The impact of a gluten free diet on a healthy microbiome

food intolerance gluten prebiotic

You may have considered restricting your gluten intake at one point or another. Whether it’s in the hope that it will alleviate your gut symptoms or that it will make you healthier– there sure are alluring and compelling reasons presented in the media as to why one would want to go gluten-free. While there are certainly some people who will benefit from a gluten-free diet, such as those with coeliac disease or who are gluten-intolerant, emerging research tells us that the rest of us should think twice before we point the finger at gluten-containing foods and adopt a gluten-free diet ourselves. What happens in cases where gluten is restricted unnecessarily? Should we be restricting it because it’s supposedly bad for us, or can doing so actually have negative health consequences? Let’s look at the evidence.

First off, what is gluten?

Gluten is a structural protein that is found in certain grains, including wheat, barley, and rye. In many baked products, gluten has an elastic texture and acts like a glue to help hold the dough together. It’s an important ingredient for maintaining the product’s structure and texture. Many gluten-free products need a suitable alterative to replicate the texture and taste of gluten-containing foods, and this often results in unrecognisable ingredients being added to the product.   

Can restricting gluten affect the gut?

When it comes to gut health, our diet is one of the most well researched factors that can influence the state of our gut. The gut microbiota is greatly influenced by what we eat, and our choices can continuously drive bacterial diversity, or suppress it. Growing research indicates that when healthy individuals restrict gluten, it can have the latter of these effects. Some potential health effects are:

  • May lead to gut dysbiosis

 There is research to suggest that unnecessary restriction of gluten can cause poorer gut health. One study followed 10 healthy subjects that followed a gluten-free diet for a month. Using stool samples, it was found that populations of healthy bacteria decreased, and unhealthy bacteria increased, resulting in gut dysbiosis [1]. Other studies have found similar results [2, 3].

  • May lower immunity

The same study also found that a low-gluten diet lowered immune stimulatory effects. These changes in bacterial composition appeared to weaken the immune response and lead to chronic inflammation [1].

  • May increase risk of heart disease

 In 2017, a large-scale study that had over 100,000 participants investigated whether there was an association between gluten consumption and coronary heart disease among non-coeliac individuals. This study found that healthy individuals following the low-gluten diet had a higher risk of poor heart health outcomes [4].

Why might this be the case?

  • Reduced intake of prebiotics

Gluten-containing foods are a common source of non-digestible carbohydrates, which remain undigested when we consume them and are a source of fuel for our good gut bacteria. When they feed on these carbohydrates, they produce beneficial compounds that bring about a range of health benefits, including supporting digestive health. A gluten-free diet may reduce the supply of these non-digestible carbohydrates, hindering the growth of our good bacteria and potentially leading to the overgrowth of pathogens [1].

  • Reduced intake of whole grains

Many gluten-containing foods are also healthy foods that are rich in nutrients. The fibre found in wheat, barley, and rye, helps to reduce, and regulate cholesterol levels and can lower your risk of heart disease [5]. It’s thought that the reduced number of whole grains may be an explanation for why there could be an increased risk of heart disease when following a gluten-free diet unnecessarily.

  • Nutritional Quality of Gluten-free Diet

In many of these studies, participants swapped their regular products for gluten-free alternatives. There is some research that suggests many available gluten-free foods are not enriched with nutrients including fibre, iron, folate and B vitamins and some products may have higher levels of trans fats and salt in comparison to gluten-containing products [6].

What can you do optimise your gut health if you need to avoid gluten?

Aim to include a broad variety of gluten-free whole grains in your diet to increase your chances of getting a wider variety of nutrients and fibres [7]. These include brown rice, red rice, black rice, sorghum, teff, millet, amaranth, buckwheat, and quinoa to name a few.

The Bottom Line

While people who have coeliac disease or who are gluten-intolerant should eliminate or limit gluten, those who restrict gluten unnecessarily may experience reduced gut health. If you have excluded gluten in the hope that it would alleviate gut symptoms, but your symptoms are still present, there could be many other potential causes including FODMAPs, stress, or the way you eat. Working with one of our gut expert, Accredited Practising Dietitians can help you get to the bottom of your gut issues while optimising the health of your gut!


[1]      Sanz Y. Effects of a gluten-free diet on gut microbiota and immune function in healthy adult humans. Gut Microbes. 2010 May-Jun;1(3):135-7. doi: 10.4161/gmic.1.3.11868. Epub 2010 Mar 16. PMID: 21327021; PMCID: PMC3023594.

[2]      Singh RK, Chang HW, Yan D, Lee KM, Ucmak D, Wong K, et al. Influence of diet on the gut microbiome and implications for human health. J Transl Med 2017.

[3]      Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, et al. The influence of a short-term gluten-free diet on the human gut microbiome. Genome Med 2016.

[4]      Lebwohl B, Cao Y, Zong G, Hu FB, Green PHR, Neugut AI, Rimm EB, Sampson L, Dougherty LW, Giovannucci E, Willett WC, Sun Q, Chan AT. Long term gluten consumption in adults without celiac disease and risk of coronary heart disease: prospective cohort study. BMJ. 2017 May 2;357:j1892. doi: 10.1136/bmj.j1892. PMID: 28465308; PMCID: PMC5421459.

[5]      Aune, D., Keum, N., Giovannucci, E., Fadnes, L. T., Boffetta, P., Greenwood, D. C., Tonstad, S., Vatten, L. J., Riboli, E., & Norat, T. (2016). Whole grain consumption and risk of cardiovascular disease, cancer, and all cause and cause specific mortality: systematic review and dose-response meta-analysis of prospective studies. BMJ (Clinical research ed.)353, i2716.

[6]      Niland B, Cash BD. Health Benefits and Adverse Effects of a Gluten-Free Diet in Non-Celiac Disease Patients. Gastroenterol Hepatol (N Y). 2018 Feb;14(2):82-91. PMID: 29606920; PMCID: PMC5866307.

[7]      Bascuñán, K.A., Vespa, M.C. & Araya, M. Celiac disease: understanding the gluten-free diet. Eur J Nutr 56, 449–459 (2017).

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