Associated with each food is a series of nutrients. In food consumption research, these are the interesting values. Nutrients in foods are what affect the body eating them. Energy, muscles, well-being, diseases, sickness, all are affected by nutrients. Food research helps find the links between nutrients and their effects and thus which foods should be eaten or avoided.
Studies have to be carefully crafted to take into account the sources of food information as well as other factors which may be having an effect such as obesity, activity, smoking, alcohol consumption (which is just another food), etc.