Let's take a look at a few known examples of why your body might be having trouble with certain foods...
👉 Gluten - probably by far the biggest culprit of food intolerance. Did you know low glutathione impairs our ability to break down gluten? Also lack of zinc, magnesium, thiamine can also be involved (and ironically, gluten-free diets tend to be deficient in thiamine).
👉 Dairy - yes the processing of modern dairy products may make it harder for some to digest, but that's not the whole picture. The enzyme required to break down lactose (lactase) is produced in the brush border of the small intestine. Things that can affect this include zinc & retinol deficiencies, extended fasting, caloric restriction or SIBO.
👉 Nightshades: Possible deficiency in Vitamin K.
👉 Oxalates: Magnesium deficiency/lack of oxalobactor species of bacteria in the gut (destroyed by antibiotics, but encouraged by eating yoghurt, kefir, etc).