Understanding the functional and genomic architecture of the rumen microbiome affecting performance traits in bovines

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Rumen microbial fermentation confers a unique ability to efficiently convert human inedible feed into foods with high nutritional value (e.g. meat, milk). However, there is a disadvantage from the environmental and energetic efficiency point of view, in that microbial fermentation also results in methane production. There is a large variation between animals in feed conversion efficiency and methane emissions, so that the substantial lack of knowledge about the functional and genomic architecture of the rumen microbiome has to be closed to efficiently breed and feed those animals. We will use deep metagenomic sequencing to gain insight into the functional and genomic architecture of the rumen microbiome, identifying the key microbial taxa and genes. Our approach will use highly-phenotyped beef cattle (n=288) to discover and prioritise putative links between the microbiome and phenotypic performance. Host genetic and nutritional effects on the microbiome will be estimated utilising the unique structure of experimental data, including different sire progeny groups and diets. Preliminary analysis suggests a link between the microbiome, phenotypic performance, animal genetics and nutrition, but was not able to provide detailed information about the functional and genomic architecture of the ruminal microbiome affecting performance traits and whether and how these interact with the host animal and nutrition. This study will provide substantial insight into the structure and function of the microbiome and identity novel microbial genes. Based on the abundance of the microbial community and genes, the research will provide novel functional and genetic networks to explain the link between the microbiome, phenotypic performance and host genetics or nutrition (e.g. the cross-talk between host and microbiome). Comparative functional genomics will broaden the potential applications of the research.

The beneficiaries of this research will include academic scientists, farmers, the livestock breeding and feed industries, national governments, climate scientists, environmentalists and the general public. The FAO predicts that by 2050, the human population will grow to over 9 billion people, and in the same time frame, global meat consumption is projected to increase by 73%. In order to address food security, as well as economic and environmental impacts of food production, sustainable intensification has been suggested by Godfray et al. (2010) - with genetic improvement of feed conversion efficiency of highest importance in farm animals. Rumen microbial fermentation confers a unique ability to efficiently convert human inedible feed (e.g. high-fibre forage) into food products, such as meat and milk, of high nutritional value. Performance traits, such as feed efficiency, vary substantially between cattle so that genetic improvement and nutritional intervention could have a substantial effect on the efficiency of using limited feed resources, as well as a major financial impact since feed is the largest variable cost in production. Furthermore, rumen fermentation contributes to greenhouse gas (GHG) emissions, in particular methane. Any marginal reduction in GHG emissions, achieved through genetic improvement, has the potential to contribute significantly to UK Climate Change Act commitments, including the need for an 11% reduction in agricultural emissions by 2020. Using animal breeding and nutritional interventions to alter the rumen microbiome is expected to improve feed efficiency, growth, body composition, meat quality or animal health and thus contribute to address the overall economic and environmental challenges. The academic partners (SRUC and Roslin Institute) have excellent links to the cattle breeding and feed industries, farmers and the entire food chain. They will ensure that any immediate impacts can be passed on, once IP has been suitably protected.
Overall, the research will deliver substantial contributions to fundamental understanding of the functional and genomic architecture of the rumen microbiome in bovines, whilst also offering insights for other ruminant species or monogastric species including humans. In particular, it will provide unprecedented new knowledge about the genomic and functional architecture of the microbiome and its impact on performance traits and methane emissions that will set the direction for animal breeding programmes and novel animal feeding strategies.
Comparative functional genomics will be used to uncover differences and similarities in functional and genetic architecture between species, providing unprecedented knowledge about the microbiome and host-microbiome interactions across species. In particular, we foresee longer-term benefits for research on host genetic effects on the rumen microbiota and its association with body composition (e.g. for human personalised medicine approaches to reduce obesity).
We will realise academic impact by publication of papers in high-impact peer-reviewed journals (open-access where possible), by presentations at scientific meetings and through deposition of datasets in public databases. We will also publish articles in trade journals to ensure that our findings are communicated to our stakeholders. SRUC and RI will present the project at public science events, such as the Roslin Open Doors Day, ensuring the general public are aware of our research and its importance. We will keep policy makers aware of the research findings and our appraisal of potential to help meet climate change targets in the medium- and longer-term. Significant findings will be communicated to the industry and general public through press releases and information on a specific project website hosted by SRUC.