Award details

Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria

Reference	BB/S006567/1
Principal Investigator / Supervisor	Professor Rainer Roehe
Co-Investigators / Co-Supervisors	Dr Marc Auffret, Professor Richard Dewhurst
Institution	SRUC
Department	Research
Funding type	Research
Value (£)	390,943
Status	Completed
Type	Research Grant
Start date	01/05/2019
End date	31/10/2022
Duration	42 months

Abstract

Rumen microbial fermentation confers a unique ability to convert human inedible feed into foods with high nutritional value (e.g. meat, milk), but produces the Greenhouse Gas methane. The overall aim is to unravel the host genetic control of its rumen microbiome (here identified as rumen microbial gene abundances (RMGA)) affecting feed conversion efficiency (FCE) and methane emissions. This will rectify the major knowledge gap about these complex interactions, as well as providing the basis to develop selection criteria and breeding strategies for improvement of FCE and mitigation of methane emissions. Our industrial partner Genus plc has a large, well-structured, genotyped, phenotyped and rumen sampled cattle population to be used as data source to estimate these complex interactions. To determine RMGA in a cost effective way, we will develop a functional microbial gene microarray (FMGM). The FMGM will include genes associated with FCE and methane emissions based on results from the whole metagenomic sequencing work.. Probes specific to ruminant Proteobacteria, Firmicutes, and Bacteroidetes will be included on the FMGM to use their ratio as biomarker for rumen dysbiosis and health. The host genomic effect on the microbiome-phenotype interactions will be estimated using REML and Bayesian analysis. The microbiome-phenotype interactions will be identified using network, partial least squares and random forest regression analyses. Functional pathway analysis will be applied to identify the functional causes of the interactions among RMGA. These functional analyses will give insight into the 'cross-talk' between the rumen microbiome and host. All findings from the analyses of the host genome-microbiome-phenotype interactions will be combined to develop novel selection criteria to breed animals based on RMGA associated with FCE and methane emissions without the need for very costly trait measurements.

Summary

The Food and Agriculture Organisation of the United Nations has predicted an increase in global meat and milk demand of 76% and 63% by 2050 due to increasing income and growing world population. This will require improved sustainable systems for livestock production. The large fore-gut of cattle, the rumen, contains billions of microbes (the microbiome) per gram of digesta (which is the substance as food undergoes digestion). These microbes ferment human inedible food (e.g. grass) into nutrients the host animal converts into high quality products such as meat and milk. This rumen microbial eco-system is essential for the animal but has one disadvantage for the environment because some microbes produce the potent greenhouse gas methane. This project will address these challenges by using rumen microbial information as animal breeding criteria for improvement of feed conversion efficiency with simultaneous mitigation of methane emissions. In this research we will estimate the extent of the link between animal genome and its rumen microbiome and investigate the causes for their link using a large breeding population. This population is provided by our commercial partner Genus plc and is well structured to ensure accurate estimation of host genetic effects on the microbiome. Our previous research showed that rumen microbial gene abundances are closely related to feed conversion efficiency and methane emissions. However, how and to what extent the host animal genome affects the abundances of microbial genes is unknown and will be investigated within this project. Because the metabolic functions of these microbial genes are mostly known, we expect to identify many novel genetic links between the host animal and specific rumen microbial functions that may even be conserved across species. Networks and functional pathways of rumen microbial genes linked to the animal genome will provide a new level of understanding of the symbiosis between microbiome and host animal. We areexpecting to identify pathways of microbial genes, e.g. to provide insight into the "cross-talk" between the rumen microbes and the host animal, being a route by which the host genome controls its own rumen microbiome. Based on these findings, optimised selection criteria and strategies to improve feed conversion ratio and mitigate methane emissions will be developed. In addition, we will use biomarkers to control that there are no adverse effects of selection using microbial genes on rumen health with potential consequences for animal health and welfare. Our large commercial partner will ensure that the outcomes of the project can be immediately implemented in the routine breeding activities and thus contribute to address the challenges of food security and environmental impact of animal production. This project is expected to provide an enormous increase in fundamental knowledge of the links between host animal genome and the rumen microbiome, which may be also relevant in other species including humans, and at the same time will develop methods and strategies to use this new knowledge for practical application in animal breeding.

Impact Summary

The FAO has predicted the need for a 70% increase in agricultural output by 2050 in order to feed the world's population, which is likely to exceed 9 billion. Sustainable systems of livestock production are needed to address this challenge, and these must not compete with humans for food. Performance traits, such as feed conversion efficiency (FCE), vary substantially between cattle so that genetic improvement could have a substantial impact on the efficiency of using limited feed resources, as well as having a major financial impact - since feed is the largest variable cost of production. Rumen microbial fermentation confers on ruminants a unique ability to efficiently convert human inedible food (e.g. high-fibre forage) into products such as meat and milk of high nutritional value. However, rumen fermentation also contributes to greenhouse gas (GHG) emissions, in particular methane resulting in the high carbon footprint of beef. Any marginal reduction in GHG emissions, achieved through genetic improvement and dietary intervention, has the potential to contribute significantly to fulfil the UK commitments to limit GHG emissions within the Paris Agreement on climate change. We expect to discover the host genomic influence on complex networks of rumen microbial genes affecting FCE and methane emissions. This knowledge will be used to develop unique selection criteria and strategies to improve these traits. The beneficiaries of this research will include governments and devolved administrations, other policy-makers, climate scientists, environmentalists and the general public by providing a unique animal breeding strategy contributing to address global challenges of food security and reducing the effects of agriculture on climate change. Academic impact will be achieved mainly by identifying the host genetic influence on the complex microbiome network and its association with performance traits. We will provide unprecedented new knowledge about the host genomic control of the rumen microbiome and its impact on performance traits and methane. Because most of the functions of the microbial genes are known, this will also provide novel insight into host genetic effects on rumen microbial functions. Business Impact is shown by the involvement of our industry partner Genus plc, the largest breeding company in the world. This will ensure that outcomes of the research project can be immediately implemented in routine breeding activities. Through artificial insemination the progress in traits like FCE and mitigation of methane emissions can therefore be rapidly disseminated worldwide. We will develop a functional microbial gene microarray (FMGM) comprising of rumen microbial genes shown to be highly significantly associated with FCE and methane emissions. This will be developed together with the biotechnology industry and they are indicating high interest. The finding of the research will have impact improving the sustainability of farming, and through findings that can be adopted by the animal feed and animal health industries. 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 data in public databases. We will also publish articles in trade journals to ensure that our findings are communicated to our stakeholders. SRUC and the Roslin Institute will present the project at public science events, such as Open Days, 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 the website hosted by SRUC and the Roslin Institute.

Committee	Research Committee A (Animal disease, health and welfare)
Research Topics	Animal Health, Animal Welfare, Microbiology
Research Priority	X – Research Priority information not available
Research Initiative	LINK: Responsive Mode [2010-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

Associated awards:

BB/S006680/1 Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria

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