The autoimmune disorder celiac disease results in mucosal inflammation and injury of the small intestine, driven by dietary gluten, resulting in a wide range of varied symptoms. Although most patients’ symptoms improve on a gluten-free diet, the restriction can lead to nutrient deficiencies including fiber. Because of that, many people with celiac disease are advised to eat more fiber, either through diet or supplements.

Now, new research suggests that the benefits of that fiber may depend on the composition of the microbiome. Although duodenal microbiota has been known to be altered in celiac disease, how the microbial fiber metabolism is affected has remained unknown.

The new study found that people with celiac disease had a significantly reduced capacity to metabolize dietary fiber in the small intestine due to the lack of Prevotellaceae bacteria. Because the finding was observed in both newly diagnosed people and in those who have been managing celiac disease for years with a gluten-free diet, this result was determined to be independent of treatment with the gluten free diet.

This work is published in the article, “Small intestinal microbial fiber metabolism dysfunction in celiac disease,” published in Nature Communications.

“Originally, we thought that the problem was that people aren’t getting enough fiber,” says Mark Wulczynski, PhD, postdoctoral fellow with McMaster’s Farncombe Nutrition Initiative. “Then we found out that people might not have the right bacteria to use the fiber that they’re already eating. Adding more fiber won’t be the solution unless you fix the underlying problems with using it.”

Celiac disease is estimated to impact approximately one percent of the population, with the only current treatment being a strict gluten-free diet. However, the new research suggests that removing gluten alone doesn’t fully restore the gut’s microbiome functional capacity. Future therapies may need to combine dietary strategies with microbiome‑directed approaches, such as microbial restoration or targeted probiotics.

“While a gluten-free diet remains essential for celiac disease, our findings suggest future therapies may also need to support the gut microbiome,” says Elena Verdú, MD, PhD, professor with McMaster’s department of medicine and director of the Farncombe Family Digestive Disease Health Research Institute. “We found reduced fiber-processing activity in the upper gut, the area damaged in celiac disease, which is surprising because this part of the gut has not traditionally been seen as a major site of fiber metabolism. This opens the door to combining dietary strategies like added fiber with probiotics that can metabolize it.”

Using preclinical models, the researchers investigated which fiber types are helpful for healing the gut. They found inulin—a fiber found in everyday foods like bananas, chicory root, garlic and onions—accelerated healing of gluten-induced intestinal injury by feeding the small intestinal microbiome.

More specifically, “colonization of germ-free mice with Prevotella increased small intestinal short chain fatty acids. In gluten-sensitized mice expressing the celiac risk gene, HLA-DQ8, an inulin-supplemented diet facilitated microbial saccharolytic function and SCFA production to accelerate mucosal healing in the small intestine during the GFD.”

To verify this in patients, researchers collected small intestinal fluid from three groups: people newly diagnosed with celiac disease, people who had followed a gluten-free diet for more than two years, and healthy controls. They analyzed the microbiome to determine which bacteria were present and whether they carried the genes needed to break down different types of fiber. They also compared these findings with participants estimated dietary fiber intake and with measurements of plant DNA in stool, providing an objective marker of fiber sources in the diet.

Celiac patients, whether newly diagnosed or treated with a gluten-free diet, showed a distinct combination of low fiber intake and a lack of bacteria known to break down fiber in the small intestine. This suggests that supporting gut health in celiac disease may require both the right fiber and the right bacteria in the small intestine.

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