RuminOmics is a European Commission funded project that aims to connect the animal genome, gastrointestinal microbiomes and nutrition to improve digestion efficiency and the environmental impacts of ruminant livestock production. A major undertaking of the project was to take rumen digesta samples from 1000 dairy cows from herds kept in UK, Italy, Finland and Sweden. Comprehensive phenotype data were recorded including milk yield, dietary intake, digestibility and methane emissions. The animals were ranked according to methane yield data expressed as g CH4 per kg dry matter intake (DMI) corrected for live weight and a selection was made of 5 the highest and lowest methane emitters from each country. Microbial DNA was extracted from digesta of each of the selected animals for metagenome sequencing using Illumina HiSeq 2000 to a depth of 90 million quality paired-end reads per sample. A reference set of nearly 4 million putative genes was generated and mapped to the UniProt KB with a relatively small proportion, just over 500000 genes, with high sequence similarity (E-value <1e-10 and identity > = 75%). MDS plots of relative gene abundance by taxonomy and functional annotation clustered according to country. However separation data by country revealed the clustering of the metagenomes according to methane emissions. KEGG orthologs (KO) involved in acetoclastic methanogenesis K13788 and K01895 were found to be significantly different in the Italian and Swedish cows respectively and all the genes involved in hydrogenotrophic methanogenesis were consistently higher in relative abundance in high methane emitters. VFA production (mmol/L) showed no significant differences and this was reflected in the relative abundance of microbial genes (cel, xyn, and amy) involved in carbohydrate degradation. Similarly, no significant differences were found in milk yield and composition (kg/day). As part of the effort to reduce the environmental impact of livestock, the results from this study showed the selection for low methane emitting animals need not necessarily come at the expense of productivity.