Understanding the functional and genomic architecture of the rumen microbiome affecting performance traits in bovines
Lead Research Organisation:
Scotland's Rural College
Department Name: Research
Abstract
By 2050, the human population will grow to over 9 billion people, and in the same time frame, global meat production is set to increase by 73%. There is a need to increase the efficiency and sustainability of animal production, reduce waste in the food chain and ensure safe and nutritious diets in order to address this challenge. Rumen microbes confers a unique ability to convert human inedible high-fibre forage into nutrients the animal can absorb to produce high-quality proteins as meat and milk. However, intensive food production puts a strain on the environment, and there is a need to produce more food ethically and in a way that does not harm the environment. The project addresses these challenges by unravelling the functional and genomic architecture of the ruminal microbiome affecting performance traits of cattle. This information will be used to identify fundamental associations between the microbiome or its genes with animal performance traits and methane emissions. In this study we will sequence all microbial genomes - the metagenome - to describe the composition of the microbial community and its functional genes. The analysis will be based on a unique dataset of 288 experimental beef cattle, with rumen DNA samples and a large array of performance information (e.g. feed conversion efficiency, growth, body composition and meat quality) available. These data are structured by breeds and sire progeny groups to estimate the animal host genetic effects on the microbiome and microbial genes. The experimental data have been the basis of numerous publications in which it was shown that at the animal performance level, and for methane emissions, there are large differences between breeds, sire progeny groups and diets. Preliminary analysis for 8 of these animals suggests that there is a link between the abundance of the microbial community or microbial genes and animal performance traits and methane emissions. However, to understand the function and genomic architecture of the ruminal microbiome, analysis of the full sample set is necessary. Algorithms will be developed to predict animal performance, e.g. feed conversion efficiency and methane emissions from the abundance of the microbial community and genes. These high value, but costly-to-measure traits could then be predicted by analysing the rumen microbiome (sampled via stomach tube on live animals or in the abattoir). However, to verify the associations between the rumen microbiome and performance traits, we need basic knowledge about the functional and genomic architecture of the microbiome. Additionally, microbial biomarkers to predict e.g. feed conversion efficiency could be identified. Due to the unique structure of the data in sire progeny groups and diets, we will be able to predict the host genetic and nutritional effect on the microbial community and microbial genes. This structure can also be used in the network analysis to identify animal genetic effects on the functional and genomic architecture of the microbiome. The project will provide unprecedented new knowledge of the genomic and functional architecture of the microbiome and its impact on performance traits and methane emissions as well as the interaction with animal genetics and nutrition. We will compare the functional and genetic architecture of the microbiome in beef cattle with that of other species to provide insights about the microbiome of different species, in particular humans. By understanding host genetic effects on the rumen microbiota and associations with body composition, we expect to provide new insights for human personalised medicine approaches to reduce obesity.
Technical Summary
Rumen microbial fermentation confers a unique ability to efficiently convert human inedible feed into foods with high nutritional value (e.g. meat, milk). However, there is a disadvantage from the environmental and energetic efficiency point of view, in that microbial fermentation also results in methane production. There is a large variation between animals in feed conversion efficiency and methane emissions, so that the substantial lack of knowledge about the functional and genomic architecture of the rumen microbiome has to be closed to efficiently breed and feed those animals. We will use deep metagenomic sequencing to gain insight into the functional and genomic architecture of the rumen microbiome, identifying the key microbial taxa and genes. Our approach will use highly-phenotyped beef cattle (n=288) to discover and prioritise putative links between the microbiome and phenotypic performance. Host genetic and nutritional effects on the microbiome will be estimated utilising the unique structure of experimental data, including different sire progeny groups and diets. Preliminary analysis suggests a link between the microbiome, phenotypic performance, animal genetics and nutrition, but was not able to provide detailed information about the functional and genomic architecture of the ruminal microbiome affecting performance traits and whether and how these interact with the host animal and nutrition. This study will provide substantial insight into the structure and function of the microbiome and identity novel microbial genes. Based on the abundance of the microbial community and genes, the research will provide novel functional and genetic networks to explain the link between the microbiome, phenotypic performance and host genetics or nutrition (e.g. the cross-talk between host and microbiome). Comparative functional genomics will broaden the potential applications of the research.
Planned Impact
The beneficiaries of this research will include academic scientists, farmers, the livestock breeding and feed industries, national governments, climate scientists, environmentalists and the general public. The FAO predicts that by 2050, the human population will grow to over 9 billion people, and in the same time frame, global meat consumption is projected to increase by 73%. In order to address food security, as well as economic and environmental impacts of food production, sustainable intensification has been suggested by Godfray et al. (2010) - with genetic improvement of feed conversion efficiency of highest importance in farm animals. Rumen microbial fermentation confers a unique ability to efficiently convert human inedible feed (e.g. high-fibre forage) into food products, such as meat and milk, of high nutritional value. Performance traits, such as feed efficiency, vary substantially between cattle so that genetic improvement and nutritional intervention could have a substantial effect on the efficiency of using limited feed resources, as well as a major financial impact since feed is the largest variable cost in production. Furthermore, rumen fermentation contributes to greenhouse gas (GHG) emissions, in particular methane. Any marginal reduction in GHG emissions, achieved through genetic improvement, has the potential to contribute significantly to UK Climate Change Act commitments, including the need for an 11% reduction in agricultural emissions by 2020. Using animal breeding and nutritional interventions to alter the rumen microbiome is expected to improve feed efficiency, growth, body composition, meat quality or animal health and thus contribute to address the overall economic and environmental challenges. The academic partners (SRUC and Roslin Institute) have excellent links to the cattle breeding and feed industries, farmers and the entire food chain. They will ensure that any immediate impacts can be passed on, once IP has been suitably protected.
Overall, the research will deliver substantial contributions to fundamental understanding of the functional and genomic architecture of the rumen microbiome in bovines, whilst also offering insights for other ruminant species or monogastric species including humans. In particular, it will provide unprecedented new knowledge about the genomic and functional architecture of the microbiome and its impact on performance traits and methane emissions that will set the direction for animal breeding programmes and novel animal feeding strategies.
