The intestinal tracts of animals are populated by hundreds, perhaps thousands of bacterial species in vast numbers - tens of billions of bacterial cells per gram of intestinal contents. Collectively these bacteria make up the microbiota, and in its overall composition and genetic makeup, the population is called the microbiome. The metagenome can be defined as the totality of DNA sequences of all the component organisms. Many of these species have not been cultured in the laboratory and most are poorly characterised. Yet they are crucial partners to their animal hosts in nutrition and health - and include the so-called 'good bacteria' of the digestive tract. For the first time, a new approach, high-throughput DNA sequencing (HTS), makes it possible to identify and count on a large scale each bacterial species in a microbiome using specific sequence 'signatures'. These are obtained from a gene, present in all bacteria, that codes for an RNA molecule that is part of the protein synthesis machinery. This gene (16S rDNA) includes both near-constant regions, useful for its specific enrichment from the metagenome, and highly variable regions where the sequence is characteristic of the bacterial species concerned. It is these variable sequence 'signatures' that will identify component bacteria. It is also feasible to infer the biochemical activities of the microbiome by using HTS to identify genes in the metagenome that encode enzymes, capable of digesting dietary substances that could enhance the nutrition of the host organism. For HTS analysis, DNA is extracted from intestinal (caecal) contents or faeces. The16SrDNA sequences are enriched by amplification, using a method called PCR, to create a pool of fragments representing all the bacteria present. These fragments are then individually analysed and their sequences, amounting to one million or more per analysis run, matched computationally to those of all known bacterial species. In this way the bacteria from which they were derived can be identified. If there is no exact match, the closest known relative can be identified. 'Proof of principle' experiments have established the practicality of this approach to unravel the complexities of intestinal microbiology. However few published studies have rigorously defined the variability inherent in the technology, or between individuals, or from day to day and as dietary intake changes. Such data are essential if the enormous power of the technology is to be exploited in rational, hypothesis-based scientific studies. We propose to obtain these data using broiler chickens, so that groups of birds of defined and matched age, breed and diet can be accessed at relatively low cost. Having established robust baselines for analysis, we will tackle some key questions about the role of the microbiota. How does the microbiome change as birds age and change diet? What is the effect of colonisation of the intestinal tract by food borne pathogens such as Campylobacter, and can this information be used to enhance levels of bacteria that may suppress the invading pathogen? We will also assess the potential of sequencing the entire metagenome, the gene pool representing the microbiota as a whole. We will seek evidence for bacterial enzymes that may add to the digestive capacity of the host and thus enhance growth and productivity of the birds. We believe this proposal will firmly establish the scientific credentials of intestinal microbiome research on food animals, and prepare the way for future research into the role of the microbiome in animal health and welfare, efficient utilisation of feed, emergence of antibiotic resistance, and the establishment of intestinal pathogens.