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Just because you consume a particular food or drink, doesn't mean all the nutrients make their way into the body, to the locations where they end up being used or stored. Sometimes they just pass right out of your gastrointestinal tract without being absorbed and other times they are broken-down immediately by the liver and excreted by the kidneys.
Nutrients have to make it through a variety of obstacles, starting from the moment they enter your mouth to the moment they are used or stored. The bioavailability of a particular nutrient refers to the ability of the nutrient to pass through some or all of these obstacles, so that they are absorbed into your body and become available for use or storage .