Development and Use of Rumen Molecular Techniques for Predicting and Enhancing productivity


Introduction:

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.

The major limitation to ruminant production in many tropical regions of Africa, Asia and Latin America is poor nutrition. The productivity of animals is restricted by the low nitrogen and high fibre content of the native grasses and crop residues, which form the basis of the diets in these regions. Chemical treatment of fibrous feedstuffs, supplementation of tropical roughages with leguminous fodder trees and shrubs (FTS) and low-cost nitrogenous sources, and use of agricultural by-products are promising methods to alleviate nutrient deficiencies associated with these basal diets. FTS often contain secondary compounds (e.g., tannins, saponins, phenolic glycosides), which can affect discrete populations of microorganisms in the rumen.

A large proportion of the global ruminant population are 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. Animal trials involving agents that specifically inhibit microbial enzymes associated with methane production probably provide the most reliable data for interpretation of the effects of inhibition of methanogenesis on digestive and animal performance parameters. This data indicates that a reduction in methanogenesis in the rumen can be associated with improvements in feed conversion efficiency without affecting intake. Furthermore, any attempt to reduce methane emissions from livestock is unlikely to be adopted unless production efficiency is at least maintained if not enhanced. The challenge therefore is to devise strategies, which reduce methane emissions from ruminants and improve production efficiency.

Rationale:

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 antinutritive 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 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 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).

Quantitative estimates of microbial populations can be performed by amplification of SSU rDNA with specific primers using real time PCR (RT-PCR). Also the more variable sequence regions of the 16S rDNA are hybridisation sites for genus, species and sometimes even strain specific hybridization probes. 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.

These technologies have the potential to revolutionize our understanding of rumen function and will enable us to overcome current limitations in rumen biotechnology, which include isolation and taxonomic identification of strains important to efficient rumen function. The future of rumen microbiology research is dependant upon the adoption of these research technologies. However, the challenge is how we utilize these technologies to improve ruminant production through a better understanding of microbial function and ecology.

The impact of reduced methane production on rumen fermentation has not been clearly elucidated, although it appears that the degree of inhibition of methane production is an important determinant of the associated effects on feed intake, feed digestibility and animal production efficiency. A consequence of inhibiting methanogens is the accumulation of H2 in the rumen that is a major metabolic end product of forage digestion. The management of H2 accumulation in the rumen under these circumstances is a critical factor, which will determine the efficiency of digestion and animal performance. When hydrogen accumulates in the rumen, bacteria shift their fermentation pattern to acetate from more reduced end products such as propionate. The adaptive changes in rumen microbial ecology to inhibition of methanogens is relatively unknown although enhanced propionate production is a consistent response and consequence of disruption to interspecies hydrogen transfer. One strategy to prevent H2 accumulating in the rumen is to provide dietary substrates that are precursors for propionate production by fermentative bacteria. Increase in the efficiency of microbial protein synthesis has also been observed with decrease in methane production.

Overall Objective:

To improve ruminant performance through a reduction in methane production. This CRP will contribute to the Agency’s project on “Use of molecular techniques for improving productivity in small-holder livestock systems” (E2.03).

Specific Research Objectives (purpose):

  • 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.
  • Develop and use molecular probes for quantifying populations of methanogens, fibre degrading bacteria, fungi and protozoa.
  • Correlate methane production to methanogen numbers.
  • Determine effects of reduced methanogen numbers on fibre degrading bacteria, fungi and protozoa.
  • Identify naturally occurring plant secondary compounds that inhibit methanogens.
  • Reduce the level of methane production by up to 40% in animals fed roughage diets.
  • Build in-country capacity to develop and use molecular techniques for studying rumen function.

Expected Research Outputs (Results):

  • Feeding strategies and or supplements that reduce methane production and improve productivity in ruminants on tropical diets.
  • Development and application of molecular techniques for studying rumen microbial ecology and effects of novel feed additives and dietary approaches.
  • Increased capacity of NARS to integrate molecular rumen techniques into research programmes on ruminant nutrition.
  • Improved knowledge of ecology of rumen microorganisms, particularly methanogenic archaea and their interaction with predominant rumen microorganisms.
  • Published and disseminated research results.

Action Plan (Activities):

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Time Schedule:

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Participants:

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Assumptions:

Institutes that are selected for participation in this CRP will have local and/or external support either through funding from other bodies or through agreements with local partners. The project will integrate with on-going research and development activities.

Logical Framework:

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Summary of the Project:

A large proportion of the global ruminant population are 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.

The Overall Objective of this CRP is to improve ruminant performance through a reduction in methane production. It is aimed to: i) 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, ii) build in-country capacity to develop and use molecular techniques for studying rumen function, iii) develop and use molecular probes for quantifying populations of methanogens, fibre degrading bacteria, fungi and protozoa, iv) correlate methane production to methanogen numbers, v) determine effects of reduced methanogen numbers on fibre degrading bacteria, fungi and protozoa, and vi) reduce the level of methane production by up to 40% in animals fed roughage diets. 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.

Planning Meeting and Training Workshop:

  • Planning Meeting and Training Workshop 19-21 April 2004
    - Summary [Download pdf]
    - Programme [Download pdf]
    - Participants [Download pdf]
  • First RCM from 12 to 16 September 2005 in Zürich, Switzerland
    - Summary [Download pdf]
    - Programme [Download pdf]
    - Participants [Download pdf]
  • Workshop on Development and use of rumen molecular techniques for predicting and enhancing productivity through a reduction in rumen methane from 26 September to 7 October 2005 in Zürich, Switzerland
    - Summary [Download pdf]

Project Officer:

E. Odongo