By naturopath Margaret Jasinska

A new study has found that SIBO (Small Intestinal Bacterial Overgrowth) is surprisingly common in people with coeliac disease and may help explain why some people continue to feel unwell even after cutting out gluten.

The small intestine is normally a relatively quiet place, with far fewer bacteria and other microbes than the large intestine (colon). When too many bacteria, fungi, or gas-producing organisms take up residence there, they can cause a range of uncomfortable symptoms: bloating, gas, stomach pain, diarrhoea, constipation, and nausea.

This matters for coeliac disease because many people still feel terrible even after switching to a strict gluten-free diet.

What did the study look at?

Researchers reviewed medical records from people with confirmed coeliac disease who had been tested for microbial overgrowth. Testing was done in two ways: either by collecting fluid directly from the small intestine during a camera procedure (endoscopy), or by breath testing,  where a person drinks a sugar solution and the gases produced by gut microbes are measured in their breath.

In total, 256 patients had the fluid culture test and 39 had breath testing.

The findings of the study

The results depended on which measurement threshold was used, but bacterial overgrowth was common, affecting anywhere from 18% to 50% of those tested, depending on the cutoff applied. Fungal overgrowth was less common, showing up in just over 4% of patients.

Importantly, the researchers did not find a link between bacterial overgrowth and the degree of gut damage seen on biopsy. This means that even if your gut lining appears to be healing, microbial overgrowth could still be present and causing symptoms.

The strongest connection was seen in people with refractory coeliac disease, which means symptoms and gut damage persist despite following a strict gluten-free diet and ruling out other causes. In this group, bacterial overgrowth was far more common.

What about the breath test results?

Of the 39 patients who had breath testing, about 23% had positive results and every positive result involved elevated methane. Methane-producing organisms are typically linked to constipation and sluggish gut movement, which is interesting because while coeliac disease is often associated with diarrhoea, many people develop constipation after going gluten-free.

The study also found that breath testing and fluid culture testing didn’t always agree with each other, a reminder that there’s no perfect test for microbial overgrowth, and results can vary depending on the method used.

What does this mean for coeliacs?

If you have coeliac disease and are still experiencing bloating, gas, pain, diarrhoea, or constipation after genuinely sticking to a gluten-free diet, microbial overgrowth could be the cause. It’s one of several possible explanations for persistent symptoms; others include accidental gluten exposure, lactose intolerance, irritable bowel syndrome, or other digestive conditions.

Microbial overgrowth in the small intestine typically causes abdominal bloating and irritable bowel type symptoms. BactoClear capsules contain herbal antimicrobials that can help relieve the symptoms of medically diagnosed irritable bowel syndrome.

When microbes over grow in the small intestine, they irritate it and can result in leaky gut syndrome. Ultimate Gut Health powder contains soothing and healing nutrients to repair a leaky gut.

Reference: https://www.nature.com/articles/s44355-026-00059-x