Microbial metagenomics---the applications of the genomics suit of technologies to nonculturable microorganisms, is coming of age. These approaches can be used for the screening and identification of nonculturable gastrointestinal (GI) microflora for assessing and exploiting them in nutrition and the health of the host. Advances in technologies designed to access this wealth of genetic information through environmental nucleic acids extraction and analysis have provided the means of overcoming the limitations of conventional culture-dependent microbial genetic exploitation. The molecular techniques and bioinformatics tools will result in reliable insights into the animals' GI microbial structure and activity of the livestock gut microbes in relation to functional interactions, temporal and spatial relationships among different microbial consortia and dietary ingredients. Further developments and applications of these methods promise to provide the opportunity to link distribution and identity of various GI microbes in their natural habitats, and explore their use for promoting livestock health and industrial development.