and methanogenesis in vitro. Chinese Journal of Animal Nutrition. 20(2):223-227.

Country/Organization

China

Type

Research paper

Year

2005

Description

Kamra, D.N., Agarwal, N. and Yadav, M.P. 2004. Methanogenesis in the rumen and the greenhouse effect on the environment. Livestock International, 8 (9): 2, 5-8.

Country/Organization

India

Type

Research paper

Year

2006

Description

Patra, A.K., Kamra, D.N. and Agarwal, N. 2006b. Effect of plants containing secondary metabolites on in vitro methanogenesis, enzyme profile and fermentation of feed with rumen liquor of buffalo. Anim. Nutr. Feed Technol., 6: 203-213.

Country/Organization

India

Type

Research paper

Year

2008

Description

Agarwal, N., Kamra, D.N., Chatterjee, P.N., Kumar, R. and Chaudhary, L.C., 2008. In vitro methanogenesis, microbial profile and fermentation of green forages with buffalo rumen liquor as influenced by 2-bromoethanesulphonic acid. Asian-Aust. J. Anim. Sci., 21: 818-823.

Country/Organization

India

Type

Special Issue or TECDOC research & review papers

Year

2011

Description

“Feeding of tropical trees and shrub foliages as a strategy to reduce ruminal methanogenesis: studies conducted in Cuba” by Delgado D.C., Galindo J. L., González R., González, N., Scull I., Dihigo L. Cairo J., Aldama A.I., and Moreira O.

Country/Organization

Cuba

Type

Research paper

Year

2006

Description

Patra, A.K., Kamra, D.N. and Agarwal, N. 2006a. Effect of plant extracts on in vitro methanogenesis, enzyme activities and fermentation of feed in rumen liquor of buffalo. Anim. Feed Sci. Technol., 128(3-4): 276-291.

Country/Organization

India

Type

Book

Year

2005

Publication URL

http://www.springer.com/life+sciences/ecology/book/978-1-4020-3790-0

Description

Methods in Gut Microbial Ecology for Ruminants edited by Harinder P.S. Makkar and Christopher S. McSweeney.

Country/Organization

Springer Publishers

Type

Special Issue or TECDOC research & review papers

Year

2011

Description

“Effects of plants containing secondary compounds and plant oils on rumen fermentation and ecology” by M. Wanapat, P. Kongmun, O. Poungchompu, A. Cherdthong, P. Khejornsart, R. Pilajun and S. Kanpakdee

Country/Organization

Thailand

Type

Research paper

Year

2009

Description

F. Klevenhusen, S.M. Bernasconi, T. Hofstetter, J. Bolotin, C. Kunz and C.R. Soliva. 2009. Efficiency of monolaurin in mitigating ruminal methanogenesis and modifying C-isotope fractionation when incubating diets composed of either C3 or C4 plants in a rumen simulation technique (Rusitec) system. British Journal of Nutrition, 102: 1308 – 1317.

Country/Organization

Switzerland

Type

Research paper

Year

2008

Description

Zhang CM, Yi XW, Yuan ZP, Liu JX, Zhu WY. 2008. Effects of adding with mixtures of linoleic and linolenic acids on rumen fermentation and methanogenesis in vitro. Chinese Journal of Animal Nutrition. 20: 223-227.

Country/Organization

China

Type

Research paper

Year

2006

Description

Duan, ZY, Guo YQ, Liu JX. 2006. Application of modern molecular biology techniques to study micro-ecosystem in the rumen. Acta Microbiologica Sinica. 46:166-169. (in Chinese with English summary).

Country/Organization

China

Type

Research paper

Year

2008

Description

K.A. Beauchemin, M. Kreuzer, F. O’Mara and T. A. McAllister. 2008. Nutritional management for enteric methane abatement: a review. Australian Journal of Experimental Agriculture, 48: 21–27.

