A massive resident bacterial population, the intestinal microbiota, within the GI tract of animals has been recognized since the dawn of microbiology. Advances in microbiology and microbial genetics have provided greater understanding of its importance.
Signals from the intestinal microbiota regulate diverse body functions. Most notably, the microbiota increase energy yield from foods, provide animals with essential micronutrients, and provide signals that optimize immune function.
Veterinarians have long been aware of the importance of microbiota, thanks to their work with ruminants, mammals that exploit microbial digestion as a way to obtain additional energy from otherwise indigestible plant material.
The microbiota also protect against colonization by pathogens and the overgrowth of endogenous pathobionts. In addition, they influence the development of obesity, allergic diseases, inflammatory diseases, and some autoimmune diseases. The microbiota directly influence an animal’s tendency to mount IgE-mediated immune reactions and thus allergies.
In healthy animals, the gram-negative Proteobacteria and Bacteroidetes and the gram-positive Firmicutes are the major bacterial phyla inhabiting the large and small intestines. The Firmicutes include Clostridiales and Lactobacillales. All of these organisms are well adapted to the intraintestinal environment and generally form stable and complex populations.
The composition of the microbiota differs between individuals, between families, and most notably between carnivores, omnivores, and herbivores. Because of their complex interactions and their stability, it may be difficult to induce longterm changes in the composition of the microbiota.
The microbiota control pathogens by direct interactions. They release bacteriocins that kill competitors, they compete for essential nutrients, and they alter the conditions required for bacterial growth. They also control pathogens by stimulating host immunity and mucosal barrier function.