Overview of the challenge and existing work underway
Enteric methane is almost entirely produced by microbial fermentation in the rumen. The mix of microbial species affects the amount of methane released and how well the animal extracts energy and nutrients from feed. The composition of this microbial mix is principally controlled by diet, although the role of an animal’s genetic makeup is now well recognised.
There is increasing evidence that ruminants themselves have evolved to influence rumen fermentation processes and therefore help adapt to different environments. These control mechanisms can influence methane production in livestock and more generally help ruminants for adapt to challenges arising from climate change.
A number of research groups around the world are exploring the rumen microbiome and its production of enteric methane to inform the basis of individual animal variation in the quantity of methane produced and its relationship with productivity traits. However, efforts have been hampered by the lack of a clear protocol for microbial sampling and subsequent DNA extraction and sequencing methods that balance information content and cost. In addition, almost all of the current studies rely on comparisons with existing databases, which are sparsely populated.
A project is already underway to develop a sequencing technology for rapid, low-cost profiling of rumen microbiomes that can be used to predict methane emissions and potentially other production traits in New Zealand and Australian sheep. Current evidence suggests that these profiles are predictors of methane emissions and potentially feed efficiency, and are to some extent also under host genetic control. This existing project aims to develop the low-cost sequencing technology, which would profile the microbiome at a cost of around NZD$60 per freeze-dried rumen sample and an efficiency greater than 50% of the efficiency of the current methods being used. Once successfully developed, the method can be used along with bioinformatics analysis to sequence and characterise microbial samples in sheep genetic improvement programmes.
The main outcome from this existing work is a method that optimises cost and information content. Our approach is that rather than sequence only a single marker gene at one extreme or the entire microbial sequence at the other, we will develop methods that sequence a proportion of each microbial genome. Like sequences will be put into bands or pins, and patterns predictive of methane emissions will be investigated. This approach has the key advantage that it does not rely on sequences matching a known database.
How will this work be extended into a flagship project?
This rapid low cost method could be made available to other GRA countries and, with greater investment, applied to other ruminants e.g. cattle. The aim would be to sequence ~2,000 new samples from a much wider range of countries, production systems and ruminant species. Rumen methane emissions, volatile fatty acid measurements and microbial profiling would be undertaken in dairy and beef systems for native breeds including Bos indicus in Australia, Brazil and Africa as well as breeds associated with intensive production systems such as Angus and Holstein Friesian.
We will also send out an open call for all member countries from the GRA to be involved in the programme. To encourage broad involvement from developing countries we have included in the budget an allowance for the costs of genome sequencing for samples from developing countries where internal resources are not available for this task. Developed countries will be expected to fund their own sequencing and all countries will be expected to provide personnel costs ‘in-kind’.
Methodology development and testing for cattle have been undertaken with samples available from New Zealand (DairyNZ). These preliminary results will be discussed with countries interested in participating in the project, prior to finalisation of the methodology and the finalisation of the programme of work that a post-doctoral scientist would then undertake.
This project will generate a method of profiling the rumen microbiome that does not require expensive infrastructure and that can be used in live animals at any stage of production. Ultimately, use of this method will help with identifying and selecting highly productive animals that emit less methane and are better adapted to climate change. The project will deepen global understanding of how the rumen adapts to different production systems, the effect of this adaptation on rumen outputs and how this affects livestock performance.
How long will it take?
With the additional resourcing indicated below, the flagship project will be completed by 30 June 2020 assuming a start date of 1 January 2018.
What additional resources are needed to ensure success?
The project will build on the existing sheep-focused activities being sponsored by New Zealand (GPLER4) along with a significant in-kind contribution from Australia (Department of primary Industries, New South Wales).
Rumen samples from other ruminants in other production systems measured for methane and for feed intake will be needed, and will come wherever possible as in-kind contributions from participating countries/research programmes.
Funding for initial sequencing will be required for comparison of cattle with the sheep methodology and with existing microbial databases. The project leader will require additional funding in order to coordinate the enhanced project, including supervising a post-doctoral scientist and the costs of that post-doctoral position itself. Costs sought from the New Zealand Government’s GRA budget are outlined in the table over the page.
 E.g. respiration chambers/portable accumulation chambers for methane, and standard feed intake and animal performance recording for production traits