Jan. 2012 – Dec. 2015 www.ruminomics.eu RuminOmics Connecting the animal genome, the intestinal microbiome and nutrition to enhance the efficiency of ruminant digestion and to mitigate the environmental impacts of ruminant livestock production, Coordinator: John Wallace Budget: EU contribution 5,95 M Participant no. Participant organisation name 1 (Coordinator) University of Aberdeen 2 Parco Tecnologico Padano, Lodi 3 Natural Resources Institute Finland, Jokioinen 4 Swedish University of Agricultural Sciences, Umeå 5 University of Nottingham 6 Institute of Animal Physiology & Genetics, Prague 7 Università Cattolica del Sacro Cuore, Piacenza 8 Centre National de la Recherche Scientifique, Grenoble 9 European Association of Animal Production 10 European Forum of Farm Animal Breeders 11 Quality Meat Scotland 1,5,11 3 2,7,9 6 4 8 10 http://3.bp.blogspot.com

RuminOmics - Aims of project Emissions Animal genetics Ruminal microbiome Tools Training Dissemination Does the animal itself determine its ruminal microbiome? If so, is this a heritable trait? How does nutrition affect this relationship? How do these interact to produce the emission phenotype?

Objectives - Experiments 1000 cows in UK, Italy, Sweden, Finland Methane N emissions Ruminal Animal FCE microbiome genotype Milk quality 20 cows in Sweden, Finland Impact of N, CHO, lipid nutrition 50 cows in UK, Italy, Sweden, Finland Full metagenome analysis of high and low emitters Rumen digesta transfer experiments Identical twins – unrelated cows Interspecies: cow-reindeer

Main achievements Extensive nutrition/performance/genetics/microbiome dataset; resource for researchers – still being analysed Tools: International ring test -> will lead to harmonization of methodology for microbiome studies Tapio I. et al.: Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community – PLoS ONE 2016, March 17 Metaproteomics’ practical usefulness is limited Milk fatty acids not strongly correlated with rumen microbiome or emissions (preliminary)

Main achievements Host effect on rumen microbiome not predictable in digesta exchange studies (composition in identical twins not more similar, large between animal variation in response), however some microbes show interesting pattern of host genetic control (e.g. Firmicutes) Potential to reduce emissions by nutrition rather limited (costs, ethics) GWAS results on cow genome regions associated with CH4 emissions, archaea/bacteria proportions, individual phyla (+ milk FAs) -> GEBV

Conclusions, 1000 cows study Relationships between emissions, digestion and efficiency are complex Generally more efficient cows produce more methane per unit of feed intake Evidence that methane emissions, feed efficiency and nitrogen efficiency are related to rumen microorganisms Relationship between milk production efficiency (kg energy-corrected milk per kg dry matter intake) and methane production (g methane per kg dry matter intake). Cows in the lower right quadrant are more efficient than average and produce less methane than average. -> opportunities to select cows with both lower methane emissions and higher feed efficiency

The systems biology challenge Genome sequence variation modification (epigenetic) Environment nutrition dieseases stress Genome expression transcription to mRNA ncRNA, miRNA translation to proteins protein modifications Proteome Metabolome Phenotype ? Rumen microbiome composition (taxa; genes) function (metatranscriptome, metaproteome)

Future challenges Feed efficiency and feed intake traits still challenging to improve, because difficulties in getting accurate phenotype measurements from large numbers of individuals Understanding the role of the microbiome Including biological background information and causal variants to genomic evaluation would improve predictions, reduce dependence on LD (-> across-breed) Difficult to pinpoint causative variants, most SNPs in GWAS studies map outside protein-coding regions Cattle functional regulatory elements have not been well annotated (-> FAANG) Epigenetic effects (-> FAANG) 27.5.2019

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