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Maybe celiac but maybe NCGS that was misdiagnosed as IBS morphing gradually into celiac. Is NCGS a new category to you? It shares many of the same GI symptoms with celiac disease but does not damage the small bowel lining like celiac.

Thiamine has antifungal properties.  The body uses thiamine to keep bacteria and yeasts from overgrowth in the digestive system.   Fluconazole use can cause thiamine deficiency.   Supplementing with thiamine in the form Benfotiamine would be beneficial as Benfotiamine promotes intestinal healing.   Thiamine and the other B vitamins tend to be low in Celiac due to malabsorption.  Talk to your doctor about supplementing vitamins and minerals.

Welcome @Natalia Revelo, your experience is profoundly difficult and, sadly, not entirely unique within the celiac community. It's the frustrating reality of "silent" or ongoing damage that isn't captured by the MARSH score alone, which only measures active villous atrophy. Your normal biopsy suggests your diet is preventing the classic autoimmune attack, but it doesn't mean your gut has fully healed or that other issues aren't at play. The inflammation from your newly discovered milk and egg allergies is a huge clue; this constant allergic response can create a low-grade inflammatory environment that severely hampers nutrient absorption, effectively creating a "leaky gut" scenario independent of celiac damage. This is likely why your iron stores deplete so rapidly—your body is both unable to absorb it efficiently and may be losing it through inflammation. While the functional medicine path is expensive, it's clearly providing answers and relief that traditional gastroenterology, focused solely on the gluten-free diet and biopsy results, is missing. To move forward, continue the gut-healing protocols your functional doctor recommends (perhaps exploring alternative options to glutamine that won't irritate your cystitis), maintain your strict avoidance of all allergens and irritants, and know that true healing is a multi-faceted process. You might seek a second opinion from a different gastroenterologist who is more knowledgeable about non-responsive celiac disease and the complex interplay of food allergies and micronutrient absorption, but your current path, while costly, seems to be leading you toward the steady health you need.

Have you had a DNA test to look for Celiac disease genes?  If she doesn't have any celiac specific genes, look for another explanation.  If she does have Celiac genes, assume they are turned on and active Celiac disease is progressing.  All first degree relatives (mother, father, siblings, children) should be genetically tested as well.   Sometimes blood tests are ambiguous or false negatives if one has anemia, diabetes or thiamine deficiency.  Certain medications like antihistamines and steroids can suppress the immune system and result in false negatives or ambiguous results on antibody tests.  

That was just the visual report, so need to wait for confirmation or otherwise from the results. They did take a biopsy from the upper end of the duodenum(D1). D2 looked unremarkable on the camera. Just wish we didn’t have to wait so long for the results as she’s naturally a very anxious person. But thanks so much for taking the time to answer me