Abstract
The gastrointestinal tract of all animals is colonized with a vast, complex and dynamic consortium of microorganisms. In spite of recent progress in molecular microbiology, this complexity makes a proper qualitative and quantitative evaluation difficult and expensive to perform. In the present review we discuss the results obtained from applying a functional concept for studying intestinal host–microbial interactions in eight mammalian species and two species of fish. We show that microbial interactions with endogenous derived substrates such as cholesterol, bilirubin, mucin and trypsin occur in all species. Exogenous compounds (e.g. carbohydrate, protein, fibre) are also acted upon by the intestinal microflora. From an evolutionary point of view, dietary differences have led to a compartmentalized variability in microbial functions. Taken together, the results in this review underscore the importance of understanding precisely how gastrointestinal metabolism serves to establish a symbiotic cross-talk between animals and their gastrointestinal flora.