There can be multiple causes of enzyme deficiency. One major cause is genetic. Many people are either born or else predisposed to certain enzyme deficiencies, the main being lactose intolerance. But there are some other causes of enzyme deficiency that can cause poor digestion, and digestive problems like nausea, gas, bloating, and other side effects. Not eating enough raw fruits and vegetables can be a big cause of digestive enzyme deficiency. People don't eat nearly the same amount of raw foods as we once did, & cooking food destroys the enzymatic value of a food. Heat ruins digestive enzymes, so if you're experiencing digestive problems and a lack of digestive enzymes, try eating more raw fruits and vegetables. This will not only give you a boost in digestive enzymes, but fiber as well, which can also help correct digestive problems.
Another cause of enzyme deficiency is amino acid deficiency. Enzymes are proteins, and pretty complex ones at that. They each require dozens or hundreds of various amino acids. If a person has an inadequate supply of amino acids, enzymes might not be produced in as plentiful supply.