Food carbohydrates vary in the type and number of sugar components, linkages, and structural complexity. These as well as their diversity and distribution in food materials is key to the overall consideration as functional foods. For this reason, functional carbohydrates naturally present in various foods have gained great attention in recent decades. However, the complexity surrounding the structure, sugar linkages as well density in most complex carbohydrates presents a special challenge to their extraction, analysis, and evaluation of physiological effects such as gut microbiota modulation. We develop extraction methods for bioactive carbohydrates, analytical methods as well evaluate the impact these carbohydrates have on human health through gut microbiota modulation.