PPIs are supposed to used short term but in some cases they are taken longer as necessary.

PPIs do not stop reflux. PPIs turn the stomach acid into stomach alkaline. What PPIs do is turn off the burning because alkaline does not burn so we think our reflux is gone. Less acid in the stomach can create an environment where bacteria are not killed off as regularly. Biologically there is a reason we have stomach acid.

One way people can get NTM (non-tuberculous mycobacteria), it's conjectured, is through reflux. They drink water or other contaminate with NTM (MAC, pseudomonas etc) they aspirate during the night and it goes into the sinuses, voice box, throat, and/or lungs. This happens routinely and then disease sets in. Recently I learned from watching Dr. Huitt's presentation from NJH that normal/healthy people can aspirate during the night. (Thanks to @becleartoday for posting this!)

What can we do about this? Know what your food triggers are and avoid them. Sleep on a high wedge at 30 degrees or on an adjustable bed. Stop food/drink 3 hours before bedtime. Wean off PPIs over a 2-3 month period. It goes something like this:

1 tablet every other day for 2 weeks
1 tablet every 3 days for 3 weeks
1 tablet every 4 days for 4 weeks