Navigating the Health of the Gut Microbiome on a Gluten Free Diet

Expert dietitian Joanna Aaron outlines the risks of following a gluten free diet without being aware of your gut microbiome

GUEST BLOG: Joanna Aaron APD, AN

Coeliac disease (CD) is a condition in which the body’s immune system attacks the villi of the small intestine when it is exposed to gluten, a protein. Gluten is naturally found in wheat, spelt, rye, barley and oats that is cross-contaminated during manufacture. CD may occur in people who carry the human leukocyte antigen (HLA) gene. The only treatment to date, is a life-long adherence to the gluten free diet (GFD).

Exposure to gluten in the small intestine can trigger inflammation and put the body at risk of severe nutrient deficiencies due to malabsorption. Healing of the villi differs for each individual. Therefore, gut health is an important factor in CD and navigating the health of the gut on a GFD is necessary.

Foods that are labelled GF must contain less than 20mg/kg of gluten (20 parts per million) which can make the GFD a fairly restrictive one and subject to inadequate nutrition. When a person is newly diagnosed with CD, their main aim is to find out how to follow a GFD and live a gluten free (GF) life.

Hence, focus would be to avoid gluten; gliadin in wheat, secalin in rye, hordein in barley and in Australia oats, though debatable is still not considered GF and introduction to it must be done with a gastroenterology team. Special care would be directed at ensuring gluten is not in the foods that are consumed or part of cross contamination.

However, one of the basic aspects of nutrition in a gluten free life is adequacy of good quality GF foods. While the GFD reduces the risk of villi damage, the lack of attention to the quality of GF food products can lead to deficiencies such as dietary fibre, calcium, iron, folate and essential vitamins. Also, the risk of cardiometabolic health may be increased in people who have a poor quality GFD.

A review conducted by Gessaroli et al, 2023 on the nutrient intake in adults and children living with CD found that the quality of GFDs tend to be high in saturated fats (teenagers), and low in fibre (adults). The review also showed that teenagers had a reduced intake of calcium and iron while protein foods were consumed in excess.

It was also highlighted that long-term poor quality GF diets has a negative impact on the gut. The article implicated that long term intake of the GFD can impact heart and bone health. While little was discussed about the gut health, long term inadequate essential nutrients from dairy and other nutrient dense foods and low fibre intake can cause gut dysbiosis.

GFD Effect on the Gut Microbiome

Joanna Aaron details the very real impact that a gluten free diet lacking proper nutrition will have on the gut microbiome

There are trillions of microorganisms such as bacteria, viruses, archaea, eukaryotes, and protozoa living in our body with Firmicutes, Bacteroidetes, and Actinobacteria being the most abundant in our gut. In CD, the diversity of the gut microbiome is compromised by the long-term quality of the GFD.

The gut microbiome is important as it is involved in producing energy for our body, building our immune system, fortifying the integrity of our gut, and keeping the protective layer of our intestine in good health. As such the health of the gut microbiome is dependent on what we feed it.

Simply put, frequent consumption of foods that are high in fat, low in dairy and inadequate in the fibre types, can change the environment in the gut causing an imbalance of microorganisms including those beneficial ones. This imbalance of microorganisms is known as gut dysbiosis. Gut dysbiosis can increase inflammatory factors in the gastrointestinal tract which may disrupt the healing process of the villi.

While the primary goal of a GFD in coeliac disease is to prevent gluten from interacting with the small intestinal villi thereby avoiding an immune response and subsequent inflammation, this goal can be compromised if the overall quality of the diet is poor. Many gluten-free processed foods are high in refined starches, added sugars, and unhealthy fats, all of which can contribute to systemic and gut-specific inflammation.

It is important to understand that a small amount of low-grade inflammation in the body is normal and reflects the immune system’s ongoing efforts to defend against potential threats. However, when the diet lacks nutrient-dense, anti-inflammatory foods such as fibre-rich grains, vegetables, fruits, legumes, and healthy fats and dairy, this low-grade inflammation can escalate.

In the context of coeliac disease, this heightened inflammatory state may lead to gut irritation and symptoms that mimic or even trigger a coeliac flare, despite strict gluten avoidance. Supporting gut health through a balanced, whole-food-based GFD is therefore essential not just for avoiding gluten, but for reducing overall inflammation and promoting long-term healing.

What Can Be Done to Improve Your Gut Microbiome

Access your own personalised gluten-free nutrition plan to cut out the confusion

If you have coeliac disease or gut-related symptoms, working with a dietitian can help you go beyond simply avoiding gluten. It usually begins with an initial consultation, where your dietitian will take a thorough health and diet history, review any test results, and assess your current eating habits.

You will then receive a personalised gluten-free nutrition plan focused on reducing inflammation, supporting gut health, and meeting your nutritional needs. This includes practical advice on reading food labels, preventing cross-contamination, choosing and personalising nutrient-dense foods, and encouraging a healthy gut microbiome with fibre and anti-inflammatory foods.

Education is a key part of the process. Your dietitian will equip you with the skills to eat safely and confidently, whether at home or when eating out. Follow-up appointments are recommended to monitor progress, fine-tune your plan, and manage any ongoing symptoms or concerns. With targeted nutrition, you can heal the gut, restore microbiome diversity, and feel confident in managing your coeliac disease long-term.

References

1. Catassi C, Verdu EF, Bai JC, Lionetti E. Coeliac disease. The Lancet 2022;399(10344):2413-26.

2. Bascuñán KA, Araya M, Roncoroni L, Doneda L, Elli L. Dietary Gluten as a Conditioning Factor of the Gut Microbiota in Celiac Disease. Advances in Nutrition 2020;11(1):160-74.

3. Cohen IS, Day AS, Shaoul R. Gluten in Celiac Disease-More or Less? Rambam Maimonides Med J 2019;10(1).

4. Gessaroli M, Frazzoni L, Sikandar U, Bronzetti G, Pession A, Zagari R, et al. Nutrient intakes in adult and pediatric coeliac disease patients on gluten-free diet: a systematic review and meta-analysis. European journal of clinical nutrition 2023;77.

5. Ma ZF, Lee YY. The Role of the Gut Microbiota in Health, Diet, and Disease with a Focus on Obesity. Foods 2025;14(3):492.

Joanna Aaron Bio

Joanna Aaron is an Accredited Practicing Dietitian. She is the founder and sole trader of I on Nutrition, a private practice with a special focus on gut health. Joanna helps her clients reset their gut health with food and nutrition. She is a member of Dietitians Australia and Dietitian Crohn’s Colitis Australian Network (DECCAN) and keeps current with the latest nutrition evidenced.