Intensifying concerns about the use of antimicrobials in meat and poultry production has enhanced interest in the application of prebiotics, probiotics, and enzymes to enhance growth and prevent disease in food animals. Growth- promoting antibiotics enhance growth of animals either by reducing the load of bacteria in the intestine, reducing colonization by intestinal pathogens, or by enhancing the growth and/or metabolism of beneficial bacteria in the intestine. Therefore other types of treatments could theoretically elicit similar responses as the use of antimicrobials.

Large herbivorous mammals such as cattle, sheep, goat or deer host “symbiotic” protozoa that are believed to be of importance for the digestion of the plant-based diets of their hosts. However, at least in under laboratory conditions, these mammalian hosts exhibit a rather normal digestive performance if the protozoa in the gastro-intestinal tract were removed by defaunation. A similar “commensalistic” relationship has been found between intestinal ciliates and arthropod hosts such as millipedes and cockroaches. In contrast, certain termites cannot survive without their symbiotic flagellates. Moreover, throughout the animal kingdom there is no simple correlation between the feeding habits of the hosts and the presence or absence of symbiotic/commensalic protozoa. Rather the taxonomic position of the host appears to be crucial for the evolution of the protozoal communities in the gastro-intestinal tract.

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.

Secondary metabolites represent a diverse group of natural products. Although precise numbers are, at best, an estimate, at least 100,000 different compounds of natural origin have been described, of which at least 80,000 of those are derived from plants. It is likely that many more than these will be isolated in the future, as increasing numbers of novel plant species are being identified and studied for their potential use in the pharmacological, medical and agricultural industries. The increased interest in phytochemicals in animal diets has been spurred on by the EU ban on the use of ‘in feed’ antibiotics, the removal of animal proteins from the diet and thus the increased variety and inclusion levels of vegetable protein sources.

Latest estimates based on comparisons of 16S rRNA-encoding gene sequences from gut microbial ecosystems reveal a daunting genetic diversity, with at least 341 distinct phylotypes evident in the ruminal bacteria (Edwards et al. 2004) and 395 in the human intestine (Eckburg et al. 2005). Some metabolic functions are fairly widespread throughout the genetic spectrum, such as glucose utilization, for example. Others, however, are not. In spite of so many phylotypes being present, single species or perhaps only two or three species often carry out key functions. Among ruminal bacteria, only three species can break down highly structured cellulose, despite the prevalence and importance of cellulose in ruminant diets, and one of those species, Fibrobacter succinogenes, is distantly related to the most abundant ruminal species. Fatty acid biohydrogenation in the rumen, which has so many health implications in terms of the fatty acid composition of ruminant-derived foods, is effectively carried out only by the Butyrivibrio group. Furthermore, the final step of biohydrogenation of C18 fatty acids, stearate formation, can be achieved only by a tiny sub-group of the butyrivibrios. Single bacterial species can also have very distinctive effects on the health of the host animal or human. Oxalobacter formigenes is a member of the ruminal and human intestinal microflora. It converts oxalic acid to formic acid, thus removing the potentially toxic oxalic acid, which is present at high concentrations in some foods such as rhubarb and spinach. In some individuals, however, O. formigenes cannot be detected, perhaps having been eliminated by antibiotic therapy. The resulting inability of the intestine to metabolise oxalic acid can cause kidney stones composed of calcium oxalate. Re-inoculation of these individuals with O. formigenes results in relief from disease. In ruminants, the conversion of tryptophan to indoleacetic acid and then to 3-methylindole causes bovine pulmonory disease. Elimination of the Lactobacillus species responsible for the indoleacetic acid to 3-methylindole conversion corrects the problem. Finally, perhaps the most celebrated example of the difference a single species can make is the ‘mimosine story’ in ruminants. Mimosine is an amino acid that is found in some plants, including Leucaena leucocephala. Leucaena had been identified as a potentially useful protein-rich feedstuff for Australian livestock. However, the mimosine caused thyroid problems by being converted to the goitrogen, 3-hydroxy-4(1H)-pyridone, in the rumen. Observations that mimosine-containing plants were not toxic to ruminants in other continents led to the discovery of Synergistes jonesii, which, when inoculated into Australian cattle, metabolised 3-hydroxy-4(1H)-pyridone and protected the animals from toxicity. Thus, in the almost overwhelming flood of information that emanates from molecular microbial ecology and genomics of gut bacteria, it should never be forgotten that this vast community consists of many important metabolic niches inhabited by species each with specific metabolic capability.