Supplementation, or fortification, refers to the process of adding vitamins, nutrients and even Omega 3s to a food that does not naturally have these items. There are several clinical studies which have explored consuming vitamins and nutrients via supplementation versus through natural foods, but the research has not shown clear results.  

How Does the Body Know the Difference?
It is thought that the foods that contain Omega 3s naturally are comprised of other vitamins and nutrients that help to break down the Omega 3s more efficiently in the body. The same goes for other vitamins and nutrients that are commonly added to foods. If the food does not contain high amounts of Omega 3s, naturally, the chemical makeup of the food may not be optimal for use in the body. This goes for both oral supplementation and the consumption of foods that state they have "Added" DHA or EPA.
The solution to the problem of absorption is simply adding foods to the diet that are naturally rich in Omega 3s. Many consumers choose the fortified products over the natural products in order to reduce overall calorie intake as many of the foods rich in natural Omega 3s are oils and higher fat fish. But these oils are the source of the Omega 3s and thus are not harmful to health when eaten in moderation.
While supplementation or eating fortified foods may not be optimal, it's better to supplement than to not have any Omega 3s  and much of  the Omega 3s are absorbed into the body, even if taken as supplements. If the only choice for the consumer is between adding no Omega 3s to the diet or adding foods fortified with Omega 3s to the diet, the fortified foods would be more beneficial over adding no Omega 3s at all.

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