Protein supplements typically come from one of two sources, either soy or whey. Both soy and whey protein supplements can have health benefits; however, they can also have some side effects, especially in individuals with food allergies.
Soy and Whey
Soy protein is produced from soybeans, and it can come in a variety of forms that you can use as protein supplements to your diet, including powder, milk, flour and yogurt. Soy also contains fiber and contains minerals and vitamins like potassium, folate and vitamin A. Whey protein is a powder manufactured from whey, the liquid that remains when milk is made into cheese. According to the University of Maryland Medical Center, whey protein powder is high in easily digestible amino acids that help to build muscle.
Allergies
According to the Mayo Clinic, soy products typically have limited side effects unless they are used or consumed by individuals allergic to soy. Symptoms of a reaction are similar to most food allergy reactions, including hives, a runny nose, a drop in blood pressure or a swollen throat. An allergic reaction to whey can occur in individuals with milk allergies or lactose intolerance, and symptoms can include an itchy throat, swelling in the face, vomiting and diarrhea.
Other Soy Problems
Soy is usually safe for most people; in fact, it is widely eaten in Asian countries as a dietary staple. However, soy has caused stomach problems, like nausea and constipation, in a few individuals. In addition, soy may affect infants' hormone levels, causing an enlarged thyroid. Soy can also cause vomiting, diarrhea, stunted growth and damage to the intestines in infants. Finally, some soy protein products, particularly those isolating the isoflavone components of soy, have caused migraine headaches.
Other Whey Problems
Whey protein supplements can lower blood sugar levels, which may be dangerous for people suffering from diabetes or hypoglycemia. Whey protein may also lower blood pressure, so people taking blood pressure-lowering medications should use caution. Other side effects can include nausea, reduced appetite, bloating, headaches and fatigue. When feeding it to an infant, use caution, as whey may cause colic in babies. Whey can interact with prescription medications, so consult with your doctor before using a whey supplement.



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