Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria
Lead Research Organisation:
Scotland's Rural College
Department Name: Research
Abstract
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 are expecting 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.
Technical Summary
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.
Planned Impact
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.
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.
Organisations
Publications
Auffret MD
(2020)
Identification of Microbial Genetic Capacities and Potential Mechanisms Within the Rumen Microbiome Explaining Differences in Beef Cattle Feed Efficiency.
in Frontiers in microbiology
Lima J
(2019)
Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle.
in Frontiers in genetics
Lima J
(2023)
Estimating Microbial Protein Synthesis in the Rumen-Can 'Omics' Methods Provide New Insights into a Long-Standing Question?
in Veterinary sciences
Lima J
(2024)
Temporal stability of the rumen microbiome and its longitudinal associations with performance traits in beef cattle.
in Scientific reports
Lima J
(2021)
Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.
in Journal of microbiological methods
Martínez-Álvaro M
(2024)
Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.
in Genetics, selection, evolution : GSE
Martínez-Álvaro M
(2022)
Bovine host genome acts on rumen microbiome function linked to methane emissions.
in Communications biology
Martínez-Álvaro M
(2020)
Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine.
in Frontiers in microbiology
| Description | Key findings associated with this award are as follows: I) Our research highlights that improvement of specific metabolisms, associated with essential microbial conversion of human inedible feed like grass by the ruminal microbiome (bacteria, protozoa, fungi, and their genes), will reduce methane emissions from cattle. These specific microbial metabolisms are reflected by the composition of the rumen microbiome which we revealed to be linked to the host cattle genome. In particular, the abundances of rumen microbial genes are highly informative to predict methane emissions. Of the abundances of 1,141 rumen microbial genes, 369 were heritable and some of these were significantly host genomically correlated to methane emissions. Because the biological functions of these microbial genes are known, interesting ruminal biological processes associated with low methane emitting cattle could be revealed. For example, high abundances of microbial genes diverting substrates necessary for methane metabolism to produce the amino acid arginine were negatively host genomically correlated (rgCH4 = -0.74 and -0.93) with methane emissions. Therefore, the composition of the rumen microbiome sampled from animals can be used to breed low methane emitting cattle without its extremely costly measurement. When this rumen microbiome-driven breeding for methane mitigation is intensively used in a cattle population we predicted based on data from our beef experiments, a reduction in methane emissions of up to 8% per year or cumulatively of up to 50% within 10 years. This microbiome-driven breeding can also be used to simultaneously improve the efficiency of animals to convert grass into meat which reduces the carbon footprint of beef and increases the profitability of its production. Our research also suggests that microbiome-driven breeding and dietary intervention are additive mitigation strategies and therefore can be efficiently combined to reduce methane emissions from cattle (Martinez-Alvaro et al., 2022a) II) In network and partial least squares analyses of the rumen microbiome, we found that one out the ten main clusters included mainly methane producing Archaea but also microbial genes involved in complex carbohydrate degradation, metabolism of sugars and amino acids and Candidatus Azobacteroides carrying nitrogen fixation genes (Martinez-Alvaro et al., 2020b). This cluster explained the highest amount of variation in methane emissions (57%) and was therefore referred to as "methanogenesis cluster". In a different network, fungi and protists were clustering together and another plant fibre degrader Fibrobacter occupied a separate cluster. Rumen microbial genes negatively related to methane emissions were involved in carbohydrate degradation via lactate and succinate and synthesis of more complex amino acids by ?-Proteobacteria. Generally, our results suggest that differences in methane production between low- and high-methane emitters in the rumen are mainly explained by other microbial communities than methanogens. The results highlight the potential of using rumen microbial genes and communities to predict this difficult and costly to measure trait methane emissions and provide therefore an excellent basis for the development of the functional microbial microarray within this project and to be used cost-effectively for breeding purposes to reduce methane. III) Our previous study revealed that there is close phenotypic link between rumen microbial gene abundances and feed conversion ratio and its components daily feed intake and average daily gain. In the current project, we found that the microbial genes, identified by Lima et al. (2019) to be associated with FCR, ADG and DMI, are heritable in the range between 9% and 44% (Martinez-Alvaro et al., 2020c). Especially, microbial genes associated with glycine and carbohydrate metabolisms were highly heritable. Our results indicate that the animal genome shapes the microbial gene abundances in the rumen, which are associated with feed efficiency traits. These findings provide new opportunities to integrate microbiome information into breeding programmes targeting feed efficiency in cattle. Using microbial gene abundances as cost-effective selection criteria for feed conversion efficiency will enable breeding for this trait on the national level. IV) We identified that cattle with higher abundance of Eubacterium in the rumen had higher feed efficiency whereas those with higher abundances of Proteobacteria and Spirochaetales (including potentially pathogenic species) showed lower feed efficiency. Based on this study we were able to identify the microbial mechanisms associated with feed efficiency related to energy providing, pathogenicity and immune response (Auffret et al., 2020). V) We revealed that the ruminal microbial composition had also an impact on the milk fatty acid profile and identified rumen metabolic activities in relation to adaptation to reduced rumen pH, carbohydrate fermentation and protein synthesis as causes (Stergiadis et al., 2021). VI) A further advantage of using the rumen microbiome as proxy information for breeding is its stability over time as reported in our longitudinal study of rumen microbiota. After adaptions to the diet, no significant variability in microbial community was detected (Snelling et al., 2019). VII) We identified the features of the bioinformatic pipelines MG-RAST and QIIME2 (Lima et al., 2021) and developed bioinformatic frameworks to analyse microbiome data using a knowledge-driven network-based analytical framework (Wang et al., 2020) and a heat diffusion multilayer network approach (Wang et al., 2021). VIII) We identified that the composition of the rumen microbiome can be used to genetically improve Omega 3 fatty acids in meat known to benefit human health (Martínez-Álvaro 2022b). Auffret, M.D., Stewart, R.D., Dewhurst, R.J., Duthie, C.-A., Watson, M., Roehe, R., 2020. Identification of microbial genetic capacities and potential mechanisms within the rumen microbiome explaining differences in beef cattle feed efficiency. Front. Microbiol. 11, 1229. Bowen, J.M., Cormican, P., Lister, S.J., McCabe, M.S., Duthie, C.-A., Roehe, R., Dewhurst, R.J., 2020. Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation. PLoS One 15, e0231759. Lima, J., Auffret, M.D., Stewart, R.D., Dewhurst, R.J., Duthie, C.-A., Snelling, T.J., Walker, A.W., Freeman, T.C., Watson, M., Roehe, R., 2019. Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle. Frontiers in Genetics 10, 701, 1-18. Lima, J., Manning, T., Rutherford, K.M., Baima, E.T., Dewhurst, R.J., Walsh, P., Roehe, R., 2021. Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions. J. Microbiol. Methods 186, 106235. Martinez-Alvaro, M., Auffret, M.D., Stewart, R.D., Lima, J., Dewhurst, R.J., Duthie, C-A., Cleveland, M.A., Watson, M., Roehe, R. (2020a). Ruminal microbial gene abundances as a selection criterion to mitigate methane emissions in beef cattle.71st Annual Meeting of the European Association of Animal Production, Porto, Portugal. Martinez-Alvaro, M., Auffret, M.D., Stewart, R., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., Wallace, R.J., Shih, B., Freeman, T.C., Watson, M., Roehe, R. 2020. Identification of complex rumen microbiome interaction within diverse functional niches as mechanisms affecting the variation of methane emissions in bovine. Frontiers in Microbiology11:659. Martínez-Álvaro, M., Auffret, M., Duthie, C., Dewhurst, R., Cleveland, M., Watson, M., Roehe, R., 2021. Bovine host genome acts on specific metabolism , communication and genetic processes of rumen microbes host-genomically linked to methane emissions, Research Square. https://doi.org/https://doi.org/10.21203/rs.3.rs-290150/v1 Martinez-Alvaro, M., Auffret, M.D., Stewart, R.D., Lima, J., Dewhurst, R.J., Duthie, C-A., Cleveland, M.A., Watson, M., Roehe, R. 2020. Host genetics affects the rumen microbial gene abundances explaining feed efficiency traits in beef cattle. In: Proceedings of the British Society of Animal Science (BSAS), Nottingham, UK. Martinez-Alvaro, M., Auffret, M.D., Duthie, C-A., Dewhurst, R.J., Zetouni, L., Cleveland, M.A., Watson, M., Roehe, R. (2021). Host genomics affects the abundances of several uncultured Methanobrevibacter species genomically associated with methane emissions in beef cattle. In: Proceedings of the British Society of Animal Science (BSAS), UK. Martinez-Alvaro, M., Duthie, C-A., Mattock, J., Dewhurst, R.J., Cleveland, M.A., Watson, M., Roehe, R. (2021). Bovine genomes influenced ruminal microbiome composition related to conjugated linoleic acid in beef. 72nd Annual Meeting of the European Association of Animal Production, Davos, Switzerland. Miller, G.A., Auffret, M.D., Roehe, R., Nisbet, H., Martinez-Alvaro, M. (2021). Predicting enteric methane production from the rumen microbial composition of beef steers fed either a high concentrate or cut grass diet. In: Proceedings of the British Society of Animal Science (BSAS), UK. Snelling, T.J., Auffret, M.D., Duthie, C., Stewart, R.D., Watson, M., Dewhurst, R.J., Roehe, R., Walker, A.W., 2019. Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements. Animal Microbiome 1:16. Stergiadis, S., Cabeza-Luna, I., Mora-Ortiz, M., Stewart, R.D., Dewhurst, R.J., Humphries, D.J., Watson, M., Roehe, R., Auffret, M.D., 2021. Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches. Front. Microbiol. 11. 590441. Wang, M., Wang, H., Zheng, H., Dewhurst, R., Roehe, R., 2020. A knowledge-driven network-based analytical framework for the identification of rumen metabolites. IEEE Transactions on NanoBioscience 19, 518-526. Wang, M., Wang, H., Zheng, H., Dewhurst, R.J., Roehe, R., 2021. A heat diffusion multilayer network approach for the identification of functional biomarkers in rumen methane emissions. Methods 192, 57-66. Martínez-Álvaro, M., Auffret, M.D., Duthie, C.-A., Dewhurst, R.J., Cleveland, M.A., Watson, M., Roehe, R., 2022a. Bovine host genome acts on rumen microbiome function linked to methane emissions. Communications. Biology. 5, 350. Martínez-Álvaro, M., Mattock, J., Auffret, M.D., Weng, Z., Duthie, C.-A., Dewhurst, R.J., Cleveland, M.A., Watson, M., Roehe, R., 2022b. Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions. Microbiome. 10, 166. Roehe, R (2022). Microbiome-driven breeding to reduce methane emissions from beef cattle. In: Proceedings of the British Society of Animal Science (BSAS), Nottingham, UK. Roehe, R., Martinez-Alvaro, M., Mattock, J., Weng, Z., Dewhurst, R.J., Cleveland, M.A., Watson, M., (2022). A novel microbiome-driven breeding strategy for feed intake and mitigation of methane emissions. 73rd Annual Meeting of the European Association of Animal Production, Porto, Portugal. |
