Award details

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

Reference	BB/N016742/1
Principal Investigator / Supervisor	Professor Michael Watson
Co-Investigators / Co-Supervisors
Institution	University of Edinburgh
Department	The Roslin Institute
Funding type	Research
Value (£)	339,898
Status	Completed
Type	Research Grant
Start date	01/12/2016
End date	30/11/2019
Duration	36 months

Abstract

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.

Summary

By 2050, the human population will grow to over 9 billion people, and in the same time frame, global meat production is set to increase by 73%. There is a need to increase the efficiency and sustainability of animal production, reduce waste in the food chain and ensure safe and nutritious diets in order to address this challenge. Rumen microbes confers a unique ability to convert human inedible high-fibre forage into nutrients the animal can absorb to produce high-quality proteins as meat and milk. However, intensive food production puts a strain on the environment, and there is a need to produce more food ethically and in a way that does not harm the environment. The project addresses these challenges by unravelling the functional and genomic architecture of the ruminal microbiome affecting performance traits of cattle. This information will be used to identify fundamental associations between the microbiome or its genes with animal performance traits and methane emissions. In this study we will sequence all microbial genomes - the metagenome - to describe the composition of the microbial community and its functional genes. The analysis will be based on a unique dataset of 288 experimental beef cattle, with rumen DNA samples and a large array of performance information (e.g. feed conversion efficiency, growth, body composition and meat quality) available. These data are structured by breeds and sire progeny groups to estimate the animal host genetic effects on the microbiome and microbial genes. The experimental data have been the basis of numerous publications in which it was shown that at the animal performance level, and for methane emissions, there are large differences between breeds, sire progeny groups and diets. Preliminary analysis for 8 of these animals suggests that there is a link between the abundance of the microbial community or microbial genes and animal performance traits and methane emissions. However, to understand the function and genomic architecture of the ruminal microbiome, analysis of the full sample set is necessary. Algorithms will be developed to predict animal performance, e.g. feed conversion efficiency and methane emissions from the abundance of the microbial community and genes. These high value, but costly-to-measure traits could then be predicted by analysing the rumen microbiome (sampled via stomach tube on live animals or in the abattoir). However, to verify the associations between the rumen microbiome and performance traits, we need basic knowledge about the functional and genomic architecture of the microbiome. Additionally, microbial biomarkers to predict e.g. feed conversion efficiency could be identified. Due to the unique structure of the data in sire progeny groups and diets, we will be able to predict the host genetic and nutritional effect on the microbial community and microbial genes. This structure can also be used in the network analysis to identify animal genetic effects on the functional and genomic architecture of the microbiome. The project will provide unprecedented new knowledge of the genomic and functional architecture of the microbiome and its impact on performance traits and methane emissions as well as the interaction with animal genetics and nutrition. We will compare the functional and genetic architecture of the microbiome in beef cattle with that of other species to provide insights about the microbiome of different species, in particular humans. By understanding host genetic effects on the rumen microbiota and associations with body composition, we expect to provide new insights for human personalised medicine approaches to reduce obesity.

Impact Summary

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.

Committee	Research Committee A (Animal disease, health and welfare)
Research Topics	Animal Welfare, Microbiology
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

Associated awards:

BB/N01720X/1 Understanding the functional and genomic architecture of the rumen microbiome affecting performance traits in bovines

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