Gluten free mania has hit full stride. I even wrote about it in my Simple Foods book. But after rethinking about this “nasty” little protein, I decided to do a little digging. Once I finished reading the research and interacting with different experts in the field of the gut microbiome, its becoming more and more apparent that the deadly gluten isn’t the one to blame.
This is not to discredit those who have been diagnosed with Celiac Disease or those who have the genes that allow their body to be susceptible to gluten in a negative way. This is absolutely a problem and a separate issue in all entirety. I am grateful for the awareness of the harmful effects of gluten for those who are unable to digest it due to disease. But for the typical American trying to become health conscious, you are only scratching the surface by going Gluten-Free. For those who don’t fall in the category of Celiac Disease, the inability to digest this protein isn’t all gluten’s fault. We have targeted it as the demon of all foods, when in fact, its your flora whom should share the brunt of this assault.
I cannot deny the positive effects why most people can curse gluten into darkness. They notice a change in their mood and brain function, etc. While these are all signs that gluten was truly a problem, there is a bigger culprit lying in the bowels of these positive correlations. (Pun partially intended)
Gluten happens to be a trigger food (especially when it never was before) that can help you self-diagnose yourself as having a not-so healthy gut. Instead of avoiding it like the plague, time to test and see what went wrong. Just avoiding it or dealing with the consequences of being intolerant to gluten is leaving yourself open to a host of future problems. Your gut needs healing and its friendly microbes back!
Believe it or not, the the flora DOES has the ability to digest gluten. 
Notably, research in our laboratory has recently shown that gluten-degrading proteases are naturally present in the upper human gastro-intestinal tract. These enzymes are not from human origin, but produced by the wealth of bacteria that colonise the oral cavity and duodenum.
Unfortunately, most of whom lived and breathed off the SAD diet probably lost their symbiotic flora. The long term habitual use of the SAD diet will most likely leave the gut inflamed and in perpetual dysbiosis.
And this study has concluded that certain strains were narrowed down in the microbiota that can break down the gluten as a food source: 
..94 strains were able to metabolise gluten…
… the human intestine exhibits a large variety of bacteria capable of utilising gluten proteins and peptides as nutrients.
The loss of our core flora probably leaves these gluten degrading microbes out on a limb, soon to be kicked out by other not so useful celled organisms.
This study observed the differences of the microbiota with children who had Celiac disease and those who were considered healthy. There was a distinctive difference between Lactobacillus , Enterococcus, and Bifidobacteria (Core). Those who were considered healthy had a higher count of all three of these strains compared to the children with treated Celiac disease. 
Given the fact that before the age of antibiotic beings passed out like candy, there was little worry about gluten. Except, of course, by those genetically predisposed to the protein. This leads me to believe, by fostering the ancestral core microbiota back to into the gut will give us this ability to digest the gluten. The core, which includes Bifidobacteria, will more than likely give a more hospitable environment for those strains to come back into the flora. There are even personal cases that support this claim. Those who restored their flora were once again able to tolerate gluten.
I’m not advocating for a diet that relies on rye, barley, and wheat as the mainstays, but avoiding these foods seems more like another “Fat Free” frenzy. Let’s target the root cause of this, your flora. Build back the flora by feeding it SBO’s and the other probiotics recommend here. If you find you are intolerant to gluten, this is good news! You have been given another clue that there is some work to be done, which will also help other lingering issues that you might be ignoring. Remember, first TEST, then you can implement a strategy to restore the flora. Soon, you will be able to cheat by having a fresh baked pizza with a frosty rye ale.