Country/Organization

Switzerland

Type

Research paper

Year

2008

Description

Guo Y.Q., Liu J.X., Hu W.l., Yuan Z.P., Zhang C.M., Lu Y, Zhu W.Y., Mcsweeney C.S., Effect of tea saponin on methanogenesis, microbial community structure and expression of mcrA gene, in cultures of rumen microorganisms. Letter in Applied Microbiology, 47: 421-426

Country/Organization

China

Type

Research paper

Year

2006

Description

Patra, A.K., Kamra, D.N. and Agarwal, N. 2006c. Effect of spices on rumen fermentation, methanogenesis and protozoa counts in in vitro gas production test. International Congress Series, 1293: 176-179.

Country/Organization

India

Type

Research paper

Year

2008

Description

Sallam, S.M.A., Bueno, I.C.S., Godoy, P.B., Nozella, E.F., Vitti, D.M.S.S., Abdalla, A.L., 2008. Nutritive value assessment of the artichoke (Cynara scolymus) by-product as an alternative feed resource for ruminants. Tropical and Subtropical Agroecosystems 8, 181 - 189.

Country/Organization

Brazil

Type

Research paper

Year

2005

Description

Hu W.L., Liu J.X., Ye J.A., Wu Y.M., Guo Y.Q, 2005. Effect of tea saponins on rumen fermentation in vitro. Animal Feed Science and Technology. 120(3/4):333-339.

Country/Organization

China

Type

Research paper

Year

2007

Description

Cabral Filho, S.L.S., Bueno, I.C.S., Abdalla, A.L., 2007. Substituição do feno de Tifton pelo resíduo úmido de cervejaria em dietas de ovinos em mantença. Ciência Animal Brasileira 8, 63-75.

Country/Organization

Brazil

Type

Research paper

Year

2005

Description

Hu W.L., Chen X.J., Duan Z.Y., Liu J.X., 2005. Effect of saponins on animal nutrition - a review. Chinese Journal of Animal Science. 41(3), 35-36, 60. (in Chinese with English summary)

Country/Organization

China

Type

Book

Year

2007

Publication URL

http://www.springer.com/environment/pollution+and+remediation/book/978-1-4020-61…

Description

Measuring Methane Production from Ruminants edited by Harinder P.S. Makkar and Philip E. Vercoe.

Country/Organization

Springer Publishers

Type

Research paper

Year

2006

Description

H.D. Hess, T.T. Tiemann, F. Noto, S. Franzel, C.E. Lascano and M. Kreuzer. 2006. The effects of cultivation site on forage quality of Calliandra calothyrsus var. Patulul. Agroforest Syst., 68: 209–220.

Country/Organization

Switzerland

Type

Research paper

Year

2008

Description

C.M. Zhang, Y.Q. Guo, Z.P. Yuan, Y.M. Wu, J.K. Wang, J.X. Liu, W.Y. Zhu 2008. Effect of octadeca carbon fatty acids on microbial fermentation, methanogenesis and microbial flora in vitro . Animal Feed Science and Technology. Animal Feed Science and Technology, Volume 146, Issues 3-4, 15 October 2008, Pages 259-269

Country/Organization

China

Type

Research paper

Year

2010

Description

Patra AK, Kamra DN, Bhar R, Kumar R, Agarwal N. 2010. Effect of Terminalia chebula and Allium sativum on in vivo methane emission by sheep. J Anim Physiol Anim Nutr (Berl). 2010 Jul 26. [Epub ahead of print].

Country/Organization

India

Type

Research paper

Year

2008

Description

T.T. Tiemann, P. Avila, G. Ramirez, C.E. Lascano, M. Kreuzer and H.D. Hess. 2008. In vitro ruminal fermentation of tanniniferous tropical plants: Plant-specific tannin effects and counteracting efficiency of PEG. Animal Feed Science and Technology, 146: 222–241.

Country/Organization

Switzerland

Type

Special Issue or TECDOC research & review papers

Year

2011

Description

“Effects of tea saponins on rumen microbiota, rumen fermentation, methane production and growth performance – A review” by J. K. Wang, J.A. Ye and J. X. Liu.