| Exploitation Route | The findings will be primarily used in animal breeding together with our collaborator the breeding company Genus plc. However, the research is expected to be the blueprint for other breeding organization to mitigation methane emissions from cattle and improve their feed conversion efficiency, meat fatty acid profiles and animal health. In addition, the research provides cutting edge information about the interactions between rumen microbiome and host animal which can be used for dietary intervention, probiotics, prebiotics and drug development to improve animal performance and health. In addition, the outcomes are used by other researcher for further research. |
| Sectors | Agriculture Food and Drink Communities and Social Services/Policy Environment Manufacturing including Industrial Biotechology Retail |
| URL | https://scholar.google.co.uk/citations?user=iYPE0ZwAAAAJ&hl=en |
| Description | I) 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. The identified biomarkers for methane emissions are useful as selection criteria to breed animals emitting less methane. They could also be applied by the feed industry to develop feed additives to mitigate methane emissions from cattle. We are in process to implement microbiome-driven breeding into a practical breeding program because our findings of the high potential to mitigate methane emissions using this strategy (depending on selection pressure and generation interval up 8% reduction of methane emissions per year). Novel breeding strategies using microbiome-driven breeding for mitigation of methane emissions without compromising animal growth and feed conversion efficiency have been developed and will enhance the sustainability of beef production. II) Cattle and other food-producing ruminants are of vital importance for human food security. To address food security, as well as economic and environmental impacts of food production, sustainable intensification has been suggested - with genetic improvement of feed conversion efficiency of highest importance in farm animals. Our research provides novel rumen microbial selection criteria to cost-effectively select animal for improved feed conversion efficiency which substantially can reduce cost of production of animals, improve to use of limited feed resources and mitigate methane emissions per kg product (meat or milk). III) Our research paves the way for the industry to understand which types of microbes - such as bacteria - are best at helping cattle to extract energy and nutrients from their food. The novel information can be used to improve feed conversion efficiency of cattle by breeding and dietary intervention. IV) Our studies also identified enzymes that are specialised for breaking down plant material, which could help in the quest to develop new biofuels. Most of the microbes and microbial enzymes uncovered have never been sequenced before and may have potential uses in the biotechnology industries. V) A further finding of our research is that the rumen microbial community and its activity affected the milk fatty acid profile with potential use to increase omega-3 fatty acids which are associated with a healthy human diet. Similarly, our finding that conjugated linoleic fatty acid in beef can be improved by microbiome-driven breeding provides the opportunity to improve the healthiness of human beef diets. VI) Furthermore, a change in rumen microbial community and its activity were related to animal health and therefore can be used as a biomarker to improve the healthiness of animals. VII) We informed the industry and general public by press releases of our findings published in high-impact peer-reviewed journals (open-access), by presentations at meetings and through deposition of datasets in public databases. We published articles in trade journals to ensure that our findings are communicated to our stakeholders. SRUC presented the project at public events, such as the Beef Open Doors Day, ensuring the public and farmers are aware of our research and its importance. We 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 have been communicated to the industry and public through press releases and information on a specific project website hosted by SRUC. Auffret, M.D., Stewart, R.D., Dewhurst, R.J., Duthie, C.-A., Watson, M., Roehe, R., 2020. Identification of microbial genetic capacities and potential mechanisms within the rumen microbiome explaining differences in beef cattle feed efficiency. Front. Microbiol. 11, 1229. Bowen, J.M., Cormican, P., Lister, S.J., McCabe, M.S., Duthie, C.-A., Roehe, R., Dewhurst, R.J., 2020. Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation. PLoS One 15, e0231759. Lima, J., Auffret, M.D., Stewart, R.D., Dewhurst, R.J., Duthie, C.-A., Snelling, T.J., Walker, A.W., Freeman, T.C., Watson, M., Roehe, R., 2019. Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle. Frontiers in Genetics 10, 701, 1-18. Lima, J., Manning, T., Rutherford, K.M., Baima, E.T., Dewhurst, R.J., Walsh, P., Roehe, R., 2021. Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions. J. Microbiol. Methods 186, 106235. Martinez-Alvaro, M., Auffret, M.D., Stewart, R.D., Lima, J., Dewhurst, R.J., Duthie, C-A., Cleveland, M.A., Watson, M., Roehe, R. (2020a). Ruminal microbial gene abundances as a selection criterion to mitigate methane emissions in beef cattle.71st Annual Meeting of the European Association of Animal Production, Porto, Portugal. Martinez-Alvaro, M., Auffret, M.D., Stewart, R., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., Wallace, R.J., Shih, B., Freeman, T.C., Watson, M., Roehe, R. 2020. Identification of complex rumen microbiome interaction within diverse functional niches as mechanisms affecting the variation of methane emissions in bovine. Frontiers in Microbiology11:659. Martinez-Alvaro, M., Auffret, M.D., Stewart, R.D., Lima, J., Dewhurst, R.J., Duthie, C-A., Cleveland, M.A., Watson, M., Roehe, R. 2020. Host genetics affects the rumen microbial gene abundances explaining feed efficiency traits in beef cattle. In: Proceedings of the British Society of Animal Science (BSAS), Nottingham, UK. Martinez-Alvaro, M., Auffret, M.D., Duthie, C-A., Dewhurst, R.J., Zetouni, L., Cleveland, M.A., Watson, M., Roehe, R. (2021). Host genomics affects the abundances of several uncultured Methanobrevibacter species genomically associated with methane emissions in beef cattle. In: Proceedings of the British Society of Animal Science (BSAS), UK. Martinez-Alvaro, M., Duthie, C-A., Mattock, J., Dewhurst, R.J., Cleveland, M.A., Watson, M., Roehe, R. (2021). Bovine genomes influenced ruminal microbiome composition related to conjugated linoleic acid in beef. 72nd Annual Meeting of the European Association of Animal Production, Davos, Switzerland. Miller, G.A., Auffret, M.D., Roehe, R., Nisbet, H., Martinez-Alvaro, M. (2021). Predicting enteric methane production from the rumen microbial composition of beef steers fed either a high concentrate or cut grass diet. In: Proceedings of the British Society of Animal Science (BSAS), UK. Snelling, T.J., Auffret, M.D., Duthie, C., Stewart, R.D., Watson, M., Dewhurst, R.J., Roehe, R., Walker, A.W., 2019. Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements. Animal Microbiome 1:16. Stergiadis, S., Cabeza-Luna, I., Mora-Ortiz, M., Stewart, R.D., Dewhurst, R.J., Humphries, D.J., Watson, M., Roehe, R., Auffret, M.D., 2021. Unravelling the Role of Rumen Microbial Communities, Genes, and Activities on Milk Fatty Acid Profile Using a Combination of Omics Approaches. Front. Microbiol. 11. 590441. Wang, M., Wang, H., Zheng, H., Dewhurst, R., Roehe, R., 2020. A knowledge-driven network-based analytical framework for the identification of rumen metabolites. IEEE Transactions on NanoBioscience 19, 518-526. Wang, M., Wang, H., Zheng, H., Dewhurst, R.J., Roehe, R., 2021. A heat diffusion multilayer network approach for the identification of functional biomarkers in rumen methane emissions. Methods 192, 57-66. Martínez-Álvaro, M., Auffret, M.D., Duthie, C.-A., Dewhurst, R.J., Cleveland, M.A., Watson, M., Roehe, R., 2022. Bovine host genome acts on rumen microbiome function linked to methane emissions. Communications. Biology. 5, 350. Martínez-Álvaro, M., Mattock, J., Auffret, M.D., Weng, Z., Duthie, C.-A., Dewhurst, R.J., Cleveland, M.A., Watson, M., Roehe, R., 2022. Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions. Microbiome. 10, 166. Roehe, R (2022). Microbiome-driven breeding to reduce methane emissions from beef cattle. In: Proceedings of the British Society of Animal Science (BSAS), Nottingham, UK. Roehe, R., Martinez-Alvaro, M., Mattock, J., Weng, Z., Dewhurst, R.J., Cleveland, M.A., Watson, M., (2022). A novel microbiome-driven breeding strategy for feed intake and mitigation of methane emissions. 73rd Annual Meeting of the European Association of Animal Production, Porto, Portugal. Roehe, R. (2023). Climate smart efficient cattle through rumen microbiome-driven breeding. In: Proceeding of the 75th Anniversary Conference of British Cattle Breeders Club, UK. Nguyen, T., Martínez-Álvaro, M., Lima, J., Gorjanc, G., Cleveland, M., Roehe, R. (2024). Informativeness of interactions between abundances of Methanobrevibacter and microbial genes for microbiome-driven breeding to reduce methane emissions in beef cattle. In: Proceedings of the British Society of Animal Science (BSAS), Belfast, UK. Roehe, R., Nguyen, T.Q., Auffret, M.D., M., Lima, J., Mattock, J., Watson, M., Dewhurst, R.J., Cleveland, M.A., Martínez-Álvaro, M. (2024). Cattle genetics influences the abundance of ruminal pathogenic microbes. 75th Annual Meeting of the European Association of Animal Production, Florence, Italy. Aho, V.T.E., Kobel, C.M., Leu, A., de León, A.V.P., Øyås, O., Lai, W., Altshuler, I., Hagen, L.H., Wollenberg, R.D., Bakshani, C.R., Willats, W.G.T., Nicoll, L., McIlroy, S.J., Hvidsten, T.R., Greening, C., Tyson, G.W., Roehe R., Pope P.B. (2025). Rumen holo-omics reveals microbial community profiles across domains of life. 6th International Metaproteomics Symposium, Oslo, Norway. |
| First Year Of Impact | 2021 |
| Sector | Agriculture, Food and Drink,Energy,Environment,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Retail |
| Impact Types | Societal Economic Policy & public services |
| Description | Reducing emissions from agriculture - the role of new farm technologies |
| Geographic Reach | National |
| Policy Influence Type | Citation in other policy documents |
| Impact | Using genomic selection within the microbiome-driven breeding strategy, Martinez-Alvaro et al., (2022) predicted based on methane emissions of beef cattle recorded in respiration chambers of the SRUC Beef Research Centre a reduction of up to 17% per generation depending on the intensity of selection and breeding only for reduction in methane emissions. Considering that in a breeding programme using genomic selection, a generation interval of 2.25 years can be achieved, the genetic gain per generation would be equivalent to an up to 8% reduction in methane emissions per year or cumulatively up to 50% in 10 years. |
| URL | https://www.gov.scot/publications/reducing-emissions-agriculture-role-new-farm-technologies/pages/7/ |