Comparative functional genomics will be used to uncover differences and similarities in functional and genetic architecture between species, providing unprecedented knowledge about the microbiome and host-microbiome interactions across species. In particular, we foresee longer-term benefits for research on host genetic effects on the rumen microbiota and its association with body composition (e.g. for human personalised medicine approaches to reduce obesity).
We will realise academic impact by publication of papers in high-impact peer-reviewed journals (open-access where possible), by presentations at scientific meetings and through deposition of datasets in public databases. We will also publish articles in trade journals to ensure that our findings are communicated to our stakeholders. SRUC and RI will present the project at public science events, such as the Roslin Open Doors Day, ensuring the general public are aware of our research and its importance. We will keep policy makers aware of the research findings and our appraisal of potential to help meet climate change targets in the medium- and longer-term. Significant findings will be communicated to the industry and general public through press releases and information on a specific project website hosted by SRUC.
Overall, the research will deliver substantial contributions to fundamental understanding of the functional and genomic architecture of the rumen microbiome in bovines, whilst also offering insights for other ruminant species or monogastric species including humans. In particular, it will provide unprecedented new knowledge about the genomic and functional architecture of the microbiome and its impact on performance traits and methane emissions that will set the direction for animal breeding programmes and novel animal feeding strategies.
Comparative functional genomics will be used to uncover differences and similarities in functional and genetic architecture between species, providing unprecedented knowledge about the microbiome and host-microbiome interactions across species. In particular, we foresee longer-term benefits for research on host genetic effects on the rumen microbiota and its association with body composition (e.g. for human personalised medicine approaches to reduce obesity).
We will realise academic impact by publication of papers in high-impact peer-reviewed journals (open-access where possible), by presentations at scientific meetings and through deposition of datasets in public databases. We will also publish articles in trade journals to ensure that our findings are communicated to our stakeholders. SRUC and RI will present the project at public science events, such as the Roslin Open Doors Day, ensuring the general public are aware of our research and its importance. We will keep policy makers aware of the research findings and our appraisal of potential to help meet climate change targets in the medium- and longer-term. Significant findings will be communicated to the industry and general public through press releases and information on a specific project website hosted by SRUC.
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
Auffret MD
(2017)
Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets.
in Frontiers in microbiology
Duthie CA
(2017)
The impact of divergent breed types and diets on methane emissions, rumen characteristics and performance of finishing beef cattle.
in Animal : an international journal of animal bioscience
Duthie CA
(2018)
The effect of dietary addition of nitrate or increase in lipid concentrations, alone or in combination, on performance and methane emissions of beef cattle.
in Animal : an international journal of animal bioscience
Duthie CA
(2016)
Impact of adding nitrate or increasing the lipid content of two contrasting diets on blood methaemoglobin and performance of two breeds of finishing beef steers.
in Animal : an international journal of animal bioscience
| Description | Key findings associated with this award are as follows: • Two hundred and four genes associated with antimicrobial resistance (AMR), colonisation, communication or pathogenicity functions were identified in the rumen of beef cattle. Both the diversity and abundance of these genes were higher in cattle offered concentrate-based (mainly grains) compared to forage-based (mainly grass silage) diets. Chloramphenicol and microcin resistance genes were dominant in samples from forage-fed animals, while aminoglycoside and streptomycin resistances were enriched in concentrate-fed animals. The concentrate-based diet also increased the relative abundance of Proteobacteria, which includes many animal and zoonotic pathogens. In conclusion, diets with high levels of fibrous forage components would be recommended over those with high grain components to lower the abundance and diversity of AMR genes and to avoid rumen microbiome dysbiosis associated with pathogenic species, particularly Proteobacteria. A high ratio of Proteobacteria to (Firmicutes Bacteroidetes) was confirmed as a good indicator for rumen dysbiosis. Finally, network analysis demonstrated that the resistance/pathogenicity genes are potentially useful as biomarkers for health risk assessment of the ruminal microbiome. These results will help to improve policies about antimicrobial treatments in beef cattle production and avoid AMR gene transmission to bovine-associated human pathogens. Further detailed information is presented in the publication Auffret et al. (2017). • We identified and validated robust rumen microbial biomarkers for methane emissions in diverse cattle breeds offered a series of different diets. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane provided the dominant biomarkers of methane emissions and methanogens were the microbial populations closely correlated with methane emissions. Microbial genes involved in the methane synthesis pathway explained a higher proportion of variation in methane emissions than using microbial community profile information. These results confirmed the advantage of using these genes as robust biomarkers of methane emissions. The presence of the lactate utilizing Megasphaera genus within the robust phylogenetic biomarkers that were negatively correlated with methane emissions highlighted the importance of lactate metabolism controlling rumen fermentation and production of hydrogen and specific volatile fatty acid and ultimately reducing methane emissions. This study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of methane emissions across diverse production systems and environments, which can be used for breeding and nutritional intervention to mitigate methane emissions from ruminants. The results have been published in Auffret et al. (2018a). • Our network and partial least squares analyses of the rumen microbiome showed that bacterial and fungal communities and microbial genes associated with nutrient metabolism and Nitrogen assimilation explain most of the differences between low and high methane emitters. These bacterial and fungal communities and microbial genes are therefore, important for prediction of methane emissions from cattle. These results have been presented at the BSAS conference by Auffret et al. (2018b). This research shows again that microbiome information is highly informative to predict methane emissions. Therefore, the proposed research to identify the host genetic effects on the bacteria and fungi communities and their microbial genes are of substantial interest for the research community and the animal breeding industry. • Our results revealed that rumen microbial gene abundances (RMGA) are good predictors for feed conversion ratio (FCR) and its components daily feed intake (DFI), average daily gain (ADG) explaining 63 to 