Celiac disease is an autoimmune condition that is triggered by the ingestion of gluten, a structural protein found in wheat, rye and barley. When someone with celiac disease eats gluten-containing food, their immune system mistakenly attacks the lining of their small intestine, causing inflammation and damage to the villi (tiny finger-like projections that are responsible for absorbing nutrients from food). Over time, this damage results in malabsorption, leading to a range of gastrointestinal symptoms including abdominal pain, diarrhea, bloating, nausea and unintended weight loss. The condition can also have far-reaching systemic effects, impacting other organs and bodily functions.

It is believed that celiac disease results from a combination of genetic and environmental factors. We know that individuals with specific genetic markers, particularly the HLA-DQ2 and HLA-DQ8 genes, are more susceptible to developing the condition; however, possessing these genes doesn’t guarantee its development. Researchers agree that environmental triggers such as gluten exposure and infections may prompt the immune system to react abnormally in genetically predisposed individuals.

Celiac disease can develop at any age, from infancy through to late adulthood, and affects around 1% of the global population. It is more common in people with a family history of celiac or other autoimmune disorders, such as type 1 diabetes. Also, women are diagnosed with celiac disease more frequently than men, although the reasons for this are still being studied.

There is currently no cure for the condition, but strict, lifelong adherence to a gluten-free diet can help to effectively manage symptoms and promote intestinal healing and regeneration of affected villi. Additionally, recent research suggests that the gut microbiome plays an important role in the disease’s development and severity of symptoms, so supporting a healthy microbiome through tailored interventions may help. 

What Does The Microbial Landscape in Celiac Disease Look Like?

In celiac disease, the gut microbial ecosystem undergoes substantial alterations in both its composition and function, commonly termed dysbiosis. Studies have shown that individuals with celiac disease often exhibit reduced microbial diversity and an imbalance in key bacterial groups within the small intestine and colon. A recurring observation across multiple studies is a reduction in protective anti-inflammatory bacterial species, such as Bifidobacteria and Lactobacilli, and an increase in potentially pathogenic gram-negative bacteria, including Bacteroides, Prevotella, and Escherichia 3 , which are associated with inflammation and gut barrier disruption. More detailed insights come from a study examining predominant bacterial populations in duodenal biopsies of pediatric patients with both active and treated celiac disease. In this study, the diversity of Bacteroides was found to be higher in the control subjects compared to the celiac groups.

Specifically, species that are typically enriched in healthy individuals, including B. distasonis, B. fragilis, B. uniformis, and B. ovatus, were depleted in celiac patients, while B. dorei, which may be linked to mucosal inflammation, was more common in those with active disease. Interestingly, although Bifidobacterium diversity was higher in celiac groups, this was largely driven by B. adolescentis and B. animalis subsp. lactis. Furthermore, lactic acid bacteria, including Lactobacillus fermentum and Weissella spp., were more frequently detected in treated patients and controls than in those with active celiac disease.

Remarkably, the gut microbiota of pediatric celiac disease patients appears to differ from that of adults. While Firmicutes dominate in adults with celiac disease, Proteobacteria are more prevalent in children with the condition. Specific bacterial genera also vary, with Mycobacterium and Methylobacterium being enriched in adults, and Neisseria and Haemophilus being more abundant in children. 5 Emerging longitudinal research suggests that microbial shifts may occur even before any clinical symptoms of celiac disease arise. In a prospective study of genetically at-risk children, those who later developed celiac disease showed early increases in pro-inflammatory species such as Dialister invisus, Parabacteroides spp., and certain Lachnospiraceae, alongside reductions in beneficial, butyrate-producing bacteria including Faecalibacterium prausnitzii, Clostridium clostridioforme, and the anti-inflammatory Streptococcus thermophilus.

How Gluten and the Gut Microbiota Interact in Celiac Disease

While shifts in the composition of the gut microbiome can precede celiac disease, gluten exposure can also play a key role in further shaping these microbial changes. The inflammation and tissue injury caused by the condition can disrupt the localized gut environment, favoring the growth of pro-inflammatory and potentially harmful bacteria while reducing beneficial microbes. At the same time, certain bacteria can influence gluten metabolism. For example, Lactobacilli produce enzymes that partially break down gluten into less immunogenic fragments, potentially protecting against inflammation. 6 However, since these protective bacteria are often reduced in celiac patients, gluten may persist in a more harmful form, exacerbating immune activation and gut damage. This shows that the relationship between gluten and the microbiome in celiac disease is a two-way street, highlighting the importance of microbiome-focused interventions to help restore microbial balance and alleviate symptoms.

Can Lifestyle Interventions Promote a More Resilient Microbiome in Celiac Disease?

Lifestyle interventions can support a healthy gut microbiome in all individuals, including those with chronic conditions, such as celiac disease. The objective in celiac disease management is to promote a microbiome that resembles a healthy state, with reduced levels of pro-inflammatory bacteria and increased populations of protective species. Beyond general healthy dietary guidance, the exciting field of personalized nutrition, guided by an individual’s unique gut microbiome profile, is emerging as a potential next step in the management of celiac disease. While a strict gluten-free diet is currently the cornerstone of celiac disease management and can lead to significant symptom improvement and gut healing, emerging research suggests that it may not fully restore the gut microbiome and can even reduce beneficial microbes such as Bifidobacteria, due to the reduced intake of dietary fibers found in gluten-containing foods. 7 This means that a more tailored dietary approach might be needed to optimize the gut microbiota in patients with celiac disease. For instance, interventions such as probiotics show promise for their potential to counteract microbial alterations in celiac disease and further support gut health. 8 Our current understanding suggests that personalizing any dietary and lifestyle interventions, based on an individual’s unique microbiome profile, might improve their effectiveness, paving the way for more precise management strategies.

Using Gut Microbiome Analysis to Guide Personalized Changes

Understanding the complex relationship between the gut microbiome and celiac disease is key to advancing personalized care. At Enbiosis, we leverage the power of whole-genome sequencing and AI to provide deep insights into what is really happening in the gut microbiome. We then use this information, backed by clinical data and real-life outcomes, to create tailored nutrition and supplement plans that actively support gut health and overall well-being.

Contact us today to find out how our evidence-backed technology can help in the management of celiac disease.