| Description | Climate Smart Beef Genetics - Innovative approaches to the reduce environmental impact of the UK beef supply chain |
| Amount | £2,088,660 (GBP) |
| Funding ID | 10045515 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2027 |
| Description | Development of an integrated metagenomic analysis system using the microbial community, their genes and biological mechanisms to predict cattle phenotypes |
| Amount | £79,112 (GBP) |
| Funding ID | 1032304 |
| Organisation | Scotland's Rural College |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 01/2018 |
| End | 09/2022 |
| Description | Precision breeding for piglet survival and the use of microbiome information to improve wellness in pigs. |
| Amount | £74,680 (GBP) |
| Organisation | Government of Vietnam |
| Sector | Public |
| Country | Viet Nam |
| Start | 07/2017 |
| End | 01/2021 |
| Description | SRUC and EU PhD studentship |
| Amount | £73,512 (GBP) |
| Organisation | Scotland's Rural College |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 03/2021 |
| Description | Sustainable production of animals by optimizing the feed-microbiome-host axis |
| Amount | 9,992,000 kr. (DKK) |
| Funding ID | 0054575 |
| Organisation | Novo Nordisk Foundation |
| Sector | Charity/Non Profit |
| Country | Denmark |
| Start | 01/2020 |
| End | 12/2024 |
| Description | UltraGreenCow: Comprehensive greenhouse gas and ammonia emissions measurement capacity for large ruminant production |
| Amount | £696,056 (GBP) |
| Funding ID | BB/Z515814/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2024 |
| End | 07/2025 |
| Description | Understanding microbiomes of the ruminant holobiont |
| Amount | € 972,476,375 (EUR) |
| Funding ID | 101000213 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 09/2021 |
| End | 09/2026 |
| Title | Additional file 2 of Microbiome-driven breeding strategy potentially improves beef fatty acid profile benefiting human health and reduces methane emissions |
| Description | Additional file 2: Table S1. Microbial gene abundances in rumen microbiome (analyzed after an additive log-ratio transformation) with significant host genomic effects referred to as host-specific functional core microbiome (HGFC). Table S2. Occupancy rates and heritabilities of micobial gene abundances (analyzed after an additive log-ratio transformation) involved in lipolysis and biohydrogenation processes in rumen found in our population. Table S3. Host genomic correlations between heritable additive log-ratio transformed microbial gene abundances and N3 and CLA Indices in beef with propbability of being positive of negative >95% (marked in bold). Table S4. The 963 different microbial genera in rumen carrying the 372 heritable additive log-ratio transformed microbial gene abundances both positively or negatively genomically correlated with N3 and CLA inidces in beef. Table S5. Composition of clusters from a co-abundance network analysis1 among phenotypic values (after correction for trial and diet) of the 110 additive log-ratio transformed microbial gene abundances genomically correlated with N3 and CLA indices with the same sign. Table S6. Composition of clusters from a co-abundance network analysis1 among estimated genomic breeding values of the 110 additive log-ratio transformed microbial gene abundances genomically correlated with N3 and CLA indices with the same sign. Table S7. Micorbial genes selected for breeding purpouses based on mean relative abundance (RA)>0.01%, significant genomic effects, host genomic correlation with N3 and CLA indices positively or negatively (P0 > 0.95) and significantly explaining part of the genomic variance inherent in the 110 additive-log transformed microbial genes. Table S8. Host genomic correlations between additive log-ratio transformed micorbial genes selected for breeding purpouses and methane emissions (g/kg dry matter intake). Table S9. Experimental design displaying the number of animals within each breed, diet and experiment. Table S10. Raw fatty acid composition (% of total fatty acids) and methane emissions (g/kg of dry matter intake) in beef cattle measured in 245 and 285 animals, respectively. Table S11. Correspondance between COG abreviations and full names. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_Microbiome-driven_breeding... |
| Title | European Nucleotide Archive Project: PRJEB31266 |
| Description | Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach adapted to the breakdown of plant-derived complex polysaccharides, and collectively the rumen microbiota encode the thousands of enzymes responsible. Here we present a comprehensive analysis of over 6.5 terabytes of Illumina and Nanopore sequence data, including assembly of 4941 metagenome-assembled genomes, and several single-contig, whole-chromosome assemblies of novel rumen bacteria. We also present the largest dataset of predicted proteins from the rumen, and provide rich annotation against public datasets. Together these data will form an essential part of future studies of rumen microbiome structure and function. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Ruminants provide essential nutrition for billions of people worldwide. The rumen is a specialized stomach adapted to the breakdown of plant-derived complex polysaccharides, and collectively the rumen microbiota encode the thousands of enzymes responsible. Here we present a comprehensive analysis of over 6.5 terabytes of Illumina and Nanopore sequence data, including assembly of 4941 metagenome-assembled genomes, and several single-contig, whole-chromosome assemblies of novel rumen bacteria. We also present the largest dataset of predicted proteins from the rumen, and provide rich annotation against public datasets. Together these data will form an essential part of future studies of rumen microbiome structure and function. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB31266 |
| Description | Climate Smart Beef Genetics - Innovative approaches to the reduce environmental impact of the UK beef supply chain |
| Organisation | Genus plc |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | This Climate Smart Beef Genetics project focuses on the practical validation of a ground-breaking new tool to breed for low methane emitting beef cattle with improved feed efficiency. The new tool referred to as ruminal microbiome-driven breeding has been developed recently in a BBSRC LINK project with Genus and was predicted to mitigate methane emissions of up to 17% per generation (Martinez-Alvaro et al., 2022). Furthermore, it was demonstrated to improve feed conversion ratio with a potential of up to 15% per generation. Due to the high population-wide impact of breeding and the case that Genus ABS is influencing approximately 45% of the beef x dairy calves' production, the use of microbiome-driven breeding is expected to substantially move the beef sector toward net zero with simultaneous improvement of farming productivity, environmental sustainability and resilience. Because the potential of microbiome-driven breeding has been predicted based on data of the SRUC populations, it has not been tested in in real breeding which will be one main aim of this project. The second main aim of the project is to demonstrate the mitigation of GHGs by a novel genetic improvement program with inclusion of microbiome-driven breeding. Within those main aims, the specific objectives we want to address are as follows: 1. Demonstration of mitigation of GHGs by a novel genetic improvement program. 2. To identify the most effective emission trait (methane production, methane/kg DMI, methane/kg carcass weight gain, residual methane emissions) to be used for genetic mitigation of methane using microbiome-driven breeding. 3. Optimization of rumen microbial genes used in microbiome-driven breeding to maximize mitigation of methane emissions across breeds. 4. Improvement of microbiome-driven breeding for methane mitigation by additionally including microbial community information in particular strains identified by metagenome-assembled microbial genomes (MAGs). 5. Demonstration of the potential additive effect using microbiome-driven breeding on mitigation of GHG emissions over and above those potentially achieved within this project developed novel genetic improvement program. 6. Validation of genetic improvement of reducing methane emissions by testing progeny of sires divergently selected for methane emissions based on breeding values estimated using microbiome-driven breeding. 7. Determination of consequences of selection for mitigation of methane emissions on performance traits. 8. Identification of alternative approaches to scale up microbiome-driven breeding by using e.g. saliva instead of rumen samples. 9. Development of an accurate microbiome-driven breeding to reduce methane emissions to be generally applicable across purebred and crossbred beef populations. 10. Assessment of the impact of genetic improvement and microbiome information on the potential reduction in GHG emissions across the UK beef population. 11. Development of an optimal breeding program using simulation studies to include microbiome information into practical breeding. The research will provide a validation of microbiome-driven breeding by actual breeding and demonstrates the mitigation of GHG emissions by a novel genetic improvement program and will show how cutting-edge research on the microbiome can be implemented effectively into practical breeding to achieve a sustainable and resilient beef cattle production moving towards net zero |
| Collaborator Contribution | Genus is providing targeted genetic solutions for farmers to create more value for the beef supply chain. Internal trials have demonstrated the superiority of targeted genetics for increasing supply chain profitability relative to traditional practices. Beef calves that are more efficient will reduce carbon footprint are increasingly demanded by supply chain stakeholders to achieve UK carbon reduction targets. Genus and SRUC have carried out ground-breaking research on beef cattle showing the potential of ruminal microbiome-driven breeding to mitigate methane emissions with an expected reduction of up to 17% per generation (MartínezÁlvaro et al., 2022) and improvement of feed conversion ratio by up to 15% per generation. A conservatively estimated 10% reduction in GHG emissions in Genus-influenced animals alone, for example, is a 337,000 metric tons reduction per year in the UK, which is permanent and increasing with ongoing genetic improvement. Novel technologies have the potential to create a step-change in emissions reduction. These selection responses were even higher than using measured methane and feed conversion ratio as basis for genomic breeding indicating the high importance of the rumen microbiome for these traits. The overall innovation is to optimise a highly promising new breeding strategy to cost effectively mitigate methane emissions and improve feed conversion ratio. |
| Impact | Microbiome-driven breeding to reduce methane emissions has been optimized to be used in different breeds. Sires have been selected by the optimized microbiome-driven breeding methodology based on their genomic breeding values for methane emissions. Progenies of the selected sires are in the process to be measured for methane emissions in SRUC's respiration chambers. Selection criteria have been developed so that reduction in methane emission does not affect growth rate and age adjusted carcass weight. The potential of microbiome-driven breeding to reduce methane emissions per day is substantial. |
| Start Year | 2023 |
