Host pathways for recognition: Establishing gastrointestinal microbiota as relevant in animal health and nutrition

It has long been recognized that gastrointestinal colonization by commensal microbiota is advantageous to the host. Relative to germ-free animals, microbiota adds digestive enzyme capability, creates nutrients (e.g. vitamins, volatile fatty acids) and excludes harmful pathogens. More recently, an appreciation for the much broader impacts of the commensal microbiota on host physiology has been established including developmental and regulatory impacts on adaptive immunity, innate immunity, nutrient digestion, absorption and metabolism. In mono-association experiments, many of these impacts are affected differently depending on the colonizing bacterial species. This suggests opportunity to modify host responses by altering intestinal microbial colonization patterns. Interestingly, new observations linking differences in intestinal microbial composition to obesity and diabetes support a role for intestinal microbiota in systemic host physiology. Host response pathways associated with these outcomes may have relevance to efficiency of nutrient utilization and/or the net rate of tissue deposition. Unfortunately, relatively little is understood about the mechanisms by which the microbiota induces host changes. With reference to the pig where possible, this review will examine identified and speculated host pathways through which microbial products are recognized and induce physiological responses. Pathways are categorized as host sampling of bacterial antigens, receptor mediated recognition of microbiota-associated molecular patterns (MAMPS), recognition of bioactive fermentation products, and microbial-origin effector molecules. We hypothesize that the relevance of the gastrointestinal microbiota in animal health and performance will be defined by elucidating the specific host response pathways. Knowledge of these pathways will, in turn, facilitate the development of targeted nutritional strategies.