Country/Organization

China

Type

Research paper

Year

2008

Description

Patra, A.K., Kamra, D.N. and Agarwal, N. 2008. Effect of leaf extracts on in vitro rumen fermentation and methanogenesis with rumen liquor of buffalo. Indian J. Anim. Sci. 78: 91-96.

Country/Organization

India

Type

Research paper

Year

2008

Description

C.R. Soliva, A.B. Zeleke, C. Clementa, H.D. Hess, V. Fievez and M. Kreuzer. 2008. In vitro screening of various tropical foliages, seeds, fruits and medicinal plants for low methane and high ammonia generating potentials in the rumen. Animal Feed Science and Technology, 147: 53–71.

Country/Organization

Switzerland

Type

Research paper

Year

2005

Description

Hu W.L., Guo Y.Q., Liu J.X., Wu Y.M., Ye J.A., 2005. Tea saponins affect methanogenesis and fermentation in faunated and defaunated rumen fluid in in vitro RPT system. Journal of Zhejiang University SCI. 6B(8):787-792.

Country/Organization

China

Type

Research paper

Year

2008

Description

Patra A.K., Kamra D.N., Agarwal N., Chatterjee P.N., 2008. Effects of Terminalia belerica and Allium sativum as feed additives on rumen fermentation, enzyme activities and microbial populations in Murrah buffaloes. Indian J. Anim. Nutr. 78 (2008) 91-96

Country/Organization

India

Type

Research paper

Year

2007

Description

Cenci, F.B., Louvandini, H., McManus, C.M., DellPorto, A., Costa, D.M., Araujo, S.C., Minho, A.P., Abdalla, A.L., 2007. Effects of condensed tannin from Acacia mearnsii on sheep infected naturally with gastrointestinal helminthes. Veterinary Parasitology, 144: 132-137.

Country/Organization

Brazil

Type

Research paper

Year

2007

Description

Guo Y.Q., Liu J.X., Zhu W.Y., McSweeney, C. 2007. Shifts of rumen microbial population detected by real-time PCR when methanogens are inhibited. Journal Animal Feed and Science. 16(Suppl.2): 107-112.

Country/Organization

China

Type

Research paper

Year

2006

Description

Hu W.L., Liu J.X., Wu Y.M., Guo Y.Q., Ye J.A. 2006. Effects of tea saponins on in vitro ruminal fermentation and growth performance in growing Boer goat. Archive of Animal Nutrition. 60(1): 89-97.

Country/Organization

China

Type

Research paper

Year

2008

Description

Bueno, I.C.S., Vitti, D.M.S.S., Louvandini, H., Abdalla, A.L., 2008. A new approach for in vitro bioassay to measure tannin biological effects based on a gas production technique. Animal Feed Science and Technology 41: 153 - 170.

Country/Organization

Brazil

Type

Research paper

Year

2005

Description

Guo Y.Q, H.U. WL, Liu J.X., 2005. Methanogens and manipulation of methane production in the rumen. Acta Microbiologica Sinica, 45(1):145-148. (in Chinese with English summary).

Country/Organization

China

Type

Research paper

Year

2008

Description

Minho, A.P., Bueno, I.C.S., Louvandini, H., Jackson, F., Gennari, S.M., Abdalla, A.L., 2008. Effect of Acacia molissima tannin extract on the control of gastrointestinal parasites in sheep. Animal Feed Science and Technology. (2007), doi:10.1016/j.anifeedsci.2007.09.016.

Country/Organization

Brazil

Type

Special Issue or TECDOC research & review papers

Year

2011

Description

“Reducing methane emissions and methanogenic population in Tibetan-sheep by dietary supplementation with coconut oil” by X. Z. Ding, R. J. Long, X. D. Huang, X. S. Guo and J. D. Mi

Country/Organization

China

Type

Special Issue or TECDOC research & review papers

Year

2011

Description

"Methane mitigation from Ruminants using Tannins and Saponins” by G. Goel and H. P.S. Makkar.