| Description | Development of an integrated metagenomic analysis system using the microbial community, their genes and biological mechanisms to predict cattle phenotypes |
| Organisation | Ulster University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This PhD project will develop a novel integrated metagenomic analysis system using information of the abundances of the microbial community and their genes augmented with functional microbial community and gene information to predict as accurately as possible phenotypic traits of the animals. Besides this, the system will provide new knowledge about functional causes of microbial communities and genes to be related to animal traits such as feed conversion efficiency, meat quality and methane emissions. Previous analyses have considered each of the interactions between microbial community or microbial genes and traits separately and thus not described the entire systems and are expected to be substantially less powerful than the integrated analysis. Within this PhD studentship not only the metagenomic analysis system will be developed, it will also be applied to discover novel causes of the interactions between microbiome and the traits and then published together with the new methodology or separately depending on the findings. The developed pipeline of an integrated metagenomic analysis system is expected to be used in precision breeding, nutrition and husbandry systems. It will be flexible to be used in research to identify fundamental functional associations between the microbiome and traits of interest. High quality information from animal experiments about the abundances of the microbial community and microbial genes are available and will be used in the development of the system. Different databases such as the KEGG will be used to identify the functions of the microbial genes important related to the animal traits. The inclusion of the correlation among traits in the analysis is novel. An advanced multiplex network-based approach which is capable to handle the correlation between traits and incorporate diverse information multiple sources will be developed. The pipeline will be provided as open source software so that its use will be widespread and improvement and adaption to specific analysis can be achieved easily after the end of the research project. |
| Collaborator Contribution | The student will be trained at Ulster University in machine learning, bioinformatics, metagenomic analysis, etc. and at SRUC in presently used metagenomic analysis, microbiology, animal genetics and nutrition, etc. The developed software will have substantial impact on many project of the microbiome at SRUC and will further strengthening our world leading research in this area. |
| Impact | There have been several abstracts submitted to different conferences. This collaboration is multi-disciplinary of host genetics, microbiology, bioinformatics. |
| Start Year | 2018 |
| Description | Sustainable production of animals by optimizing the feed-microbiome-host axis |
| Organisation | Norwegian University of Life Sciences (NMBU) |
| Department | Noragric, Norwegian University of Life Sciences |
| Country | Norway |
| Sector | Academic/University |
| PI Contribution | Experimental research of the impact of seaweed on reduction in methane emissions from cattle and the bioinformatics. |
| Collaborator Contribution | Generating different omics data from samples taken from the experimental animals and carrying out the bioinformatics. |
| Impact | Proteomics data are in the process to be generated. It multi-disciplinary research of Genetics, Proteomics, Metabolomics and Bioinformatics. |
| Start Year | 2020 |
| Description | The use of intestinal microbiota as a biomarker for swine wellness and performance |
| Organisation | Zoetis |
| Country | United States |
| Sector | Private |
| PI Contribution | In this study, we develop a biomarker based on intestinal microbiota of swine to determine the amount of stress, feed conversion efficiency and growth rate in pigs. Establishing these links is an important step towards identifying novel treatments (manipulations which affect the microbiota with consequentially benefits for swine wellness and performance). To assess the interaction of stress and gut microbiota in pigs, including the consequences for production parameters, a social stress treatment was applied. Manipulation of the social environment is a potent source of stress for pigs. Here the stress treatment comprised of low stocking density, reduced feeder space and regular regrouping. Each of these individual components has been demonstrated to increase stress levels in pigs. Their combination here ensures a reliable stress state will be induced and also maintains the commercial relevance of the work. |
| Collaborator Contribution | Zoetis has financially contributing to the project and has provided their expertise in genomics and metagenomics. |
| Impact | Preliminary results have been presented to the partner. |
| Start Year | 2017 |
| Description | Understanding microbiomes of the ruminant holobiont |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Rennes Centre |
| Country | France |
| Sector | Public |
| PI Contribution | The key objective of the EU-funded HoloRuminant project is to study the role of the microbiome on animal health and production efficiency. Researchers will undertake a multi-omics approach to analyse the microbiome and the host, as well as the impact of their interaction at key stages during ruminant life. The ultimate goal is to characterise and identify ruminant-associated microbiomes associated with improved production efficiency, health and welfare. |
| Collaborator Contribution | The goal of the project is to elucidate the role of ruminant-associated microbiomes and their interplay with the host in early life and throughout fundamental life events. HoloRuminant will use a holistic multi-omics approach to characterise the acquisition and evolution of microbiomes from different body sites, their inheritability and their influence on the host's resistance to disease and environmental efficiency of production. Specifically we will: determine microbiomes' functions by combining multi-level information for microbes, host and their interaction; define microbiomes' roles during challenging life periods such as perinatal, weaning, and after exposure to pathogens; and evaluate the effect of ruminant microbiomes on critical phenotypes for sustainable production, health and welfare. This will allow the identification of novel microbial markers for monitoring, predicting and selecting phenotypes of interest. By engaging actors from the livestock value chain, we will evaluate the socio-economic impact and acceptability of the innovations proposed among stakeholders and the public. HoloRuminant will provide highly innovative, standardized methodologies that will radically advance our understanding of the ruminant holobiont. This knowledge and the tools created will allow the use of microbiome-based diagnostics and solutions for improving ruminant sustainabilty. |
| Impact | The collaboration has commence and no outputs have been generated yet. |
| Start Year | 2021 |
| Title | KOunt.v1.1.0.tar.gz |
| Description | Version 1.1.0 of KOunt the KEGG Abundance tool |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Impact | The software is used to identify KEGG genes from metagenomic sequences which can be used for many applications to determine the microbial functions. In our research we are using the software to identify functional KEGG genes from metagenomic sequences of the ruminal microbiome. This information is used for microbiome-driven breeding to mitigate methane emissions from ruminants. |
| URL | https://figshare.com/articles/software/KOunt_v1_1_0_tar_gz/22250662/1 |
| Title | MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs) |
| Description | The Model of Agricultural Production and its Impact on the Environment (MAgPIE) is a global land use allocation model framework, which is coupled to the grid-based dynamic vegetation model LPJmL, with a spatial resolution of 0.5°x0.5°. It takes regional economic conditions such as demand for agricultural commodities, technological development and production costs as well as spatially explicit data on potential crop yields, land and water constraints (from LPJmL) into account. Based on these, the model derives specific land use patterns, yields and total costs of agricultural production for each grid cell. The objective function of the land use model is to minimize total cost of production for a given amount of regional food and bioenergy demand. Regional food energy demand is defined for an exogenously given population in 10 food energy categories, based on regional diets. Future trends in food demand are derived from a cross-country regression analysis, based on future scenarios on GDP and population growth. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Metagenomics is a powerful tool for assaying the DNA from every genome present in an environment. Recent advances in bioinformatics have enabled the rapid assembly of near-complete metagenome-assembled genomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterize thousands of genomes simultaneously, to enable identification and functional characterization. This software allowed us to assemble from over 800 Gb of rumen metagenomic sequence data, derived from 43 Scottish cattle, 913 draft bacterial and archaeal genomes, using both metagenomic binning and Hi-C-based proximity-guided assembly. |
| URL | https://github.com/WatsonLab/MAGpy |
| Description | "Finding consensus on how Scottish agriculture can contribute to meeting our international and national climate change commitments" |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Roehe, R. (2019). Methane emissions in Scotland: Sources and potential solutions. Nourish Scotland Conference "Finding consensus on how Scottish agriculture can contribute to meeting our international and national climate change commitments", Edinburgh, UK (invited speaker) |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.nourishscotland.org |
| Description | 75th British Cattle Breeding Conference will create discussion, debate and vision |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Our research on microbiome-driven breeding to reduce methane emissions and improvement of feed conversion was presented to farmers, breeding organizations, press, AHDB, etc. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.cattlebreeders.org.uk/news/3524/75th-british-cattle-breeding-conference-designed-to-crea... |
| Description | BBC Landward Scotland Low-methane cattle |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Will cows that burp less be key to a greener future? With the world's attention focused on climate change, the agricultural industry is under pressure to clean up its act. A particular problem it is responsible for is the amount of methane created as a by-product of cattle farming. Methane, a greenhouse gas that contributes to global warming, is belched out by cows as part of their digestion process. However, scientists have discovered that it is possible to breed more eco-friendly cows. Researchers at Scotland's Rural College have discovered that some cows produce less methane than others. This is due to their microbiomes - the mix of different microbes in the gut. The microbiome varies in each cow causing some to produce more methane than others. On Landward Professor Rainer Roehe explains that his team has been monitoring cattle in respiration chambers and discovered that some animals emit only half of the methane emissions of others. he team determined that a cow's saliva can reveal whether its stomach is a perfect host for methane-producing microbes, or not. "Saliva production on an animal is very high," says Professor Roehe. "A cow can produce one hundred and fifty litres of saliva [per day] and there is variation between animals of fifty litres. "Saliva production has a big influence on the environment in the rumen [stomach] where the microbes are living. It has an impact on the PH. If the PH is very high then we know these animals are producing a lot of methane. If the PH is low then these animals are producing less methane." So by establishing which cows produce smaller amounts of methane, it will be possible to selectively breed more of them and reduce the amount of gas released into the atmosphere. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.bbc.co.uk/programmes/p0b2wrkt |