73% of their variation (Lima et al., 2019). These amounts of explained variation were depending on the trait predicted by the abundancies of 14 to 20 rumen microbial genes. FCR and ADG were influenced partly by the same microbial genes and combined in the same microbial network clusters. The results indicate the high potential of RMGA to predict difficult and costly to measure trait such as feed conversion efficiency, but have to be confirmed in practical breeding programmes (Roehe et al., 2018). In addition, the available data is not large enough to provide the statistical power to identify significant host genetic effects on the association of RMGA with performance traits. However, this was also not the aim of this on-going BBSRC project because it focuses on the understanding of the functional and genomic architecture of the rumen microbiome affecting performance traits in bovines. • The cow rumen is adapted for the breakdown of plant material into energy and nutrients, a task largely performed by enzymes encoded by the rumen microbiome. We assembled 913 bacterial and archaeal genomes from over 800 Gb of rumen metagenomic sequence data derived from 43 Scottish cattle. Most of these genomes represent previously un-sequenced strains and species. The draft genomes contain over 69,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in public databases. Inclusion of the 913 genomes presented here improves metagenomic read classification by sevenfold against our own data, and by five-fold against other publicly available rumen datasets. Thus, our dataset substantially improves the coverage of rumen microbial genomes in the public databases and represents a valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome (Stewart et al., 2018). Using whole metagenomics sequence of rumen samples from 284 cattle, we achieved to assemble 4,941 metagenome-assembled genomes (MAGs) of microbes never identified before. These novel microbial genomic and protein resources will provide a fundamental basis for studies to improve our understanding of functions of the rumen microbiota. This information can then we used for breeding purposes or dietary intervention for e.g. to mitigate methane emissions, improve feed conversions efficiency and animal health (Steward et al. 2019). Auffret, M.D., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., Wallace, R.J., Freeman, T.C., Stewart, R., Watson, M., Roehe, R. 2017. The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle. Microbiome 5, 159. Auffret, M.D., Stewart, R., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., Wallace, R.J., Freeman, T.C., Snelling, T.J., Watson, M., Roehe, R. 2018a. Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos Taurus breeds and basal diets. Front. Microbiol. 8, 2642. Auffret M D, Martínez-Álvaro M, Wallace R J, Freeman T C, Blasco A, Watson M and Roehe R. 2018b. Network analysis to study ruminal microbial community and functional microbial gene interactions associated with methane emissions in beef cattle In British Society of Animal Science (BSAS) Annual Conference, Dublin, Ireland. Roehe, R., Auffret, M.D., Southwell, A.J, Duthie, C-A., Rooke, J.A., Wallace, R.J., Freeman, T.C., Snelling, T.J, Watson, M., Dewhurst, R.J. (2018). The potential of using rumen microbial gene abundances to improve feed efficiency in beef cattle. Proceedings of the 11th World Congress on Genetics Applied to Livestock Production (WCGALP), Aukland, New Zealand. Stewart, R.D., Auffret, M.D., Warr, A., Wiser, A.H., Press, M.O., Langford, K.W., Liachko, I., Snelling, T.J., Dewhurst, R.J., Walker, A.W., Roehe, R., Watson, M. 2018. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nature Communication 9, 870. Stewart, R.D., Auffret, M.D., Snelling, T.J., Roehe, R., Watson, M. 2019. Compendium of 4941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. Nature Biotechnology 37, 953-961. |
| Exploitation Route | The findings can be used for breeding, dietary intervention, probiotics, prebiotics and drug development to improve animal performance and health. Most of the microbes and microbial enzymes uncovered have never been sequenced before and may have potential uses in the biofuels and biotechnology industries. |
| Sectors | Agriculture Food and Drink Communities and Social Services/Policy Environment Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| URL | https://scholar.google.co.uk/citations?user=iYPE0ZwAAAAJ&hl=en |
| Description | The beneficiaries of this research results will be farmers, the livestock breeding and feed industries, national governments, environmental activist on climate change, environmentalists and the general public (health). • The emergence and spread of antimicrobial resistance (AMR) of pathogenic bacteria is an increasing medical and veterinary problem and the most urgent current threat to human and animal health. Our research provides an improved understanding of the abundance of antimicrobial resistance genes and genes associated with microbial colonisation and pathogenicity in the animal foregut (rumen). Dietary intervention is expected to have a major role in reducing the contribution of animal production to AMR of pathogenic bacteria. The results will help to improve policies about antimicrobial treatments in cattle production and to help avoid AMR gene transmission to bovine-associated human pathogens. • 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 used by the feed industry to develop feed additives to mitigate methane emissions from cattle. • Cattle and other food-producing ruminants are of vital importance for human food security. In order 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 reduced cost of production of animals, improves the use of limited feed resources and mitigates the methane emissions per kg product (meat or milk). • 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. Our study also identifies 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. We inform 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 general 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 general public through press releases and information on a specific project website hosted by SRUC. The outcomes of this project resulted in very successful further research of BBSRC project BB/S006567/1. Auffret, M., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., Freeman, T.C., Watson, M., Wallace, R.J., Roehe, R. (2017). Impact of diet on the diversity of resistance and pathogenicity related genes in the rumen microbial community of apparently healthy cattle. Proceedings of the British Society of Animal Science, Chester, Cambridge University Press, UK. Auffret, M.D., Duthie, C-A., Rooke, J.A., Freeman, T.C., Dewhurst, R.J., Watson, M., Roehe, R. (2017). Diet affects the dominance of antimicrobial resistant genes in the rumen microbial community of cattle. 