So I ran across this article in the New Yorker, it is long, really long. But it is part of an investigation with what the **** is up with gluten. As it seems and some recent studies show, gluten may not necessarily be the problem.
http://www.newyorker.com/magazine/2014/11/03/grain

In the end, if you have gastric distress, you may need to follow a fodmap diet to see what exactly is causing the issue. If you are eating breads with added gluten, it may be because they are trying to short cut the whole grain bread baking process which may cause gastric distress.

There needs to be more research and studies done.

I think it is interesting that the theory may have to do with gut bacteria. Gut bacteria has gotten a lot of interest lately. So I am hoping they do more research in that area and they have even started looking into 'stool supplements'. Sounds gross but it may be a partial solution.

I think gut bacteria has a lot to do with it. More so when it comes to non-celiac gluten sensitivity. With Celiac Disease, it is autoimmune and I think they will need to dive deeper.