Newer biological agents that are designed to have multiple effects on a host require better ways to determine both their safety and toxicity. Indeed ecologically potent factors such as agents that can alter the gut milieu and change host responses are now being realized as a viable alternative to more focused pharmaceuticals. Even in the pharmaceutical arena there is a growing awareness of the preventative and therapeutic potential of alternative agents. Probiotics and prebiotics amongst other agents fall into this category and can have both direct and indirect effects on the pathogenesis and progress of disease. This review details some of the new approaches using non-invasive tests to enable firstly a better definition of a stressed through to a damaged gastrointestinal mucosa. They constitute ways to apply dynamic function testing in animal models and humans to provide reference points to which other measurements can be related e.g. altered circulating cytokines, altered gene expression. As such this phenotypic scaffold, alone and combined with newer molecular parameters, will improve our understanding of the interaction of luminal factors within the alimentary tract and the impact that these have on physiologically challenged mucosa and in disease both at the gastrointestinal level and also in remote organs. Practically, the dynamic function tests, primarily breath tests, can now be used as diagnostic and prognostic indicators of the efficacy of new biologics such as probiotics and prebiotics that in part elicit their effects by altering the ecology of particular regions of the intestine.