The rumen of the dairy cow contains a rich and diverse collection of microbes that during feed digestion produce significant quantities of methane gas and ammonia, both of which contribute to greenhouse gas emissions. Strategies to redirect rumen carbon and nitrogen metabolism away from these products provide opportunities for significant productivity improvements in livestock systems not only by improving nutrient retention, but also by reducing greenhouse gas emissions. In order to develop these strategies, a greater knowledge of the diversity of the microbes within their rumen and their genomic capability is required. Many have used several techniques to study the rumen microbes, and the technology continues to improve. Among them include researchers at the Department of Primary Industries Victoria (DPI Vic) and the Dairy Futures Cooperative Research Centre (CRC) who are addressing the issue of regulation of methane emissions in dairy cattle, while scientists in Queensland and New South Wales, as part of the most recent Beef CRC program, focus on beef cattle. In this brief review, we examine how the techniques used in rumen microbial ecology have changed, and how technology improvements continue to allow us to examine the rumen microbiota of cattle and other ruminants, so as to better understand and possibly select animals with superior traits, leading to improvements in feed efficiency, methane emissions and nitrogen retention.