Fermentation is a metabolic process in which microorganisms — mainly lactic acid bacteria and yeasts — convert sugars or proteins in food into new compounds. The most common results are lactic acid, acetic acid, carbon dioxide and small amounts of alcohol. These changes preserve the food, deepen its flavor and can make certain nutrients easier for your body to absorb.
Many fermented foods still contain live microbes when you eat them, while others mainly provide what you might think of as microbial byproducts: organic acids, enzymes and other metabolites. Digestion in your stomach and small intestine reduces the number of live microbes that reach your colon, but the compounds they produce can still influence the environment there.
In the colon, these compounds can affect which microbes thrive. Organic acids, for example, create conditions that may favor organisms supporting digestion and gut barrier function. Because everyone carries a different starting mix of microbes, individual responses vary.