All animals, including humans, are adapted to life in a microbial world. Anaerobic habitats have existed continuously throughout the history of the earth, the gastrointestinal tract being a contemporary microniche. Since microorganisms colonize and grow rapidly under the favorable conditions in the gut they could compete for nutrients with the host. This microbial challenge has modified the course of evolution in animals, resulting in selection of complex animal-microbe relationships that vary tremendously, ranging from competition to cooperation. The ecological and evolutionary interactions between herbivorous dinosaurs and the first mammalian herbivores and their food plants are reconstructed using knowledge gained during the study of modern living vertebrates, especially foregut and hindgut fermenting mammals. The ruminant is well adapted to achieve maximal digestion of roughage using the physiological mechanism at the reticulo-omasal orifice which selectively retains large particles in the reticulo-rumen. However, the most obvious feature of all ruminants is the regurgitation, rechewing and reswallowing of foregut digesta termed rumination. Foregut fermenting mammals also share interesting and unique features in two enzymes, stomach lysozyme and pancreatic ribonuclease which accompany and are adaptations to this mode of digestion. The microbial community inhabiting the gastrointestinal tract is represented by all major groups of microbes (bacteria, archaea, ciliate protozoa, anaerobic fungi and bacteriophage) and characterized by its high population density, wide diversity and complexity of interactions. The development and application of molecular ecology techniques promises to link distribution and identity of gastrointestinal microbes in their natural environment with their genetic potential and in situ activities.