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I suggest you eliminate dairy from your son's diet next.  Cow's milk protein, Casein, can trigger tTg IgA antibody production, the same as gluten, because casein contains segments of proteins that resemble gluten protein segments.   Mucosal reactivity to cow's milk protein in coeliac disease https://pmc.ncbi.nlm.nih.gov/articles/PMC1810502/ I cannot consume dairy products.  Some people find they can tolerate A2 dairy without a reaction. Corn is another frequently hard to tolerate food because the protein zein in corn also resembles the protein structure of gluten.   Do research in Dr. Derrick Lonsdale and TTFD thiamine.  Taking TTFD really can make a dramatic difference, speaking from personal experience. https://hormonesmatter.com/energy-deficiency-asd/ Keep us posted on your progress!

It sounds like you're doing everything right with your gluten-free diet, yet still experiencing significant discomfort, which must be frustrating. Since your stool sample came back normal but symptoms persist, pushing for further investigation—like a colonoscopy or biopsy—is a reasonable next step. You might also want to discuss the possibility of additional conditions, such as IBS, microscopic colitis, or other inflammatory issues, with your doctor. Tracking your symptoms, diet, and triggers in detail could help identify patterns. Don’t hesitate to advocate for yourself—if your current doctor isn’t addressing your concerns, seeking a second opinion or a referral to a gastroenterologist could be beneficial. You’re right to seek answers, and I hope you find relief soon. Many people with celiac disease, especially those who are in the 0-2 year range of their recovery, have additional food intolerance issues which could be temporary. To figure this out you may need to keep a food diary and do an elimination diet over a few months. Some common food intolerance issues are dairy/casein, eggs, corn, oats, and soy. The good news is that after your gut heals (for most people who are 100% gluten-free this will take several months to two years) you may be able to slowly add some these items back into your diet after the damaged villi heal. This article may be helpful:    

Hi all, I was diagnosed with coeliac in August 2020. This was via a blood test, as it was during COVID, so I’ve never had a biopsy or colonoscopy or anything like that.    I have been following a gluten-free diet since and would expect to feel much better, however, I am still experiencing issues with my bowels. Very strict, so I know there’s no cross contamination etc.    It usually seems to be after I have had a bowel movement, my bowels feel on fire, cramping, sore and very uncomfortable. I know it isn’t normal, and isn’t right and I have saw a doctor before, I provided a stool sample and apparently everything was fine- but I know it isn’t.    I am just wondering if anyone else experiences this? What would you advise I do in regards to seeing a doctor, I was thinking of asking for a colonoscopy or biopsy, I just want to know what is going on and why I’m still experiencing this. Any advice is welcome and appreciated.. thank you. 

Thanks. My son has been on B2 for two to three years now. I found literature about B1 earlier and put him on a B1 supplement, but not thiamine tetrahydrofurfuryl disulfide specifically. He also gets D and Magnesium. He goes to his doctor in June and I am going to ask for bloodwork to look for any deficiencies. What I suspect is that he is having a gluten-like reaction to the proteins in other grains. It is well known that a small percentage of celiac patients react to the protein in oats. Oats are in gluten-free Oreos, so we removed them. He got a little better. The science with oats is pretty solid. My son's nutritionist knows about it and it is easily found in PubMed. I suspect my son is reacting to something else. The next thing that I only just removed was corn, at least things with corn protein. I need to give that a couple of months. If that doesn't work, I will try to replace his cheese with goat-milk cheese, although that will be hard.    My son was migraine free for over a year on a strict gluten-free diet before this past fall. I can test his foods for gluten and I have given in to diet rigidity. He eats my homemade refried beans and rice for lunch every day, so his rigid diet contains pretty healthy components. Given his antibody levels (tTG-IgA very low) and that I tested everything under the son that he ingests when his migraines returned and nothing tested positive for gluten, I think he really is gluten-free. So my personal working hypothesis is that he is having a reaction to a similar protein, one in another grain. However, the neurologist sees migraines come and go in lots of normal people, so it might just be that he is now having multiple (3-10) migraines monthly and it is hormonal or weather-related or something that is entirely distinct from an antibody reaction. I just would like them to go away again, as would he.    Thanks again! Elizabeth

Welcome to the forum, @jamiet06, Yes, it does point in that direction.  Your report says "Correlation with clinical findings and results of serological studies is recommended"  is saying you should undergo a gluten challenge and be tested for antibodies associated with Celiac Disease.   These antibodies are produced in celiac disease in response to gluten, but you have to eat generous amounts of gluten for the antibodies to show up in the bloodstream. A gluten challenge means you eat 10 grams or more of gluten  (4 to 6 slices of gluten containing bread or equivalent or more) per day for a minimum of two weeks.