Metagenomics techniques applied to the rumen microbiota have demonstrated tremendous diversity originally among populations of bacteria and, more recently, among the methanogenic archaea, including those associated with protozoa. Although with some potential limitations, cluster analyses of sequences recovered from clone libraries have revealed differences in populations among animals fed forage v. grain, including amylolytic ruminococci and novel groups of clostridia adhering to the rumen particulates. Rapid profiling procedures, such as denaturing gradient gel electrophoresis (DGGE), can be used to infer likely differences in community structure of bacteria and archaea among numerous replicates of animals and times after feeding diets that are more representative of intense ruminant animal production. Metagenomics procedures also are being applied to issues related to ruminal output of fatty acid isomers influencing milk fat composition and consumer acceptance, the environmental impact of nitrogen in animal waste and methane emissions, and future potential approaches to improve ruminal fibre digestibility. If varying concentrations of ruminal metabolites and fluxes quantified from microbial processes can be combined with results from metagenomics applied to rumen microbiota, then we should reduce the unexplained variability in models in which the prediction of nutrient supply to the intestine is synchronised with nutritional guidelines for more efficient feed conversion by ruminants.