Still Symptomatic After Going Gluten-Free? SIBO May be Part of the Picture
For many people with Celiac Disease, going gluten-free leads to major improvement in digestive symptoms. But for others, bloating, gas, abdominal discomfort, or diarrhea continue even after gluten has been removed from the diet.
Small intestinal bacterial overgrowth (SIBO) may, in fact, be contributing to ongoing digestive symptoms. Research suggests that roughly 18–20% of patients with celiac disease may also have SIBO, with even higher rates seen in people whose symptoms persist despite following a gluten-free diet.
At first glance, this relationship may seem surprising. One condition is an autoimmune disease triggered by gluten, while the other involves excessive bacterial growth in the small intestine. But the connection becomes easier to understand when you look at how the small intestine normally protects itself and what happens when those protective systems break down.
How the Small Intestine Normally Prevents Bacterial Overgrowth
The small intestine is designed to contain relatively low levels of bacteria compared to the large intestine. Several defense systems help keep bacterial populations under control, including intestinal motility, digestive secretions, immune defenses, and the migrating motor complex (MMC), sometimes described as the gut’s “housekeeping wave.”
When these systems are disrupted, bacteria are more likely to remain in the small intestine and multiply.
What Happens in Celiac Disease
In active celiac disease, the immune system reacts abnormally to gluten and damages the lining of the small intestine. This damage interferes with nutrient absorption, but it can also disrupt the intestine’s normal protective functions.
Researchers believe several changes associated with celiac disease may increase the risk of SIBO. We describe three key changes below:
Slowed Intestinal Motility
One of the most important protective mechanisms impaired by celiac disease is the effective movement of the small intestine. Studies have shown that untreated celiac disease is often associated with delayed intestinal transit and changes in gut motility.
When the small intestine is not moving normally, food and bacteria are more likely to remain in place and accumulate rather than being cleared effectively.
Researchers also believe hormonal changes in celiac disease may contribute to slowed intestinal movement, further increasing the risk of bacterial overgrowth.
Malabsorption and Nutrient Fermentation
Damage to the intestinal lining also reduces the body’s ability to absorb nutrients properly. When carbohydrates, fats, and other nutrients remain unabsorbed inside the small intestine, they can become fuel for bacteria. This creates an environment that encourages fermentation, gas production, and bacterial proliferation.
Changes in the Intestinal Barrier
Some researchers believe that celiac disease may weaken the small intestine’s normal antimicrobial defenses. Ongoing inflammation may impair the intestine’s ability to regulate bacterial populations and prevent microbes from persisting in the small bowel.
Why Symptoms Can Overlap
One reason the relationship between celiac disease and SIBO can be difficult to recognize is that the two conditions often produce very similar symptoms.
Both can cause:
bloating
abdominal discomfort
diarrhea
gas
weight loss
fatigue
nutrient deficiencies
SIBO can also worsen malabsorption in patients with celiac disease, contributing to lower levels of iron, albumin, beta-carotene, and other nutrients.
Because the symptoms overlap so closely, persistent digestive problems are not always easy to interpret. Ongoing symptoms may reflect continued gluten exposure, persistent intestinal inflammation, bacterial overgrowth, or multiple conditions working together.
SIBO and Nonresponsive Celiac Disease
Researchers are especially interested in SIBO in patients with what is known as nonresponsive celiac disease. This term is generally used when symptoms continue despite following a gluten-free diet for at least 6 to 12 months.
Studies suggest that SIBO may be more common in these patients than in celiac patients who respond well to treatment. A pooled analysis found that approximately 28% of symptomatic patients with persistent symptoms on a gluten-free diet had evidence of SIBO.
Importantly, however, SIBO is not always the only explanation for ongoing symptoms. Many patients with nonresponsive celiac disease also have other coexisting conditions, including microscopic colitis, irritable bowel syndrome, lactose intolerance, pancreatic insufficiency, or refractory celiac disease.
In one study, 67% of patients with both SIBO and nonresponsive celiac disease also had another significant gastrointestinal disorder contributing to symptoms.
What Researchers Still Do Not Fully Understand
Although the association between celiac disease and SIBO is increasingly recognized, many questions remain unanswered.
Researchers still do not fully understand whether in celiac patients, SIBO is directly caused by celiac-related intestinal damage, changes in motility, shifts in the microbiome, or if it is a combination of factors. Estimates of how common SIBO is in celiac disease also vary widely between studies, partly because researchers use different diagnostic methods.
What is clear is that persistent digestive symptoms in celiac disease should not automatically be assumed to mean ongoing gluten exposure alone. In some patients, bacterial overgrowth may also be contributing to the clinical picture.
Key References
Charlesworth, R. P. G., & Winter, G. (2020). Small intestinal bacterial overgrowth and celiac disease – coincidence or causation? Expert Review of Gastroenterology & Hepatology, 14(5), 305–306. https://doi.org/10.1080/17474124.2020.1757428
Leffler, D. A., Dennis, M., Hyett, B., Kelly, E., Schuppan, D., & Kelly, C. P. (2007). Etiologies and predictors of diagnosis in nonresponsive celiac disease. Clinical Gastroenterology and Hepatology, 5(4), 445–450. https://doi.org/10.1016/j.cgh.2006.12.006
Losurdo, G., Marra, A., Shahini, E., Girardi, B., Giorgio, F., Amoruso, A., Pisani, A., Piscitelli, D., Barone, M., Principi, M., Di Leo, A., & Ierardi, E. (2017). Small intestinal bacterial overgrowth and celiac disease: A systematic review with pooled-data analysis. Neurogastroenterology & Motility, 29(6), e13028. https://doi.org/10.1111/nmo.13028
Rubio-Tapia, A., Barton, S. H., Rosenblatt, J. E., & Murray, J. A. (2009). Prevalence of small intestine bacterial overgrowth diagnosed by quantitative culture of intestinal aspirate in celiac disease. Journal of Clinical Gastroenterology, 43(2), 157–161. https://doi.org/10.1097/MCG.0b013e3181557e67
Shah, A., Thite, P., Hansen, T., Kendall, B. J., Sanders, D. S., Morrison, M., Jones, M. P., & Holtmann, G. (2022). Links between celiac disease and small intestinal bacterial overgrowth: A systematic review and meta-analysis. Journal of gastroenterology and hepatology, 37(10), 1844–1852. https://doi.org/10.1111/jgh.15920
