Reducing the environmental footprint, allied with enhancing food quality and safety are key elements of the new agenda to improve the sustainability of livestock farming. Improving nutrient use efficiency is a key challenge in ruminant production systems with improvements in dietary forage utilisation, enabling reductions in use of cereal and/or protein rich supplements, being one of the primary means to achieve this goal (Kingston-Smith & Thomas, 2003). Consumers are also becoming increasingly aware of the relationships between diet and health, in particular food quality and safety. Research into functional food components has focused on increasing the quantities of those nutrients present naturally in ruminant products which are considered to play important roles in health promotion and disease prevention. Food safety on the other hand has focused on the ability to eliminate or decrease food-chain pathogens that can be harboured in the gut of ruminants in order to improve both human and animal health. Microbial transformations in the digestive tract (in particular the rumen) have a major impact on our ability to improve nutrient use efficiency, food quality and safety. The rumen microflora is very diverse making it a challenging ecosystem to manipulate. Application of cultivation independent methodologies has also revealed that only as little as 11% of the bacterial diversity has been cultivated to date (Edwards et al. , 2004). This paper reviews how increasing our understanding of microbially mediated processes in the rumen is central to achieving improvements in nutrient use efficiency, food quality and safety.