@Mep, it's complicated...
I have one autoimmune condition, inflammatory bowel disease (IBD), which happily, is in remission 99% of the time. I think because I use the specific carbohydrate diet (SCD) and the LCHF diet.
Last year, I added 2 tablespoons of freshly ground flaxseed to my daily diet for three weeks - (what I later learned is an "illegal" food on the SCD) - and before I understood what was happening I was thrown out of remission and into a full blown IBD flare that lasted 9 months. When I'm that ill, what I can and cannot do is greatly limited.
I have two other conditions that may or may not be autoimmune diseases: subclinical hyperthyroid, which my lab work showed in 2002 but I never had the proper lab work to determine if I have antibodies attacking my thyroid.
I also have non-celiac gluten sensitivity (NCGS), diagnosed based on medical history, vitamin B12 and iron deficiency, and a lab test developed to identify severity of gluten senstivity. In December, I had the genetic test to determine if I have the genes for celiac disease. I don't. At that point my gastroenterologist confirmed that I have NCGS. (To have the antibody test for NCGS, I'd have to resume eating gluten which I'm not going to do. Wish now I'd had that test before I stopped eating gluten.)
The big question is whether my NCGS is caused by gluten, or by the herbicide glyphosate because in the US glyphosate is sprayed on wheat and so many other crops. I don't know, but interestingly, more and more experts are beginning to ask this question.
I live in the US. Glyphosate, a herbicide, wasn't used on crops until 1974, so something else may have played a role in the development of my NCGS. A possibility was ongoing exposure to a pesticide sprayed on the carpets of our home monthly to control fleas prior to 1974. It took hours to dry, and I walked barefoot on those carpets. Don't know.
The reason I detailed all this out is because toxins such as heavy metals, pesticides, and herbicides can cause health problems too. So it's not just a "leaky gut" or intestinal permeability that leads to unexplained health issues. What I recently learned is that specific toxins can interfere with processes in the body by
displacing specific vitamins and minerals. If you haven't watched the new documentary, What's With Wheat, yet, that's a good place to start learning about this.
Returning to the topic of autoimmune disease... One of the most respected authors on autoimmune disease in the US is Sarah Ballantyne, Ph.D., author of The Paleo Approach: Reverse Autoimmune Disease and Heal Your Body (2013). The only reason I haven't read the entire book yet is because my autoimmune conditions are all stable right now and I'm focused on learning other things - (I'm obsessed with finding new non-medication ways to improve my blood glucose levels further. Next, I want to learn how to improve the diversity and health of my gut flora). Eventually I'll get back to Dr. Ballantyne's work. A couple of members of our local gluten-free support group have benefitted greatly from this book.