| Description | BBC TWO programme horizon 'Feast to Save the Planet' |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Public presentation of our developed microbiome-driven breeding to reduce methane emissions of beef cattle broadcast on BBC TWO programme horizon 'Feast to Save the Planet' |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.bbc.co.uk/iplayer/episode/m000qzyd/horizon-2021-feast-to-save-the-planet |
| Description | Breeding for reduced Methanobrevibacter to mitigate methane emissions from beef cattle (at BSAS 2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The use of the most abundant methanogen as breeding trait to reduce methane emissions from beef cattle. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.bsas.org.uk/conference-2024 |
| Description | Breeding to Reduce Methane Emissions from Beef Cattle |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | At SRUC's Beef and Sheep Research Centre, we recorded the feed intake of beef cattle using electronic feeders and subsequent methane emissions using respiration chambers. In addition, we obtained samples of rumen contents, either using a stomach tube on live animals or directly from the rumen of slaughtered animals in the abattoir. We sequenced microbial DNA extracted from the rumen samples to identify the relative abundance of different microbes (e.g. bacteria and Archaea) and microbial genes. We found that the relative abundance of Archaea, which are the main organisms producing methane in the rumen of cattle, are a good predictor of methane emissions. However, the relative abundance of key microbial genes provided an even better predictor for methane emissions. Most of the identified microbial genes are involved in the metabolism of methane or pathways providing substrates (e.g. hydrogen) for methane metabolism. We also revealed that the relative abundance of methanogenic Archaea is controlled by the host animal's genetics. This means that breeding can be used to reduce the methanogenic Archaea and thus methane emissions. The relative abundance of different microbial genes was also found to be a good predictor of feed conversion efficiency so that both methane emissions and feed conversion efficiency can be predicted from different microbial genes in the same sample. The relationship between the abundance of microbial genes and methane emissions was independent of the diet so that breeding could be combined with dietary intervention to cumulatively mitigate methane emissions Benefits This research provides new breeding strategies to improve the sustainability of Scottish beef production in terms of efficiency and mitigation of GHG emissions. During a 12-week feeding period, we calculated feed cost savings of £23/head of cattle between the most feed efficient third and least efficient third in a Stabiliser cattle population. For 388,700 prime cattle slaughtered in Scottish abattoirs during 2017, this would mean a cost reduction of £8.9 million, considering only 3 months of the growing-finishing period. The use of microbiome information to predict feed conversion efficiency will save the large cost of recording feed intake and growth in test stations. It is, therefore, a cost-effective and practical strategy for genetic improvement of feed conversion efficiency. Since beef cattle have never been selected for reduction in methane emissions before, we obtained a large variation in methane emissions from 170g/day to 330g/day among beef cattle of the same breed offered the same forage-based diet. This large variation of methane emissions, and the host genetic control of methane-producing Archaea, will result in a selection response for reduction of methane emissions (expected to be about 3% of the mean per year). Measuring methane emissions in respiration chambers for breeding purposes is very accurate but too costly and cannot provide the number of animals neccessary to be recorded for accurate breeding. In contrast, a more cost-effective method to predict methane emissions is by using the relative abundance of different microbial genes, based on rumen samples taken using a stomach tube on live animals or directly from the rumen of slaughtered animals. This method will provide a dataset of predicted methane emissions from a large number of individual animals to be used to make accurate breeding decisions to select animals emitting less methane. More broadly, our research suggests that rumen microbial genes are excellent biomarkers for complex traits linked to other important issues - such as animal health and welfare, meat fatty acid profiles (healthy diets for people) and antimicrobial resistance. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://sefari.scot/research/breeding-to-reduce-methane-emissions-from-beef-cattle |
| Description | CBS Mornings |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | U.K. researchers study genetic link to methane emissions in cattle, key to reducing greenhouse gases Methane is a potent greenhouse gas, and reducing its emissions is one of the most important keys to curbing global warming. Cows are one of the main offenders, but experiments are proving that their level of gassiness is determined by genetics. CBS News' Mark Phillips spoke to researchers hoping that breeding cows with the right genes could prove a cost-effective way to reduce cattle methane emissions by as much as 50%. Cows are responsible for about 40% of global methane emissions. Methane is the gas passed or belched by the world's 1.4 billion cattle. In Scotland, cattle can be found grazing on the lush green pastures. Some environmentalists believe that when it comes to global warming, meat, especially beef, is among the worst foods that can be eaten. According to scientists, the methane cows belch out while turning feed into food is a far more powerful greenhouse gas than even the carbon dioxide produced by burning fossil fuels. Researchers at an experimental farm run by Scotland's Rural College believe that they have found a way to satisfy the world's ever-growing appetite for beef, while also producing less methane. Rainer Roehe, a professor of animal genetics and microbiome at the college, has been studying the digestive process in cows and has found that microbiome at the college, believes that one cow is not like another. He's found that the microbes in their stomachs not only vary from cow to cow, they determine how much methane the cow produces. "There are huge variations in the stomach," Roehe told CBS News correspondent Mark Phillips. Cows have four stomachs and don't digest what they eat - the bugs in their gut do. Their food mixes with a kind of microbe soup in the rumen, or first stomach, and is then re-chewed, before passing through the rest of the system. Roehe's work shows that genetics can predict which animals will have the right microbe cocktail to produce the least methane. In other words, you can breed low-methane-producing cattle. We are predicting that we reduce methane by 50%," Roehe said. How does he know this? He measures it. The cows are put in hermetically sealed chambers on the farm for three days and I the gases they emit are analyzed. Producing methane is considered a waste of energy for a cow. The less they produce, the more efficient they are at turning cattle feed into human food. According to Oxford University's Joseph Poore, judged against the nutrition it provides, beef is simply too environmentally expensive and found that a 50% reduction in greenhouse gas production is different from a 100% reduction, which is what we would get if people stopped eating meat. "Beef provides about 6% of our protein and 2% of the global calorie, worldwide," Poore said. "If you look at the environmental impacts, beef is about 30% of our greenhouse foods greenhouse gas emissions, so you got a massive imbalance between the kind of environmental impacts of this product and the nutrition it provides." In In the rugged terrain of the Scottish highlands, Cattle raising is arguably the most efficient food-producing use to which these fields can be put because nothing much will grow there other than grass. There are lots of other areas of the world like that. As with so much of the environmental argument, there is a lot to chew over. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.cbsnews.com/video/uk-researchers-study-genetic-link-to-methane-emissions-in-cattle-key-t... |
| Description | COP26 Reducing Methane Emissions: Breeding, Feeding and Animal Health |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | International COP26 event: Reducing Methane Emissions: Breeding, Feeding and Animal Health Microbiome-driven breeding to mitigate methane emissions from beef cattle One cost-effective method for farmers to reduce methane emissions from their livestock is to selectively breed animals with lower emissions. SEFARI researchers, in collaboration with the University of Edinburgh and Genus plc, a breeding company, have revealed that the composition of the microbiome in the rumen, the largest of a cow's four stomachs, is linked to cattle host genetics. The microbiota (i.e. Bacteria, Protozoa and Fungi) in the rumen is a unique symbiotic ecosystem that allows cattle to ferment inedible fibrous plant material, like grass, into nutrients and produce high-quality beef and milk for human consumption. During this conversion, methane is produced by specific microbes (Archaea) as a natural by-product - although how much varies from cow to cow. Sampling the microbiome composition in cattle herds is a cost-effective way to identify lower methane-emitting cattle as well as those with improved characteristics, such as feed conversion efficiency and meat quality, and predict these traits in a large cohort of cattle. Based on this research, SEFARI scientists are developing a rumen microbiome-driven breeding strategy, which can reduce methane emissions by up to 8% per year or cumulatively up to 50% after 10 years of selection. Improving the feed efficiency of cattle also reduces the carbon footprint of beef and increases the profitability of beef production. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://sefari.scot/blog/2021/12/20/cop26-and-reducing-methane-emissions-breeding-feeding-and-animal... |
| Description | Cattle genetics influences the abundance of ruminal pathogenic microbes potentially associated with higher GHG emissions |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the newest research to reduce methane emissions by microbiome-driven breeding |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://eaap2024.org/ |
| Description | Contributions to regular Scottish Government Livestock Genetics Meetings |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Discussion of the Road Map to reduce GHG emissions from beef cattle using breeding. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Defra Visit to explain microbiome-driven breeding |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Presentation of microbiome-driven breeding to reduce methane emissions and discussion of the findings with the Defra Visiting group. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.gov.uk/government/organisations/department-for-environment-food-rural-affairs |