68th Annual Meeting of the European Federation of Animal Science, Tallinn, Estonia. Roehe, R., Auffret, M.D., Duthie, C-A., Rooke, J.A., Freeman, T.C., Watson, M., Wallace, R.J., Dewhurst, R.J. (2017). Prediction of methane emissions and feed conversion efficiency of beef cattle based on the rumen microbial community at phylum or genus level. Proceedings of the British Society of Animal Science, Chester, Cambridge University Press, UK. Wassan, J.T., Wang, H., Browne, F., Walsh, P., Kelly, B., Palu, C., Konstantinidou, N., Roehe, R., Dewhurst, R. J., Zheng, H. (2017). An Integrative Approach for the Functional Analysis of Metagenomic Studies. Intelligent Computing Theories and Application. In: 2017 International Conference on Intelligent Computing, Springer. p. 421-427. Haiying Wang, H., Zheng, H., Dewhurst, R.J., Roehe, R. (2017). Microbial co-presence and mutual-exclusion networks in the Bovine rumen microbiome. In: 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE. p. 114-119. Haiying Wang, H., Zheng, H., Dewhurst, R.J., Roehe, R. (2017). Microbial co-presence and mutual-exclusion networks in the Bovine rumen microbiome. In: 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE. p. 114-119. Roehe, R., Auffret, M.D., Southwell, A.J, Duthie, C-A., Rooke, J.A., Wallace, R.J., Freeman, T.C., Snelling, T.J, Watson, M., Dewhurst, R.J. (2018). The potential of using rumen microbial gene abundances to improve feed efficiency in beef cattle. Proceedings of the 11th World Congress on Genetics Applied to Livestock Production (WCGALP), Auckland, New Zealand. Auffret, M., Martinez-Alvaro, M., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., Wallace, R.J., Freeman, T.C., Stewart, R.D., Watson, M., Roehe, R. (2018). Changes in rumen microbiome interaction explain the methane emissions differences in beef cattle. In: 69th Annual Meeting of the European Association of Animal Production, Dubrovnik, Croatia, p. 205. Auffret, M., Stewart, R.D., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., Wallace, R.J., Freeman, T.C., Snelling, T.J., Watson, M., Roehe, R. (2018). Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos Taurus breeds and basal diets. Proceedings of the British Society of Animal Science, Dublin, Ireland, UK. Auffret, M., Stewart, R.D., Dewhurst, R.J., Duthie, C-A., Rooke, J.A., Wallace, R.J., Freeman, T.C., Snelling, T.J., Watson, M., Roehe, R. (2018). Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos Taurus breeds and basal diets. Proceedings of the British Society of Animal Science, Dublin, Ireland, UK. Auffret, M., Martinez-Alvaro, M., Wallace, R.J., Freeman, T.C., Blasco, A., Watson, M., Roehe, R. (2018). Network analysis to study ruminal microbial community and functional microbial gene interactions associated with methane emissions in beef cattle Proceedings of the British Society of Animal Science, Dublin, Ireland, UK. Lima, J., Auffret, M.D., Stewart, R.D., Dewhurst, R.J., Duthie, C-A., Snelling, T.J., Walker, A.W., Freemann, T.C., Watson, M., Roehe, R. (2019). Investigating the impact of rumen microbial genes on feed conversion efficiency, growth rate and feed intake in beef cattle. In: Proceedings of the British Society of Animal Science (BSAS), Edinburgh, UK. Auffret, M.D., Stewart, R.D., Dewhurst, R.J., Duthie, Freemann, T.C., Watson, M., Roehe, R. (2019). Impact of rumen microbiome-host interaction on feed efficiency of beef cattle explained by microbial adhesion and mucosa interaction genes. In: Proceedings of the British Society of Animal Science (BSAS), Edinburgh, UK. Roehe, R., Martinez-Alvaro, M., Auffret, M.D., Duthie, C-A., Stewart, R.D., Dewhurst, Watson, M., Dewhurst, R.J. (2019). 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), Edinburgh, UK. Wassan, J.T., Zheng, H., Wang, H., Browne, F., Walsh, P., Manning, T., Dewhurst, R.J., Roehe, R. (2019). A Phylogeny-aware Feature Ranking for Classification of Cattle Rumen Microbiome. In: 2019 International Conference on Bioinformatics and Biomedicine (BIBM), IEEE. p. 1900-1906. Further publications building on the research of this project are provided in the narrative impact section of the BBSRC project BB/S006567/1. |
| First Year Of Impact | 2017 |
| Sector | Agriculture, Food and Drink,Communities and Social Services/Policy,Environment,Manufacturing, including Industrial Biotechology |
| Impact Types | Societal Economic Policy & public services |
| Description | SRUC Beef Research Stakeholder Event |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | Impact of the microbiome on feed efficiency and mitigation of methane emissions in beef cattle was presented and that the microbiome can be changed by breeding and nutritional intervention. The will have impact on sustainable intensification of beef production in the UK and worldwide, mitigations of Greenhouse Gas emissions and food security. |
| 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 | Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria |
| Amount | £390,943 (GBP) |
| Funding ID | BB/S006567/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 01/2022 |
| 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 | 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 | 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 under accession PRJEB10338 |
| Description | All raw metagenomic sequence data of the DNA extracted from rumen samples of bovine have been submitted to the European Nucleotide Archive under project PRJEB21624. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | The sequence data were used to identify microbial genes and their abundances. 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 |
| URL | https://www.ebi.ac.uk/ena/data/search?query=PRJEB10338 |
| Title | European Nucleotide Archive under project PRJEB21624 |
| Description | All raw sequence data have been submitted to the European Nucleotide Archive under project PRJEB21624. RUG and hRUG assembled genomes and proteomes are available from ENA and also from Edinburgh DataShare DOI:10.7488/ds/2296) All other relevant data are available in this article and its Supplementary Information files, or from the corresponding author upon request. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Our research paves the way for research to understand which types of microbe - 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 nutritional intervention. Our study also identifies 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. |
| URL | https://www.ebi.ac.uk/ena/data/view/ERX2087036 |
| Title | MOESM1 of Correction to: The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle |
| Description | Additional file 1: Figure S1.Relative abundance (%) of 20 groups of functional genes representing 204 selected genes (number of animals, n = 50 samples). The sum of the relative abundance (%) of genes grouping within the same function is shown in this figure. Figure S2A. Total abundance of 204 selected genes based on diet treatments (n = 50). *P value |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/MOESM1_of_Correction_to_The_rumen_microbiome_as_a_reser... |
| Title | MOESM1 of Correction to: The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle |
| Description | Additional file 1: Figure S1.Relative abundance (%) of 20 groups of functional genes representing 204 selected genes (number of animals, n = 50 samples). The sum of the relative abundance (%) of genes grouping within the same function is shown in this figure. Figure S2A. Total abundance of 204 selected genes based on diet treatments (n = 50). *P value |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/MOESM1_of_Correction_to_The_rumen_microbiome_as_a_reser... |
| Description | Development of an Easy-to-use Metagenomics Platform for Agricultural Science |
| Organisation | NSilico Lifescience Ltd |
| Country | Ireland |
| Sector | Private |
| PI Contribution | Experimental sampling, expertise in gut microbiology, animal genetics, animal nutrition, animal models of methane production and performance traits and statistical analysis. |
| Collaborator Contribution | Expertise in bioinformatics and machine learning. |
| Impact | The outputs and outcomes are presented in the following presentations: I) Konstantinidou, N., Walsh, P., Lu, X., Bekaert , M., Lawlor, B., Kelly, B., Zheng, H., Browne, F., Dewhurst, R., Roehe, R., Wang, H. (2016). MetaPlat: A cloud based platform for analysis and visualisation of metagenomics data. In: CERC 2016 Collaborative European Research Conference. Cork, Ireland. II) Browne, F., Haiying Wang, Huiru Zheng, R. Roehe, R. J. Dewhurst, and P. Walsh. 2016. A network analysis of methane and feed conversion genes in the rumen microbial community. In: 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE. p. 1477-1484. III) Wang, H., H. Zheng, F. Browne, R. Roehe, R. J. Dewhurst, F. Engel, M. Hemmje, and P. Walsh. 2016. Analysis of rumen microbial community in cattle through the integration of metagenomic and network-based approaches. In: 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE. p. 198-203. |