Country/Organization

Germany

Type

Research paper

Year

2007

Description

Kumar, R., Kamra, D.N., Agarwal, N. and Chaudhary, L.C. 2007. In vitro methanogenesis and fermentation of feeds containing oil seed cakes with rumen liquor of buffalo. Asian-Aust. J. Anim. Sci. 20: 1196-1200.

Country/Organization

India

Type

Research paper

Year

2006

Description

Chatterjee, P.N., Kamra, D.N. and Agarwal, N. 2006. Effect of roughage source, protein and energy levels on in vitro fermentation and methanogenesis. Indian J. Anim. Nutr. 23: 72-77.

Country/Organization

India

Type

Research paper

Year

2008

Description

T.T. Tiemann, C.E. Lascano, M. Kreuzer and H.D. Hess. 2008. The ruminal degradability of fibre explains part of the low nutritional value and reduced methanogenesis in highly tanniniferous tropical legumes. J. Sci. Food Agric., 88: 1794–1803.

Country/Organization

Switzerland

Type

Research paper

Year

2007

Description

Yuan Z.P., Zhang C.M., Zhou L., Zou C.X., Guo Y.Q., Li W.T., Liu J.X., Wu Y.M. 2007. Inhibition of methanogenesis by tea saponin and tea saponin plus disodium fumarate in sheep. Journal Animal Feed and Science. 16(Suppl.2): 560-565.

Country/Organization

China

Type

Research paper

Year

2010

Description

Patra AK, Kamra DN, Agarwal N. 2010. Effects of extracts of spices on rumen methanogenesis, enzyme activities and fermentation of feeds in vitro. J Sci Food Agric. 2010 Feb;90(3):511-20.

Country/Organization

India

Type

Research paper

Year

2006

Description

Hu W.L., Wang J.K., Guo Y.Q., Lv J.M., Liu J.X. 2006. Rapid gas chromatogram determination of methane, organic acids in in vitro ruminal fermentation products. Journal of Zhejiang University (Agric & Life Sci). 32(2): 217-221 (in Chinese with English summary)

Country/Organization

China

Type

Research paper

Year

2009

Description

A. Z. Bekele, C. Clément, M. Kreuzer and C. R. Soliva. 2009. Efficiency of Sesbania sesban and Acacia angustissima in limiting methanogenesis and increasing ruminally available nitrogen in a tropical grass-based diet depends on accession. Animal Production Science, 49: 145–153.

Country/Organization

Switzerland

Type

Research paper

Year

2008

Description

Kamra, D.N., Patra, A.K., Chatterjee, P.N., Kumar, R., Agarwal, N. Chaudhary, L.C., Effect of plant extracts on methanogenesis and microbial profile of the rumen of buffalo: a brief overview. Aust. J. Experimental Agric. 48 (2008): 175-178

Country/Organization

India

Type

Research paper

Year

2008

Description

T.T. Tiemann, C.E. Lascano, H.R. Wettstein, A.C. Mayer, M. Kreuzer and H.D. Hess. 2008. Effect of the tropical tannin-rich shrub legumes Calliandra calothyrsus and Flemingia macrophylla on methane emission and nitrogen and energy balance in growing lambs. Animal, 2: 790–799.

Country/Organization

Switzerland

Type

Research paper

Year

2005

Description

Kamra, D.N. 2005. Rumen Microbial Ecosystem. Current Science, 89: 124-135.

Country/Organization

India

Type

Research paper

Year

2007

Description

Bueno, I.C.S., Vitti, D.M.S.S., Abdalla, A.L., Louvandini, H., 2007. Consumo voluntário, digestibilidade aparente e cinética digestiva de três forrageiras em ovinos. Ciência Animal Brasileira 8, 713-722.

Country/Organization

Brazil

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