| Description | Drovers "Driving the Best Market" |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Cow Gut DNA Study Finds Bugs that Could Up Meat and Milk Yields! Cutting-edge DNA technologies have discovered thousands of bugs in cows' stomachs that could improve meat and dairy production, and keep cattle healthy. The findings build the clearest picture yet of how the microbes in a cow's rumen - the first of its four stomachs - help cattle to digest, and extract energy from, their food. Researchers from SRUC, the University of Edinburgh's Roslin Institute and the Rowett Institute at the University of Aberdeen analysed the rumen contents of hundreds of cows and discovered thousands of bacteria, as well as archaea - a separate group of single-celled organism. Pinpointing which microbes are essential for livestock wellbeing and food production could inform future breeding programmes. These microbes enable cattle, and other ruminants, to convert plants and low-value products that humans cannot eat into food with high nutritional value, such as meat, milk and cheese. The microscopic organisms provide cattle with nutrients and energy, contribute to the animals' health and, as a bi-product, release methane which is a concern for global warming. The latest research follows on from a study by the same team last year, in which DNA data from 42 cows was analysed. Until this study, the diverse mix of bacteria and archaea that live in the rumen was poorly understood. Scientists had been unable to link DNA analysis to food digestion, animal health and greenhouse gas emissions. The team used the latest DNA technologies, including a handheld sequencing device that can quickly generate DNA data that is incredibly long and detailed. This allowed the researchers to completely sequence the genomes, from beginning to end, of several new bacterial species. They studied samples from 283 cows, identified almost 5,000 new strains of microbe and more than 2,000 novel species - microbes that previously no-one knew existed. Hundreds of thousands of novel enzymes, whose instructions are encoded in the DNA, may have potential uses as biofuels, or in the biotechnology industries. By analysing their genetic information, the team pinpointed previously unknown enzymes that can extract energy and nutrition from plant material. The study is published in the journal, Nature Biotechnology. Rainer Roehe, Professor of Animal Genetics and Microbiome at SRUC, said: "We've identified some 5,000 novel genomes of microbial species in the rumen that all play a vital role. Not only do they enhance breeding and nutrition to reduce greenhouse gas emissions from cattle, they also improve production efficiency, product quality and animal health." Professor Mick Watson, Head of Genetics and Genomics at The Roslin Institute, said: "The cow rumen is a gift that keeps on giving. We were surprised by how many completely new microbes we have discovered, which is far more than in our previous study. The findings will inform studies of cow health and meat and dairy production for many years to come." |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.drovers.com/article/cow-gut-dna-study-finds-bugs-could-meat-and-milk-yields |
| Description | Environmental factor effects on rumen microbiome multi-omics traits in beef cattle (at BSAS 2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The impact of environmental factors on the rumen microbiome are important to be considered for microbiome-driven breeding to reduce methane emissions and improve feed efficiency. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.bsas.org.uk/conference-2024 |
| Description | Government World |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Cutting-edge DNA technologies have discovered thousands of bugs in cows' stomachs that could improve meat and dairy production, and keep cattle healthy. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.government-world.com/cow-gut-dna-study-finds-bugs-that-could-up-meat-and-milk-yields/ |
| Description | How can the UK reduce meat consumption and cut emissions? |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | The Guardian published our research on microbiome-driven breeding to reduce methane emissions as one solution to reduced the environmental impact of cattle production. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.theguardian.com/environment/2022/aug/16/how-can-the-uk-reduce-meat-consumption-and-cut-e... |
| Description | Improving 'Scotch Beef' environmental impact |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Beef production is very important for Scotland's economy (economic output of £851 million in 2017) and for providing the high quality and iconic 'Scotch Beef' brand. However, it is widely recognised that there is an environmental impact caused by cattle through their production of methane. Methane is a highly potent greenhouse gas (GHG) produced by ruminants and a reduction of these emissions will help to meet the legally binding Scottish Government target of net-zero GHG emissions by 2045 to limit climate change. The cow's largest stomach, the rumen contains a very dense microbial ecosystem comprising of different Bacteria, Archaea, Protozoa and Fungi. This ecosystem within the rumen is essential in cattle due to its ability to convert indigestible fibrous plant material (e.g. grass) into absorbable nutrients used to produce high quality beef. As a by-product of the microbial conversion of feed, in particular fibrous grass, the rumen microbial Archaea population produces methane, which is expelled through mouth and nose into the environment. In collaboration with the Universities of Edinburgh and Aberdeen, SEFARI scientist's prize winning and subsequent research showed that efficient beef production with less methane emissions is achievable by: • Genetic improvement of animals for increased feed conversion efficiency which produce more meat per kg of feed consumed using the correlated abundances of specific microbes and their genes present in the rumen • Selection for lower abundance of key microbes and their genes involved in producing substrates needed by Archaea so that they produce less methane in the rumen of cattle This research provides new breeding strategies to improve the sustainability of Scottish beef production in terms of efficiency and mitigation of GHG emissions. The breeding strategy is cost-effective because it avoids expensive measurements of feed conversion efficiency using electronic feeders and methane emissions in respiration chambers. Rumen microbial genes are also excellent biomarkers for animal health (including antimicrobial resistance) and welfare traits, as well as meat fatty acid profiles ensuring healthier human diets. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://sefari.scot/sites/default/files/documents/SEFARI%20Food%20Booklet.pdf |
| Description | Innovate UK KTNs plant and animal sector advisory boards |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the microbiome-driven breeding strategy to Innovate UK KTNs plant and animal sector advisory boards. |
| Year(s) Of Engagement Activity | 2024 |
| Description | International SMARTCow Study Tour |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Roehe, R. (2019). SmartCow: SRUC's beef research facilities to study associations of the rumen microbiome with traits important for beef production. International SMARTCow Study Tour, Edinburgh, UK |
| Year(s) Of Engagement Activity | 2019 |
| Description | International Training Course of EU project SMARTCow |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Roehe, R. (2019). Microbiome proxies for methane emissions and feed efficiency. International Training Course of EU project SMARTCow, Webinar |
| Year(s) Of Engagement Activity | 2019 |
| Description | Livestock Genetic and Performance Improvement Stakeholder Policy |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Discussion of KPI to develop and summary document for policy to reduce GHG emissions from beef cattle. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Low-emission cow |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | The low-emission cow published in several German News Paper Rheinpfalz am Sonntat, Saechsische Zeitung, Stuttgarter Zeitung, Suedkurier, Neue Zuericher Zeitung. Die Mikro-bengemeinschaft im Pansen habe sich seit Urzeiten entwickelt. <> Günstiger erscheint es, Rinder aufzuziehen, die von ornherein weniger Treibhausgas bilden. <>, sagt Rainer Roehe vom Scotland's Rural College in Edinburg. Für die Zucht sind solche <> inder interessant. Aber es ist nicht ausgemacht dass jedes diese Eigenschaft weitergibt. Deshalb muss man die Nachkommen testen. Respirationskammern wären viel zu teuer und seien nicht in nötiger Zahl vorhanden, sagt Roehe. Er und sein Team haben stattdessen ein Verfahren entwickelt, das kostengünstig und grossflächig einsetzbar sein soll. Es analysiert die Zusammensetzung der Mikrobengemeinde im Pansen. Einige sorgen beispielsweise dafür, dass die Kuh viel Speichel bildet, was am Ende die Methanproduktion erhöht. Die Forscher haben neben dem <> noch 29 weitere Gene in den Mikroorganismen identifiziert, die relevant für die Methanbildung sind. Nach diesen Genen fahnden sie im Pansensaft der Nachkommen und ermitteln, wie häufig diese vorkommen. <>, sagt Roehe. Konsequent eingesetzt könnte mikrobiombasierte Züchtung den Methanausstoss der Rinder binnen zehn Jahren um die Hälfte reduzieren, glaubt der Forscher. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://magazin.nzz.ch/wissen/klimafreundliche-kuh-wie-man-rinder-dazu-bringt-weniger-methan-auszust... |
| Description | Methane emissions from beef cattle reduced by 7% per year. |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Our research are published by the Scottish Farmer. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.pressreader.com/uk/the-scottish-farmer/20230204/282351158921555 |
| Description | Microbiome-driven breeding to mitigate methane emissions to The Scottish Government |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Presentation of microbiome-driven breeding to mitigate methane emissions and improve feed conversion efficiency including a discussion of how this new methodology can be implemented into breeding for reduction of GHG emission from beef cattle in Scotland. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Mid-Lothian Science Zone Steering Group Visit |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Mid-Lothian Science Zone Steering Group was visiting SRUC and I presented our research on microbiome-driven breeding to reduce methane emissions and improve feed efficiency. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://midlothiansciencezone.com/about/ |
