The biggest thing with PPI's are that they suppress acid production which leaves your body with no way of breaking down foods in order to digest them. What this causes is that your body is no longer getting all of the nutrients it needs from the foods.
Not to be a stickler but are there any studies or evidence that you can point to for this assertion? I understand that it makes sense, but a lot of times in medicine making sense isn't enough. There have been plenty of things that I would think that have been disproven via studies. So I tend to be cautious about these things.
The way I came up with this assertion is because it is said by multiple sources that PPI's are used for acid suppression. Although I have not found any studies that show how much acid is suppressed by these medications, I have seen numerous times that they can suppress acid almost 100%. I have also done research on why some of the long term effects happen while on PPI's and from what I gather is that the reason why there are deficiencies is due to there not being enough acid to break down the foods. Based on this information I did research to determine what is needed in order for our digestive tract to work correctly and found that in order for our bodies to digest food properly, it needs to be broken down by stomach acid. All of this makes me have a theory of why long term effects happen when on PPI's. I also understand that everyone will react differently and one form of PPI medication may not work the same for one person as it does another and not everyone that takes PPI's will experience the long term effects.
Why it makes sense to me is through experience I have noticed a difference in how long it takes for my stomach to empty since I stopped taking PPI's. I have also noticed energy increases and being able to be at the same energy levels on less sleep. But again it is my experience which may be different than other's experiences. I understand where you are coming from though as I question everything I see. I don't rely upon one resource or one study for anything. I tend to research a specific piece with multiple resources and then start to tie things together to come up with an answer.
Article that shows different PPI's and how much they suppress acid: http://www.medscape.com/viewarticle/754326_3
This article includes a lot of information that I see among many different sources referring to the importance of stomach acid and side effects of not having the correct levels of acid: http://primaldocs.com/opinion/the-truth-about
This article has information regarding some of the effects regarding PPIs: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974811/
To me these sources, plus many more, only provide pieces to the puzzle. I have not yet seen a study or any evidence that puts all the pieces together, but based on studies, articles, knowledge that tends to be common among many sources, and my own experiences, I've pieced together an answer that makes sense to me. I also understand that this may not make sense to some as they have tried things based on this reasoning and had unsuccessful results, but that just might be due to the underlying problem itself.
So far I have not seen anything that goes against this information either. I've seen a lot of conflicting information on how to treat GERD or "cure" it, but nothing that disproves any of my research.