It is because of beneficial bugs in the gut that we can get some extraordinary substances from foods. Of the hordes of bacteria in the digestive tract, very few of them live in the acid environment of the stomach, which breaks down food and prepares it for digestion. A small number of them reside in the small intestine, where much of food digestion takes place. The vast majority of gut bacteria inhabit the large intestines, the colon.
There, they tackle foods that are resistant to digestive enzymes—notably foods rich in the complex carbohydrates known as fiber. From them, they create micronutrients that boost health in ways that are still under study. They also aid in the digestion of protein and, to some extent, fat. In the process of digesting foods, gut bacteria release a great array of molecules known as metabolites that have effects on virtually every system of the body. The actions of the microbiome extend well beyond the gut.