| Description | PHYS.ORG |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Cow gut study finds bugs that could up yields! Cutting-edge DNA technologies have discovered thousands of bugs in cows' stomachs that could improve meat and dairy production, and keep cattle healthy. The findings build the clearest picture yet of how the microbes in a cow's rumen-the first of its four stomachs-help cattle to digest, and extract energy from, their food. Researchers analyzed the rumen contents of hundreds of cows and discovered thousands of bacteria, as well as archaea-a separate group of single-celled organism. Pinpointing which microbes are essential for livestock wellbeing and food production could inform future breeding programs. These microbes enable cattle, and other ruminants, to convert plants and low-value products that humans cannot eat into food with high nutritional value, such as meat, milk and cheese. Global Warming The microscopic organisms provide cattle with nutrients and energy, contribute to the animals' health and, as a bi-product, release methane which is a concern for global warming. The latest research follows on from a study by the same team last year, in which DNA data from 42 cows was analyzed. Until this study, the diverse mix of bacteria and archaea that live in the rumen was poorly understood. Scientists had been unable to link DNA analysis to food digestion, animal health and greenhouse gas emissions. The team used the latest DNA technologies, including a handheld sequencing device that can quickly generate DNA data that is incredibly long and detailed. This allowed the researchers to completely sequence the genomes, from beginning to end, of several new bacterial species. New Strains They studied samples from 283 cows, identified almost 5,000 new strains of microbe and more than 2,000 novel species-microbes that previously no-one knew existed. Hundreds of thousands of novel enzymes, whose instructions are encoded in the DNA, may have potential uses as biofuels, or in the biotechnology industries. By analyzing their genetic information, the team pinpointed previously unknown enzymes that can extract energy and nutrition from plant material. The study was carried out by researchers at the University of Edinburgh's Roslin Institute, in collaboration with Scotland's Rural College (SRUC) and the Rowett Institute at the University of Aberdeen. It is published in the journal, Nature Biotechnology. "The cow rumen is a gift that keeps on giving. We were surprised by how many completely new microbes we have discovered, which is far more than in our previous study. The findings will inform studies of cow health and meat and dairy production for many years to come," says Professor Mick Watson, Head of genetics and genomics at The Roslin Institute. "We've identified some 5,000 novel genomes of microbial species in the rumen that all play a vital role. Not only do they enhance breeding and nutrition to reduce greenhouse gas emissions from cattle, they also improve production efficiency, product quality and animal health," says Professor Rainer Roehe, professor of animal genetics and microbiome at SRUC. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://phys.org/news/2019-08-cow-gut-bugs-yields.html |
| Description | Planet A ® Visiting Group from France |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of our developed microbiome-driven breeding to reduce methane emissions to the visiting Group of Planet A ® from France. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Press release "Cow gut DNA study finds bugs that could up meat and milk yields" |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Cow gut DNA study finds bugs that could up meat and milk yields! Cutting-edge DNA technologies have discovered thousands of bugs in cows' stomachs that could improve meat and dairy production, and keep cattle healthy. The findings build the clearest picture yet of how the microbes in a cow's rumen - the first of its four stomachs - help cattle to digest, and extract energy from, their food. Researchers from SRUC, the University of Edinburgh's Roslin Institute and the Rowett Institute at the University of Aberdeen analysed the rumen contents of hundreds of cows and discovered thousands of bacteria, as well as archaea - a separate group of single-celled organism. Pinpointing which microbes are essential for livestock wellbeing and food production could inform future breeding programmes. These microbes enable cattle, and other ruminants, to convert plants and low-value products that humans cannot eat into food with high nutritional value, such as meat, milk and cheese. The microscopic organisms provide cattle with nutrients and energy, contribute to the animals' health and, as a bi-product, release methane which is a concern for global warming. The latest research follows on from a study by the same team last year, in which DNA data from 42 cows was analysed. Until this study, the diverse mix of bacteria and archaea that live in the rumen was poorly understood. Scientists had been unable to link DNA analysis to food digestion, animal health and greenhouse gas emissions. The team used the latest DNA technologies, including a handheld sequencing device that can quickly generate DNA data that is incredibly long and detailed. This allowed the researchers to completely sequence the genomes, from beginning to end, of several new bacterial species. They studied samples from 283 cows, identified almost 5,000 new strains of microbe and more than 2,000 novel species - microbes that previously no-one knew existed. Hundreds of thousands of novel enzymes, whose instructions are encoded in the DNA, may have potential uses as biofuels, or in the biotechnology industries. By analysing their genetic information, the team pinpointed previously unknown enzymes that can extract energy and nutrition from plant material. The study is published in the journal, Nature Biotechnology. Rainer Roehe, Professor of Animal Genetics and Microbiome at SRUC, said: "We've identified some 5,000 novel genomes of microbial species in the rumen that all play a vital role. Not only do they enhance breeding and nutrition to reduce greenhouse gas emissions from cattle, they also improve production efficiency, product quality and animal health." Professor Mick Watson, Head of Genetics and Genomics at The Roslin Institute, said: "The cow rumen is a gift that keeps on giving. We were surprised by how many completely new microbes we have discovered, which is far more than in our previous study. The findings will inform studies of cow health and meat and dairy production for many years to come." |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.sruc.ac.uk/news/article/2467/cow_gut_dna_study_finds_bugs_that_could_up_meat_and_milk_yi... |
| Description | RESAS webinar Mitigation of methane (greenhouse gas) emissions from beef cattle |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Title of the webinar presentation entitled "Microbiome-driven breeding for low methane-emitting efficient beef cattle" will provide a breeding solution to mitigate methane emissions from beef cattle. In the presentation it will be shown that: • Methane is a highly potent greenhouse gas that has been emphasised at COP26 to be one main target for limitation of climate change • Livestock production results in 32% of all methane emissions (UN report, 2021), mainly due to enteric methane emissions from cattle • There are large differences in methane emissions between cattle so that some animals emit only half of the methane emissions considering that they were fed the same diet, are from the same breed and reared as well as tested on the same farm (SRUC Beef Research Centre) • The animal genetics is at least partly causing these substantial differences in methane emissions • Methane is produced by the methanogenic microbes in the largest of four stomachs of cattle the rumen and released through mouth and nose into the atmosphere • The rumen microbial community can be used to accurately predict methane emissions and therefore used to cost-effectively breed cattle without expensive measuring of methane emissions • Based on our SRUC Beef research data, this microbiome-driven breeding is expected to result in up to 8% reduction in methane emissions per year or cumulatively of up to 50% reduction over 10 years of selection. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://vimeo.com/649462381/daae3514db |
| Description | Rumen microbiome - a new selection criteria to reduce methane emissions and improve feed efficiency in beef cattle |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Rumen microbiome - a new selection criteria to reduce methane emissions and improve feed efficiency in beef cattle. Virtual presentation at the Royal Welsh Show, Wales, UK. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.youtube.com/watch?v=4nNkBnG5Yg0 |
| Description | SRUC and University of Guelph virtual event: A Green Rural Recovery: Sustainable Natural Economies of Canada and Scotland |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | SRUC teams up with University of Guelph for virtual event Leading scientists from Scotland and Canada are set to meet virtually to discuss solutions around greener agricultural systems. Experts from Scotland's Rural College (SRUC) and the University of Guelph in Ontario will examine how technology is being used to boost the natural economy at next month's virtual event. Professor Rainer Roehe from SRUC, who will showcase his research into the mitigation of methane emissions from beef cattle, and Prof Asim Biswas from the University of Guelph, will discuss the use of smart farming techniques in Ontario's grain production. Supported by the Scottish Government, the event will include opening remarks from Mairi Gougeon MSP, Cabinet Secretary for Rural Affairs and Islands, as well as an in-depth panel discussion. Further presentations will be made by Prof Richard Dewhurst, who will talk about the Digital Value Dairy Chain project, led by SRUC, and the University of Guelph's Prof Claudia Wagner-Riddle will explain how an integrated data sharing platform can expand the value of soil health and soil ecosystem services research. The Digital Value Dairy Chain project, which aims to create 600 new jobs in South-West Scotland and Cumbria, recently received more than £21 million from the UKRI Strength in Places fund. Professor Wayne Powell, Principal and Chief Executive of SRUC, said: "We are delighted to be hosting this joint webinar. Supported by the Scottish Government, it is the latest event in a long-running series of collaborations between the University of Guelph and SRUC. It is particularly timely, illustrating examples of key research that aims to build back the natural economy greener and more sustainably from the Covid-19 pandemic." Malcolm Campbell, Vice-President (Research) at the University of Guelph, said: "At University of Guelph we are absolutely delighted to be partnering with fantastic colleagues at SRUC to promote collaboration between our countries that will catalyse innovation and fuel economic development." The University of Guelph and SRUC have collaborated on joint research and teaching for many years. In particular, the Ontario Agricultural College (OAC) and SRUC have many research interests in common, including Animal Bioscience, Food Agriculture and Resource Economics, Animal Welfare, Environmental Systems, Plant agriculture, Genetic Improvement of Livestock, Organic Farming, Grassland, and Food and Agricultural Policy. The Zoom event, A Green Rural Recovery: Sustainable Natural Economies of Canada and Scotland is free to attend. It takes place on Tuesday 12 October from 4pm-5.30pm (BST). To sign up visit bit.ly/GreenRuralRecovery |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.farmbusiness.co.uk/uncategorized/sruc-teams-up-with-university-of-guelph-for-virtual-eve... |
| Description | SRUC awarded £700k by BBSRC to measure cattle emissions |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Researchers at Scotland's Rural College (SRUC) have been awarded nearly £700,000 for equipment which will form part of an ultra-modern research facility to measure emissions from beef cattle, supporting the UK Government's goals to achieve net-zero greenhouse gas emissions by 2050. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.thescottishfarmer.co.uk/news/24544783.sruc-awarded-700k-measure-cattle-emissions/ |