| Start Year | 2015 |
| 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 | 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 | Award winning Scottish research could pave the way for 'low-emission cattle' |
| 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 | Award winning Scottish research could pave the way for 'low-emission cattle'A Scottish study that potentially paves the way for the breeding of low-emission livestock has won an internationally respected research prize. The study, the result of a collaboration involving Scotland's Rural College (SRUC), The University of Edinburgh's Roslin Institute and The University of Aberdeen, identified a genetic link between host animals, the microbial community in their digestive tract and the methane that they produce. The findings could ultimately help farmers respond to the growing global demand for meat, while minimising the associated environmental impact. The results were reported in the international research journal PLOS Genetics and won the journal's 2017 annual prize for outstanding research. Researchers have for some time discussed the possibility of breeding cattle that generate less methane but it was not known to what extent the cattle genome would influence the make-up of gut microbes. In the winning study, the researchers explored the interactions between an animal's genetic background, its diet and the composition of its microbial community. They identified microbial community profiles that can be used to recognise cattle that use their feed more efficiently while also emitting less methane. Professor Rainer Roehe from the Future Farming Systems research group of Scotland's Rural College said: "In our research, we were surprised to find that the host animal's genetics shapes its own microbiome to the extent that it does and that this is highly informative when predicting traits like methane emissions and feed conversion efficiency. "In the future we expect that the use of gastrointestinal microbial information will have a great impact in animal breeding and that it will also be of great value in medicine and nutritional recommendations that can be tailored to the individual in many different species, including humans." Professor John Wallace from the University of Aberdeen Rowett Institute said: "I am delighted to have been involved in this project, what we - Rowett, SRUC and Roslin, combining our expertise in microbial ecology, animal genetics and bioinformatics, respectively - achieved is very much a first. "The results have huge implications for breeding farm animals on the basis of their gut microbes, for better digestion of the feed, lower greenhouse gas emissions and many other possible applications." Professor Mick Watson, Director (Agrigenomics), Edinburgh Genomics at the University of Edinburgh's Roslin Institute said: "We employed a relatively new technique called metagenomics, which involves analysing the genetic composition of an entire organism including the microbes that exist within it. "Our study demonstrates the power of combining this approach with big data analysis tool to solve a real world problem - in this case breeding more efficient animals." The PLOS Genetics prize comes with a $5,000 award to the authors. The public nominates worthy papers from the previous year and the PLOS Genetics Editors-in-Chief and Senior Editors make their final selection based on the scientific merit and community impact of the research. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.sruc.ac.uk/news/article/1953/award_winning_scottish_research_could_pave_the_way_for_low-... |
| 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 | Battle of the belch - cutting-methane-from cattle |
| 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 | Reuters media cover of our microbiome research to improve feed conversion efficiency and to reduce methane emissions. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.reuters.com/video/2017/12/04/battle-of-the-belch-cutting-methane-from?videoId=373095957 |
| 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 | DNA study of cow stomachs could aid meat and dairy production |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | To inform Scottish Farmer about the our research. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.thescottishfarmer.co.uk/news/16080592.DNA_study_of_cow_stomachs_could_aid_meat_and_dairy_... |
| Description | DNA study of cow stomachs could aid meat and dairy production |
| 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 | DNA study of cow stomachs could aid meat and dairy production Published Wednesday, 28th February 2018 in Research news Meat and milk production from cattle could one day be boosted, thanks to analysis of microbes in cows' stomachs. The study, carried out by researchers from SRUC and the University of Edinburgh's Roslin Institute, paves the way for research to understand which types of microbe - such as bacteria - are best at helping cattle to extract energy from their food, experts say. It also identifies enzymes that are specialised for breaking down plant material, which could help in the quest to develop new biofuels. The researchers focused on microbes found in a cow's rumen - the first of its four stomachs. The rumen is home to diverse strains of microorganisms, such as bacteria, archaea and fungi, which help the animal to extract energy and nutrients from its food. The team used an advanced technique called metagenomics, which involves analysing the genetic composition all of the microbes that exist within an organism, in this case a cow. They studied samples of rumen gut contents from 43 cows and identified 913 diverse strains of microbes living in the rumen. Most of the microbes uncovered have never been seen before and may have potential uses in the biofuels and biotechnology industries. By analysing their genetic information, the team pinpointed previously unknown enzymes that can extract energy and nutrition from plant material. Beef and dairy cattle, and other milk-producing ruminants, provide food and nutrition to billions of people worldwide. Understanding how these animals convert plant-based diets into energy will be vital for securing the future of the world's food supplies, experts say. The research, published in the journal Nature Communications, was carried out in collaboration with experts at The Rowett Institute at the University of Aberdeen. The Roslin Institute receives strategic funding from the Biotechnology and Biological Sciences Research Council. Professor Rainer Roehe from SRUC said: "The newly identified microbial species in the rumen of beef cattle will greatly improve our understanding of how the rumen microbial ecosystem works. Using breeding and nutritional interventions, we will be able to use this information to help improve cattle health and performance throughout the world." Professor Mick Watson, of the University of Edinburgh's Roslin Institute, said: "This has been a truly fascinating study, and really we are only beginning to understand what these microbes do. The fact most of them were very different to microbes that have already been discovered surprised us, so we just can't wait to study them further. If we can improve the efficiency of digestion in cows and other ruminants, we may be able to produce more food for people whilst using fewer resources. This is a key aim of improving global food security." |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.sruc.ac.uk/news/article/2029/dna_study_of_cow_stomachs_could_aid_meat_and_dairy_producti... |
