Effects of a Gluten-Free Diet on the Gut Microbiota

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Gluten free. Image Credit: Baibaz / Shutterstock
Gluten free. Image Credit: Baibaz / Shutterstock

Why a Gluten Free Diet?

Gluten is a protein found in grains such as wheat, barley, and rye, and is comprised of gliadins. For some people, eating foods that contain gluten can cause digestive problems due to gluten-related disorders.

Gluten-related disorders can range from mild to severe in symptoms, and include celiac disease and non-celiac gluten sensitivity.

For patients suffering with gluten-related disorders, it is necessary to stick to a gluten-free diet. More recently, people who do not suffer from gluten-related disorders have started to adopt a gluten-free diet as part of a lifestyle choice.

The rising popularity of gluten-free diets as a lifestyle choice means that they outnumber the number people who must eat a gluten-free diet for their gluten-related disorder.

How Does a Gluten-free Diet Affect the Microbiota?

The gut microbiota consists of the numerous microorganisms that live in our gut. It has been shown that the gut microbiota is key to protecting our gut against pathogens, and that it has the ability to make and regulate molecules going into the blood.

Intestinal microbiome, 3D illustration showing anatomy of human digestive system and enteric bacteria Escherichia coli, E. coli, colonizing jejunum, ileum, other parts of intestine. Gut normal flora - Illustration Credit: Kateryna Kon / Shutterstock
Intestinal microbiome, 3D illustration showing anatomy of human digestive system and enteric bacteria Escherichia coli, E. coli, colonizing jejunum, ileum, other parts of intestine. Gut normal flora - Illustration Credit: Kateryna Kon / Shutterstock

Also, the microbiota has the ability to process molecules that the host does not have the capacity to process. For example, the microbiota can metabolize carbohydrates that the host cannot digest, and produce vitamins that the host cannot.

It is heavily influenced by diet, therefore there have been various studies done to investigate how a gluten-free diet affects the gut microbiota.

Bonder and co. investigated the effect of a short-term gluten-free diet on the microbiota. For this study, the authors recruited 21 adult volunteers who did not suffer from symptomatic gluten-related disorders, and followed them through 4 weeks on a gluten-free diet, 5 weeks on a “wash-out” diet and a further 4 weeks on the individuals’ habitual diet.

Fecal samples were collected from the volunteers before the gluten-free diet, then weekly during the gluten-free diet and the habitual diet. DNA was then extracted from the stool samples, and the 16S rRNA sequence was determined to see the bacterial composition in the microbiome.

The authors found that while there was no difference in the overall microbiome diversity of individual volunteers, certain species changed in abundance on a gluten-free diet. This included reductions in Veillonellaceae family, Ruminococcus bromii and Roseburia faecis, and increases in Victivallaceae, Clostridiaceae and Coriobacteriaceae families. Most of these species are known to play a role in starch metabolism.

In another study, by de Palma and co., 10 volunteers without symptomatic gluten-related disorders were recruited, and over one month their diet was changed to gluten-free. When the fecal microbiota was analyzed by a combination of techniques, it showed that the number of beneficial bacteria (Bifidobacterium, Lactobacillus) decreased while numbers of potentially pathogenic bacteria (Enterobaceriaceae, E. coli) increased.

In the case of patients with celiac disease, it has been shown that their microbiota is altered: there is a decrease in protective species and an increase in species that could become pathogenic.

Initial studies showed that the imbalance in the microbiota of celiac patients was still somewhat unbalanced after 2 years on a gluten-free diet. This was noticed in the reduced number of potentially pathogenic bacteria, such as E. coli and Staphylococcus species, while the number of protective species such as Bifidobacterium and Lactobacillus was still reduced.

This has been supported by other studies, which showed a reduction in other protective species such as Enterococcus, and an increase in other potentially pathogenic species such as Bacteroides, Salmonella, Shigella, Klebsiella and Enterobacteriaceae family. These changes could also influence inflammation in the gut.

Overall, these studies show that dysbiosis of the gut microbiota seen in celiac disease patients is not fully reversed by the adoption of a gluten-free diet.

In conclusion, these studies show that a gluten-free diet can cause changes in the gut microbiota, and that this could potentially be harmful.

What are the Difficulties in Studying the Microbiota?

While there are consistent findings from these studies, there are some limitations. One limitation is that there are many ways of studying the microbiota, ranging from culture-based methods to DNA sequencing-based methods.

Each technique has its own advantages and disadvantages, and it is difficult to know if differences between these techniques can be accounted for.

Another limitation is the classification of the species in the microbiota: it is traditionally thought that bacteria belonging to the same species have highly similar DNA sequences, but this is not always the case.

Also, some studies group similar 16S rRNA sequences into “operational taxonomic units” (OTUs) based on similarity, but these OUTs may be made up of species that are not related at all.

It should also be noted that genes can pass easily between bacteria, therefore this could create species that are difficult to classify due to the presence of genes that originate from other species.


Further Reading

Last Updated: Sep 25, 2019

Dr. Maho Yokoyama

Written by

Dr. Maho Yokoyama

Dr. Maho Yokoyama is a researcher and science writer. She was awarded her Ph.D. from the University of Bath, UK, following a thesis in the field of Microbiology, where she applied functional genomics to Staphylococcus aureus . During her doctoral studies, Maho collaborated with other academics on several papers and even published some of her own work in peer-reviewed scientific journals. She also presented her work at academic conferences around the world.


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  1. Yvonne Weeks Yvonne Weeks United States says:

    The studies cited prove more that gluten free diet foods cause dysbiosis then they prove gluten free diets do. Not to mention the small sample sizes are hardly conclusive.
    How about some studies where the participants eat real food and not processed GF junk food, which by the way isn't even wholly GF as per the FDA allowing 9PPM and Spain allows 20PPM of gluten in GF foods.
    How about a study that looks at replacing the PREbiotic fiber that is given up when patients go GF since gluten containing foods are the primary source of prebiotics in the Standard American Diet.  Or gluten free diets that focus on nutrient density instead of replacing processed junk with processed junk.
    The right kinds of studies matter, and these are not focusing on the right questions if you want to prove that gluten free is the actually problem versus the Gluten free diet choices most people adopt. I propose that a study that compares GF diets that have a focus on healthy, nutrient dense,  and foods with proper prebiotics against a diet of GF substitution foods would come up with vastly different results to the microbiome. I don't think the same species would be lacking in a healthy diet that focuses on replacing the prebiotics that gluten containing foods provide.

The opinions expressed here are the views of the writer and do not necessarily reflect the views and opinions of News Medical.
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