| Description | SRUC awarded £700k by BBSRC to measure cattle emissions |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | The UltraGreenCow project is set to be one of the few locations in the world which can measure all emissions from livestock. SRUC researchers have been awarded nearly £700,000 for equipment* which will form part of an ultra-modern research facility to measure emissions from beef cattle, supporting the UK Government's goals to achieve net-zero greenhouse gas emissions by 2050. The winning project, titled 'UltraGreenCow: Comprehensive greenhouse gas and ammonia emissions measurement capacity for large ruminant production' has become one of 29 projects to receive a portion of the £13 million of funding available from the Biotechnology and Biological Sciences Research Council (BBSRC) for mid-range equipment for biosciences research. The UltraGreenCow project, led by SRUC researchers Dr Gemma Miller, Professor Rainer Roehe and Prof Carol-Anne Duthie, will build upon SRUC's existing GreenCow facility. UltraGreenCow is set to be one of the few locations in the world which can measure all emissions from livestock (including methane, nitrous oxide, ammonia and carbon dioxide). The increased knowledge of trade-offs between these pollutants will provide essential data for mitigation measures, such as feed additives, at a time when farmers are under intense pressure to reduce emissions. Project co-lead Dr Miller, Research Fellow at SRUC, said: "In the UK, agriculture is responsible for 11% of Greenhouse Gases (GHGs) and 87% of ammonia emissions. Around 50% of GHGs and 75% of ammonia emissions from agriculture are associated with livestock or their wastes. Therefore, reducing emissions of these gases from agriculture is vital to meeting these ambitious commitments. However, there is a real risk that implementing a mitigation measure to reduce one gas could lead to increases in one or more of the others. "Currently there are very few facilities with the capability to measure emissions of all these gases simultaneously from individual animals, which is apparent in the low number of studies reporting all of them. "Gaining comprehensive data supporting reductions in all emissions will improve cohesion between different policy objectives and help improve farmer and consumer confidence, leading to greater uptake of mitigation measures." For more information about research work at SRUC, visit: www.sruc.ac.uk/research. *Equipment includes: NH3 and N20 gas sampling and analysis system Air handling units Combined hydronic unit System control hardware and software |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.sruc.ac.uk/all-news/sruc-awarded-700k-to-measure-cattle-emissions/ |
| Description | Scientists developing EBV for lower methane emission |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Farmers could be selecting cattle bred to produce lower methane emissions in the near future, according to a leading scientist. Methane is an important greenhouse gas, with 28-times the potential global-warming capability of carbon dioxide. Levels in the atmosphere have recently risen to a historic peak and the increase has been blamed on livestock production, in particular beef and dairy farming. The gas is a by-product of microbial feed conversion, mainly of fibrous grass, by a dense population of bacteria, archaea, protozoa and fungi within the rumen. See also: Farmer Focus: Methane rules will hit NZ farm profits Work carried out at the SRUC by professor of animal genetics and microbiome Rainer Roehe showed that methane production is linked to the archaea micro-organism. In trials the quantity of archaea was a good predictor of methane emissions, said Prof Roehe, who was speaking at a Royal Welsh Agricultural Society webinar. The number of these micro-organisms is linked to higher gut pH levels and this, in turn, is influenced by an animal's saliva production. Crucially, research has shown that the level of saliva produced is strongly linked to the genetic make-up of an individual animal. "Average saliva production is 150 litres a day but this can vary, up or down, by 25 litres between individuals," said Prof Roehe. This means one animal may have a genotype that means it produces 50 litres more saliva than another animal. Cattle producing more saliva will therefore have more archaea in their guts and produce more methane. Tests developed have shown that rumen sampling via stomach tube can indicate accurately the abundance of microbial genes in an individual. It is therefore possible to identify which animals are methane producers and hence an estimated breeding value (EBV) could be developed, Prof Roehe said. The high level of trait heritability means cattle producers could reliably select sires based on their potential to produce less methane, he concluded. The work, backed by numerous cattle breeding societies, is ongoing, with traits expected in the coming years. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.fwi.co.uk/news/environment/scientists-developing-ebv-for-lower-methane-emission |
| Description | Scotland's Rural College awarded £700,000 by BBSRC to measure GHG |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Scotland's Rural College (SRUC) has been awarded nearly £700,000 for equipment which will form part of an ultra-modern research facility to measure emissions from beef cattle. Burping and flatulating cattle are a major contributor to harmful greenhouse gases. The Biotechnology and Biological Sciences Research Council (BBSRC) grant to SRUC supports UK Government goals to achieve net-zero greenhouse gas emissions by 2050. Scotland plans to reach net zero five years earlier, by 2045. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.pressandjournal.co.uk/fp/business/farming/6567079/scotlands-rural-college-awarded-700000... |
| Description | Selecting the best performing animals with low methane emissions |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Methane is a highly potent greenhouse gas (GHG) produced by ruminants, mainly cattle and sheep. A reduction of these emissions will help to meet the legally-binding national target of net-zero GHG emissions by 2045 to limit climate change and build long-term environmentally sustainable livestock production. Specific feed additives, such as seaweed or 3-Nitrooxypropanol, can reduce methane emissions from cattle, but are costly. Animal breeding is efficient, permanent and cumulative in its response and thus cost-effective. The challenge to breed low methane-emitting animals is to cost-effectively measure or predict emissions continuously on large cohorts of animals. SEFARI scientists in collaboration with the University of Edinburgh and University of Aberdeen have found a way to predict methane emissions from cattle, based on their microbiome, specifically the bacteria and methanogenic Archaea living in the cow's largest stomach - the rumen. • Specific ruminal bacteria are essential for the animal to convert food into nutrients used to produce milk and meat, whereas the methane producing Archaea are nonessential and their reduction mitigates methane emissions: • The composition of the microbiome in the rumen can be used to predict methane emissions and is linked to the animal host genetics • Selective breeding, based on rumen microbiome composition can be used to reduce methane emissions from cattle but also improve characteristics, such as feed conversion efficiency and meat quality Based on this, SEFARI scientists are developing a system based on the rumen microbiome to implement selection for low methane emitting animals with improved production efficiency and product quality into practical breeding. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://sefari.scot/sites/default/files/documents/SEFARI%20Livestock%20_%20Research%20Examples%20Apr... |
| Description | University of São Paulo (Pirassununga, SP) Brazil |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Roehe, R. (2019). Lecturing the course "Microbiomes: Principles and Applications in Animal Science" at the University of São Paulo (Pirassununga, SP) Brazil |
| Year(s) Of Engagement Activity | 2019 |
| Description | Visit of Canadian Farmers |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation and Discussion with Canadian Farmer to use microbiome-driven breeding to reduce methane emissions. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Visit of staff of the breeding company Genus at the Roslin Institute |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the microbiome-driven selection to improve animal performance and reduce the GHG gas methane from cattle. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Webinar Towards Net Zero Agriculture: GHG Mitigation Research at SRUC |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A presentation of microbiome driven breeding strategies to reduce enteric methane emissions |
| Year(s) Of Engagement Activity | 2024 |
| Description | Workshop Seaweed as Agri-food |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation: Using seaweed as an additive in animal feed to reduce methane emissions. The workshop is part of a Universities Innovation Fund (UIF) project by SRUC and SAC Consulting, looking at the future collaboration opportunities between SRUC and the Seaweed and Agri-food sectors in the following areas 1. Seaweed as an innovative ingredient in food products 2. Seaweed as a fertiliser for crops 3. Seaweed as an additive in Animal feed to reduce methane emissions |
| Year(s) Of Engagement Activity | 2021,2022 |
| Description | itv NEWS |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Thousands of bugs discovered in cows stomachs 'could improve meat and dairy Meat and dairy products could be improved by thousands of bugs in cows' stomachs that have been found by scientists using special DNA technology. Researchers at the University of Edinburgh's Roslin Institute studied how microbes in a cow's rumen help cattle digest and extract energy from their food. Inside the first of a cow's four stomachs they found thousands of bacteria which are essential for livestock wellbeing and food production. Sorry, this content isn't available on your device. The cow rumen is a gift that keeps on giving Professor Mick Watson A special handheld device was then used to generate DNA and allow the team to completely sequence the genomes and shorten the data process. Professor Mick Watson, head of genetics and genomics at The Roslin Institute, said: "The cow rumen is a gift that keeps on giving. "We were surprised by how many completely new microbes we have discovered, which is far more than in our previous study. "The findings will inform studies of cow health and meat and dairy production for many years to come." Researchers studied samples from 283 cows and identified almost 5,000 new strains of microbes and more than 2,000 novel species. The study in numbers 283 cows studied Almost 5,000 new strains of microbes identified More than 2,000 novel species found University of Edinburgh The findings were made in collaboration with Scotland's Rural College (SRUC) and the Rowett Institute at the University of Aberdeen. Rainer Roehe, professor of animal genetics and microbiome at SRUC, said: "We've identified some 5,000 novel genomes of microbial species in the rumen that all play a vital role. "Not only do they enhance breeding and nutrition to reduce greenhouse gas emissions from cattle, they also improve production efficiency, product quality and animal health." The study is published in the journal Nature Biotechnology. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.itv.com/news/2019-08-12/thousands-of-bugs-discovered-in-cows-stomachs-could-improve-meat... |