| 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 | Gassy Cows Warm The Planet. Scientists Think They Know How To Squelch Those Belches |
| 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 | Media cover of the Research on the selection of cattle for low methane emissions. Gassy Cows Warm The Planet. Scientists Think They Know How To Squelch Those Belches, Cattle pass a lot of gas, and the methane from their flatulence and especially, their belches, is an expanding burden on the planet. The greenhouse gas has a warming potential 25 times that of carbon dioxide. Livestock account for 14.5 percent of all greenhouse gas emissions, with over half of that coming from cattle, according to a 2013 report from the United Nations' Food and Agriculture Organization. Given that, some environmentalists might choose to eschew milk and beef, but scientists think they've figured out a way for us to one day have our cattle and eat them, too - gas-free. The key is breeding less-gassy cattle, and scientists now know it's possible because of a study that won the Public Library of Science Genetics Award on Thursday. The study, originally published in the journal PLoS Genetics last year, showed that a cow's genetics determine which microbes populate its gut - and some of those microbes produce the methane that eventually makes its way into the atmosphere. "The cow genetics will dictate which bacteria they will have in their own stomach," says Filippo Miglior, a geneticist at Canadian Dairy Network and the University of Guelph, who did not work on the study. "[The research team] proved that." The researchers divided 72 cows into nine groups. Each group consisted of siblings - cows similar to each other in their genetic makeup. Half of the cows in every group got one diet, and the other half got a different diet. To measure how much methane they were emitting, the researchers shut each cow in a chamber to suck up its gasses coming. It turned out that the different groups differed in the amounts of methane they emitted - by a lot. "The highest [group emitted] 200 grams per day, and the lowest [group's] methane emission was at 140 grams per day. So there is a large difference," says Rainer Roehe, the lead author on the study and a geneticist at Scotland's Rural College. Roehe says the different diets made a difference in how much methane the cows emitted, but when they ranked the cow families based on how much gas they were expelling, the least gassy family emitted the least methane no matter what they ate. On the flipside, the cows in the family that gave off the most gas were still the biggest offenders regardless of what they were eating. Roehe says that suggests genetics is playing a big role in shaping which microbes exist in any individual cow's gut and is the reason why some cows belch and fart less than others. "It's very exciting because we did not know that the microbial community is so heavily influenced by the host genetics," he says. "This gives an opportunity to select animals based on those genetics and thus reduce methane emissions." But it won't be that easy to do, says Migilor. Putting cows into a chamber that analyzes their outgassing is extremely expensive. "To measure methane emissions, it can cost $700 to $1,000 per cow," Miglior says. That's a lot of money for a breeder to blow through just looking for an environmentally friendly stud. But Roehe and his team think they have a solution for that, too. The researchers took microbial samples straight out of each cows' guts. When they analyzed the samples, Roehe and his colleagues found 20 microbial genes that give bacteria the ability to produce methane. The abundance of those genes in a cow's gut correlated strongly with how much methane the cow actually gave off. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.youtube.com/watch?v=1hu-3jZJKhw |
| Description | Genetics and microbiome of cattle methane production: 2017 PLOS Genetics Research Prize Winning Research |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | The PLOS Genetics Editors-in-Chief and Senior Editors would like to congratulate: Rainer Roehe, Richard J. Dewhurst, Carol-Anne Duthie, John A. Rooke, Nest McKain, Dave W. Ross, Jimmy J. Hyslop, Anthony Waterhouse, Tom C. Freeman, Mick Watson and R. John Wallace, authors of the article chosen as the recipient of the 2017 PLOS Genetics Research Prize: 'Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance' In the winning research article [1], Rainer Roehe and colleagues from Scotland's Rural College and the Universities of Edinburgh and Aberdeen set out to understand how the host genetics affects the rumen microbiome, and thus influence rumen microbial methane production and rumen microbial digestion. Anthropogenic production of methane contributes significantly to greenhouse gases and global warming, for which emissions from ruminant digestive tracts, e.g. gassy cows, are a major source. In their article, Rainer Roehe and colleagues tackle the genetics of cattle methane production with a metagenomic approach. This is a daunting research question: methane is produced by methanogenic archaea in the rumen of cattle, and therefore might be influenced by diet, host genetic factors, and the composition of the microbiome. The authors investigated the relative contributions of these factors by associating methane emissions measured individually in respiration chambers with genetic background (sire progeny groups) and diet. The analysis indicated a significant sire genetic effect on their progenies' methane production and thus a contribution of the host genome. The authors also used the power of cattle family structures to identify that a fraction of the variation in the composition of the microbial community is controlled by the host genome. Roehe et al. further showed that the composition of the microbial community and particularly of the microbial genes is highly correlated with methane emissions. Importantly, the authors note that this metagenomic profile could provide a selection parameter that is much easier to implement in a real breeding program than direct measurement of methane emissions, which is difficult and expensive. This study paves the way for an approach to reduce methane produced by cattle farming using modern breeding approaches. It should be noted that the study is necessarily based on a relatively small number of animals. The question of whether selection for a particular microbiome composition in cattle has any adverse effects, e.g. on the health of the animals, will need to be investigated. Nonetheless, the study by Roehe et al. advances our understanding of how genes and environment interact in the cattle gut, and provides a plausible scenario for an application that could greatly benefit society. Corresponding author, Rainer Roehe says: "We are honored to receive this award from the high impact journal PLOS Genetics. Our research article answered the fundamental question that the host genetics shapes its own microbiome. In addition, the paper provides many new results, in particular based on the abundance of microbial genes to be used to identify mechanisms of the interactions between microbiome and host. In the future, we expect that the use of gastrointestinal microbial gene information will have a large impact in animal breeding, personalized medicine, nutritional recommendations, etc., in many different species." The PLOS Genetics Research Prize was born from the editors' desire to recognize the outstanding work published in PLOS Genetics and launched in 2015 as part of the journal's 10-year anniversary celebrations. Members of the genetics community nominated their favourite Research Article published in PLOS Genetics in 2016, and the Senior Editors selected the winning article from these nominations, based on scientific excellence and the community impact of the work. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://blogs.plos.org/biologue/2017/09/21/genetics-and-microbiome-of-cattle-methane-production-2017-... |
