This project will integrate at the highest possible level expertise and technologies to increase the efficiency and decrease the environmental footprint of ruminant production, significantly advancing current knowledge in this sector. The project will exploit state-of-the-art –omics technologies to understand how ruminant gastrointestinal microbial ecosystems, or microbiomes, are controlled by the host animal and by the diet consumed, and how this impacts on greenhouse gas emissions, efficiency and product quality. New models and tools will be developed to enable the livestock industry to decrease environmental damage from methane and nitrogen emissions, and to improve efficiency of feed utilisation. A large-scale genetic association study involving 1000 dairy cows will relate feed intake, digestion efficiency, milk production/composition and methane emissions to the ruminal microbiome and host genome, leading to new indicator traits and tools for use in both traditional and genomic selection. Cow-reindeer metagenomic studies will establish how host species influence ruminal microbiology and function. Bovine twins studies will define how the rumen microbiome varies in an identical host genetic background. Nutrition work will assess how dietary oils, nitrogen and carbohydrates affect the ruminal microbiome and product quality. A meta-barcoding 16S rRNA analysis protocol will be developed to investigate ruminal microbiomes more accurately, rapidly and cheaply. Saliva and faeces will be analysed as possible tools for non-invasive assessment of ruminal microbiome and function. A novel method for on-farm methane analysis will be refined for easy application. Results will be publicly available through an online data warehouse that will provide tools to build new queries and create novel information. Transversal work packages include dissemination and industrial liaison, targeted towards the enlarged EU, and candidate and developing countries.