The complex relationship between the host ruminant and its inhabitant microbiota has been the focus of research for decades initially centred around identification of the types of microbiota that reside within the rumen through to a greater understanding of their functional contribution to the host’s energy requirements. As new technology has become available, what originally involved the isolation and detailed studies of single strains in the laboratory has now moved to large scale sequencing of “total” rumen microbiota nucleic acids (genomics and transcriptomics), proteomics and metabolomics. Notwithstanding the limitations of these new techniques, the adoption of these techniques has been rapid and applied to most ruminant systems. Initially to define the variance in rumen bacterial populations on diet shifts from forage based diets to those with higher proportions of grain. Most notable in the last decade the emphasis has been focused around the understanding of the rumen microbiota’s contribution to agricultural greenhouse gas emissions, predominantly methane. While now there is increased interest on defining the rumen microbiota of an efficient production animal (meat and dairy) and the influence of the host genetics on shaping the microbiota of the rumen.