| 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 | 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 | 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 | 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 | Research to breed more climate-friendly cattle selected for PLOS Genetics Research Prize |
| 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 | A study that identified a genetic link between host animals, the microbial community in their digestive tract, and the methane that they produce, has won the PLOS Genetics Research Prize for 2017. The winning research, a collaboration between Scotland's Rural College, The University of Edinburgh and The University of Aberdeen, UK was reported last year in PLOS Genetics. The prize is now in its third year and comes with a $5,000 award to the authors. The public nominates worthy papers from the previous year and the PLOS Genetics Editors-in-Chief and Senior Editors make their final selection based on the scientific merit and community impact of the research. Rainer Roehe and colleague's paper were selected in part, for its potential to reduce methane released from cattle and other livestock, which represents a significant portion of greenhouse gas emissions. Researchers have discussed the possibility of breeding cattle that generate less methane, but it was unknown to what extent a cattle's genome would influence the makeup of its gut microbes. In the winning study, the researchers explored the interactions between an animal's genetic background, its diet and the composition of its microbial community. They identified microbial profiles that can be used to recognize cattle that use their feed more efficiently while also emitting less methane. The study represents the first step toward breeding low-emission cattle, which will become increasingly important in the face of growing global demand for meat. The findings also support the idea that a host animal's genetics control the composition of its microbial community to a large extent. The work gives proof of principle that by determining the community or gene abundances of microbes in the gut, scientists can also gain information about certain traits relating to metabolism, health and behavior. Corresponding author, Rainer Roehe says: "We are honored to receive this award from the high impact journal PLOS Genetics. In our research, we were impressed to find that the host genetics shapes its own microbiome to that extent and that microbial gene abundances are so highly informative to predict traits like methane emissions and feed conversion efficiency. In the future we expect that the use of gastrointestinal microbial information will have a great impact in animal breeding, personalized medicine, nutritional recommendations, etc. in many different species." |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.eurekalert.org/pub_releases/2017-09/p-rtb091417.php |
| Description | Rumen genotyping advances could enhance cattle breeding |
| 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 | Future cattle selection decisions could extend to breeding for rumen microbiome characteristics, say researchers who have recently mapped more bovine rumen microbe genomes than ever before. A British study published this week (28 February) has doubled the number of rumen microbes sequenced and available on public databases. A multinational effort had previously logged 410 microbes, but following the study, published in Nature Communications, there are now 913 available for further research. This progress is still "early days", but could influence cattle breeding, bovine nutrition and even biofuel technology in the years ahead, researchers said. Led by researchers from the University of Edinburgh's Roslin Institute and Scotland's Rural College (SRUC), the study analysed rumen microbes in 43 commercial beef cattle (Limousin, Aberdeen Angus, Charolais) at the SRUC's Beef and Sheep Research Centre. New enzymes were discovered that allow bovines to extract energy and nutrition from forage, which the Roslin Institute said could lead to advances in the biofuels sector. Professor Mick Watson, Roslin Institute, said breeding companies are becoming increasingly interested in the rumen microbiome. He added that making selection decisions based on the genotype of rumen microbes could be a possibility in the future, but stressed there is a long way to go. "The study found different proteins to those studied before, there were lots of novel proteins in the Scottish beef cattle," he told Farmers Weekly. "Breeders and farmers are selecting cattle for beef performance traits and perhaps without knowing they are changing and adapting the rumen microbiome from generation to generation for feed efficiency and growth." Professor Rainer Roehe from SRUC said: "The newly identified microbial species in the rumen of beef cattle will greatly improve our understanding of how the rumen microbial ecosystem works. "Using breeding and nutritional interventions, we will be able to use this information to help improve cattle health and performance throughout the world." |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.fwi.co.uk/livestock/rumen-genotyping-advances-enhance-cattle-breeding |
| 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 | ScienceDaily publication of our rumen microbiome research |
| 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 | Our research was disseminated worldwide by ScienceDaily. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.sciencedaily.com/releases/2018/02/180228085347.htm |
| 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 | Scot scientists target climate-friendly cows to cut greenhouse gas 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 | Scot scientists target climate-friendly cows to cut greenhouse gas emissions. Work by Scottish scientists could see farms being stocked with climate-friendly cattle bred for their efficiency at turning fodder into meat while producing as little greenhouse gas as possible. Agriculture accounts for about a fifth of Scotland's climate warming emissions and methane makes up more than half of emissions from Scottish agriculture. Much of it is produced by livestock. Academics have for some time discussed the possibility of breeding cattle that generate less methane. Now researchers from Scotland's Rural College (SRUC), the University of Edinburgh's Roslin Institute and the University of Aberdeen have identified a link between an animal's genetic make-up, the bacteria in its digestive system and the amount of methane it produces. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.scotsman.com/news/environment/scot-scientists-target-climate-friendly-cows-to-cut-greenh... |
| 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 | Study of microbes found in cow stomachs could lead to energy extraction breakthrough, aiding in production of biofuels |
