Proton pump inhibitors create many nutritional imbalances. Acid reflux has for the longest time been associated with low levels of HCL in the stomach creating cycles of under- and over-production of HCL. The pharmaceutical industry has worked hard to convince people that this is due to a constant excess of HCL that needs to be suppressed, which it isn't.
The best way would be to balance the intestinal tract and flora, as fungal candida can continue to create imbalances that lead to many conditions.