Giving up gluten can harm your gut, damaging important bacteria

Scientists have found that long-term reduction in gluten consumption – often perceived as a health measure – may instead disrupt the balance of gut microbiota, reduce levels of key microbes, and cause ethanol accumulation associated with inflammation and metabolic risks.

A study published in the journal Nutrients assessed whether and how a long-term gluten-free diet affects the composition and function of gut microbiota in healthy adults.

Gluten and intestinal microflora

Gluten is the main food component of wheat, containing large peptides such as gliadins and glutenins. Because of their size, they are difficult for human digestive enzymes to break down, so they pass through the intestines undigested and cause changes in the microbiota. Gluten is associated with several diseases, including non-celiac gluten sensitivity, celiac disease, and gluten ataxia.

People who adopt a gluten-free lifestyle often report improved digestion, weight control, and overall well-being. However, evidence for these effects in healthy people is still limited, and avoiding gluten without a medically indicated diet may carry nutritional and metabolic risks.

One study found that after one year of following a gluten-free or low-gluten diet (LGD), patients with celiac disease had an increased risk of developing metabolic syndrome, likely due to the high glycemic index of many gluten-free foods. Such risks require long-term monitoring, as diet-induced changes in the microbiota may contribute to metabolic disorders.

About the study

This was a randomized controlled trial assessing the effects of long-term adherence to the LGD on the composition and metabolic activity of the gut microbiota in 40 healthy adults in France. Participants typically consumed approximately 160 g of bread and pasta per day, corresponding to 14–15 g of gluten.

Volunteers switched from a conventional high-gluten diet (HGD) to LGD in two 8-week cycles. Stool samples were collected at baseline (M0), after 8 weeks (M2), and in 20 individuals, after 16 weeks of LGD (M4). Microbiota was analyzed using 16S rRNA gene sequencing and PCR. Metabolism was assessed using 1H NMR spectroscopy of fecal fermentation products.

Research results

A total of 1,742,283 16S rRNA reads were processed from faecal samples after HGD and LGD. There was a significant decrease in microbiota alpha diversity during LGD, with a greater decrease after 16 weeks, suggesting an effect that increases over time. Beta diversity showed a clear shift in microbial communities during LGD compared to baseline.

At the phylum level, Verrucomicrobiota and Actinomycetota significantly decreased, while Bacteroidota and Bacillota increased. However, the Bacillota/Bacteroidota ratio did not change, which the authors consider an important detail. At the family level, Veillonellaceae increased, while Akkermansiaceae decreased.

Bifidobacteria were significantly reduced by qPCR (p = 0.0021), although this did not always reach statistical significance in sequencing. Levels of Escherichia coli, Faecalibacterium prausnitzii and the Lactobacillus–Pediococcus group were unchanged.

The classes Bacteroidia, Verrucomicrobiae and Clostridia changed at the species level. Akkermansia muciniphila decreased significantly by M4. The lactate-producing Lachnobacterium bovis also decreased. At the same time, some butyrate producers such as Roseburia and Faecalibacterium increased, which the authors believe helped maintain stable butyrate levels.

The cellulose-fermenting species R. callidus and Ruminococcus champanellensis also declined in M4. Members of the Lachnospiraceae family, including Eubacterium sp. and Blautia caecimuris, declined—even though Lachnospiraceae includes many butyrate producers.

After LGD, Enterobacteriaceae increased 10-fold, while total anaerobes remained unchanged. Levels of microbes capable of breaking down gluten decreased 10-fold by M2. Enterobacteriaceae, including potential ethanol producers such as E. coli, may contribute to inflammation when overgrown.

Metabolic changes

No significant differences in concentrations of faecal fermentation products were found between M2 and M4. In M2, a slight decrease in the proportion of acetate and an increase in propionate were observed. The proportion of ethanol increased more than threefold in M2 and M4. Ethanol accumulation is an important metabolic alarm signal, as it is associated with inflammation and metabolic syndrome.

A significant decrease in isobutyrate was also noted in M4. Despite the changes in microbiota, the levels of acetate, propionate and butyrate generally remained stable, which the authors attribute to the excess capacity of different bacteria to produce butyrate.

Most of the gluten-degrading strains belonged to the class Clostridia. There was also one isolate from Actinomycetota, two from Gammaproteobacteria, and three from Erysipelotrichia. Five strains belonged to the family Lachnospiraceae within Clostridia. One isolate from the family Oscillospiraceae was identified as Flavonifractor plautii, and three individuals were found to have Erysipelotrichaceae strains.

Conclusions

A 16-week LGD altered the composition and metabolic activity of the gut microbiota in healthy French subjects, inducing signs of dysbiosis. These changes could be due not only to the exclusion of gluten, but also to the replacement of wheat with rice and corn, which altered the fiber and polyphenol composition of the diet.

Further long-term studies may clarify the effects on immunity, physiology, and metabolism. However, data already indicate that long-term LGD in healthy individuals may disrupt the microbial balance and increase ethanol levels, potentially creating metabolic risks.