| 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 | To develop new techniques in maximizing food and fuel production in the modern age, researchers from The University in Edinburgh in the United Kingdom are turning to an unlikely source for answers: The living bacteria inside the guts of bovine animals. A new study claims that microbes may be the solution to figuring out how to improve production of meat and milk, as well as biofuels made from organic materials like corn. The focus of the study involved identifying which microbes in the stomachs of cows are most utilized for extracting energy from the foods they eat. It also looked at corresponding enzymes to determine how this energy conversion is catalyzed - both processes believed to hold the key to revolutionary developments in 21st-century resource creation. Led by scientists from the school's Roslin Institute, in conjunction with Scotland's Rural College (SRUC), the paper looked specifically at microbes living in the first stomach of cows, known as the rumen. Among the 43 cows they examined, the team identified 913 diverse strains of living microbes. A vast majority of these microbes have never before been identified, suggesting that there's a whole lot we don't know about the nature of the bovine gut microbiome. The enzymatic reactions were also eye-opening, revealing potential methods that humans can mimic to better extract energy and nutrition from plant material. The implications of all this for future advancements in fuel creation are enormous, experts claim. They say that beef and dairy production could be increased on a substantial scale, helping to provide more food and nutrition to the world's growing population. "This has been a truly fascinating study, and really we are only beginning to understand what these microbes do," stated Professor Mick Watson, one of the study's authors. "The fact most of them were very different to microbes that have already been discovered surprised us, so we just can't wait to study them further. If we can improve the efficiency of digestion in cows and other ruminants, we may be able to produce more food for people whilst using fewer resources. This is a key aim of improving global food security." Moral of the study: Nature almost always has the answer to humanity's practical problems. Cows are a perfect specimen for this type of research because they thrive on plant-based foods, converting it into the energy they need to produce milk and healthy meat. Gaining a better understanding of how their bodies do this just might be the key to developing an improved food production system for humans all over the world. "The newly identified microbial species in the rumen of beef cattle will greatly improve our understanding of how the rumen microbial ecosystem works," added Professor Rainer Roehe, another researcher involved with the project who believes that taking a page from nature's playbook is the best approach for humanity moving forward. "Using breeding and nutritional interventions, we will be able to use this information to help improve cattle health and performance throughout the world." |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://power.news/2018-03-20-study-of-microbes-found-in-cow-stomachs-could-energy-extraction-breakt... |
| Description | The potential of using rumen microbial gene abundances to improve feed |
| 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 | The main aim of this study was to elucidate whether rumen microbial gene abundances (RMGA) can be used to predict residual feed intake (RFI), feed conversion ratio (FCR) and its component traits: daily feed intake (DFI), average daily gain (ADG), and thus RMGA could be applied as indirect trait for breeding of feed efficiency in beef cattle. RMGA were generated by whole metagenomic sequencing of rumen microbial DNA samples from 42 beef cattle, with extreme low and high FCR, selected from two feed efficiency trials. The results of the PLS analysis indicated that RMGA showed substantial potential to be used as predictors for RFI, FCR and its components DFI and ADG explaining 55 to 73% of their variation. While only 12 and 23 microbial genes were significantly associated with RFI and DFI, respectively, there were 166 and 167 affecting ADG and FCR. RFI and DFI were influenced partly by the same microbial genes and combined in the same microbial network clusters as was also the case for FCR and ADG. The results elucidate the likely potential of RMGA to predict the difficult and costly to measure trait feed efficiency, but have to be confirmed under the more challenging conditions of practical breeding programmes. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://sefari.scot/document/roehe-r-2018-the-potential-of-using-rumen-microbial-gene-abundances-to-... |
| Description | Understanding the role of rumen microbes |
| 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 | New research that analyses microbes in cows' stomachs could help boost meat and milk production leading to greater food security in the future. Scientists from Scotland's Rural College (SRUC) and the University of Edinburgh's Roslin Institute undertook a study that could lead to research to understand which types of microbe, such as bacteria, are best at helping cattle to extract energy from their food, experts say. The initial study also identifies enzymes that are specialised for breaking down plant material, which could help in the quest to develop new biofuels. The researchers focused on microbes found in a cow's rumen which is the first of its 4 stomachs. The rumen is home to diverse strains of microorganisms, such as bacteria, archaea and fungi, which help the animal to extract energy and nutrients from its food. The team used an advanced technique called metagenomics, which involves analysing the genetic composition all of the microbes that exist within an organism, in this case a cow. In total, they studied samples of rumen gut contents from 43 cows and identified 913 diverse strains of microbes living in the rumen. Most of the microbes uncovered have never been seen before and may have potential uses in the biofuels and biotechnology industries. By analysing their genetic information, the team pinpointed previously unknown enzymes that can extract energy and nutrition from plant material. Beef and dairy cattle, and other milk-producing ruminants, provide food and nutrition to billions of people worldwide. Understanding how these animals convert plant-based diets into energy will be vital for securing the future of the world's food supplies, experts say. Understanding rumen microbial ecosystem The research, published in the journal Nature Communications, was carried out in collaboration with experts at The Rowett Institute at the University of Aberdeen. Professor Rainer Roehe from SRUC said: "The newly identified microbial species in the rumen of beef cattle will greatly improve our understanding of how the rumen microbial ecosystem works. "Using breeding and nutritional interventions, we will be able to use this information to help improve cattle health and performance throughout the world." Professor Mick Watson, of the University of Edinburgh's Roslin Institute, said: "This has been a truly fascinating study, and really we are only beginning to understand what these microbes do. The fact most of them were very different to microbes that have already been discovered surprised us, so we just can't wait to study them further. "If we can improve the efficiency of digestion in cows and other ruminants, we may be able to produce more food for people whilst using fewer resources. This is a key aim of improving global food security." |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.dairyglobal.net/Nutrition/Articles/2018/5/Understanding-the-role-of-rumen-microbes-28030... |
| 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 | World Angus Forum 2017 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the microbiome research associated with this award. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://worldangusforum2017.com/ |
| 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... |