Gluten, gluten-free diet and gut microbiota

The relationship between gluten and gut microbiota is currently the subject of growing scientific interest, especially in order to understand how a gluten-free diet may influence the balance of intestinal bacteria.

Abstract
A gluten-free diet is the main treatment for celiac disease and is increasingly widespread also among non-celiac individuals. Several studies have shown that adopting a gluten-free diet may be associated with changes in the composition of the gut microbiota, including a reduction in Bifidobacterium and Lactobacillus and an increase in Enterobacteriaceae. The most common interpretation attributes such changes to the reduction of fermentable carbohydrates present in gluten-containing cereals. However, fermentable substrates for the microbiota may also derive from many other dietary sources. Gluten is also a protein partially resistant to digestion, and its degradation may generate peptides that reach the intestine and are further metabolized by the microbiota. This article analyzes the available evidence on the relationship between a gluten-free diet and gut microbiota and discusses the still little explored hypothesis of a possible ecological role of peptides derived from incomplete gluten digestion in the intestinal microbial ecosystem.

Highlights
1 – A gluten-free diet may modify the gut microbiota.
2 – In some studies a reduction in Bifidobacterium and Lactobacillus is observed.
3 – The most common explanation is the reduction of fermentable fibers present in wheat.
4 – However, the microbiota can also obtain fibers from legumes, fruit, vegetables and resistant starch.
5 – Gluten is a protein partially resistant to digestion and some of its peptides reach the intestine.
6 – The microbiota possesses enzymes capable of degrading these peptides.
7 -The possible ecological role of gluten peptides in the microbiota is a field of research that is still little explored.

The paradox of the gluten-free diet

A gluten-free diet represents the indispensable treatment for celiac disease and is increasingly widespread also among non-celiac individuals. However, in recent years several studies have observed that adopting a gluten-free diet may be associated with changes in the composition of the gut microbiota.

In particular, some studies have reported:

1. reduction in Bifidobacterium

2. reduction in Lactobacillus

3. increase in Enterobacteriaceae

These alterations have been observed not only in patients with celiac disease but also in healthy individuals who adopt a gluten-free diet.

The explanation most frequently proposed attributes such changes to the reduction of fermentable carbohydrates present in gluten-containing cereals, such as fructans and arabinoxylans.
However, this interpretation raises some questions.

The gut microbiota can in fact use fermentable fibers coming from many other dietary sources, including legumes, fruit, vegetables, seeds and resistant starch. Moreover, gluten is a protein that during digestion generates numerous peptides partially resistant to enzymatic degradation, some of which may reach the intestine and be further metabolized by the microbiota.
This raises a question that is still little explored:

is it possible that the human microbiota, especially in populations with high consumption of gluten-containing cereals, has also developed a metabolic adaptation toward peptides derived from incomplete gluten digestion?

At present there are no definitive answers, but this hypothesis represents an interesting field of research for better understanding the relationship between gluten, diet and gut microbiota.

1. Gluten-free diet and changes in the microbiota
Several studies show that adopting a gluten-free diet may be associated with changes in the gut microbiota.
In particular, the following have been observed:
1 – decrease in Bifidobacterium
2 – decrease in Lactobacillus
3 – increase in Enterobacteriaceae
These changes have been detected both in subjects with celiac disease even after years of a gluten-free diet, and in healthy individuals adopting a gluten-free diet [1][2][3].
A study conducted on healthy subjects showed that a short-term gluten-free diet is associated with:
1 – reduction in Bifidobacterium
2 – reduction in Lactobacillus
3 – increase in Escherichia coli and Enterobacteriaceae [1].
Alterations of the microbiota have also been observed in celiac patients treated with a gluten-free diet, suggesting that normalization of the microbiota does not always occur completely despite clinical remission of the disease [2][4].
Some studies report that 60–80% of celiac patients still show intestinal dysbiosis despite a correct gluten-free diet. Probiotics and dietary modifications can modulate the microbiota in celiac patients, but no therapy has yet demonstrated that it can stably correct dysbiosis

2. The most common interpretation: reduction of fermentable carbohydrates
The explanation most frequently proposed is that a gluten-free diet entails a reduction of fermentable complex carbohydrates, with a consequent decrease in the substrates available for beneficial intestinal bacteria. By eliminating cereals such as wheat, rye and barley, the intake of some components of the wheat food matrix is in fact reduced, including:
1 – fructans
2 – arabinoxylans
3 – some fermentable fibers
These compounds are important substrates for the gut microbiota and contribute to the production of beneficial metabolites such as short-chain fatty acids [5][6].
According to this interpretation, therefore, the alterations observed in the microbiota would be mainly due to the modification of the food matrix and the intake of fermentable fibers, rather than to the absence of gluten itself [5].

3. A critical point: fibers can come from many other sources
However, fermentable substrates for the microbiota can come from many other dietary sources, including:
1 – legumes
2 – fruit
3 – vegetables
4 – seeds
5 – tubers
6 – rice
7 -resistant starch
Numerous studies indicate that the following are particularly important for microbiota health:
1 – fermentable fibers
2 – complex plant polysaccharides
3 – resistant starch
components that do not depend exclusively on wheat consumption.
Therefore, claiming that the wheat food matrix is indispensable for maintaining intestinal eubiosis is not supported by definitive evidence.

4. What happens to gluten during digestion
Gluten is a complex protein composed mainly of:
1 – gliadins
2 – glutenins
During gastrointestinal digestion some protein sequences are particularly resistant to enzymatic hydrolysis. This happens because gluten contains sequences rich in proline and glutamine, which make complete degradation by human digestive enzymes difficult [7][8].
Consequently, some peptides derived from gluten digestion may reach the small intestine and the colon in the form of partially digested protein fragments.

5. The role of the microbiota in gluten degradation
Several intestinal bacteria possess enzymes capable of further degrading peptides derived from gluten.
Among the most studied genera are:
1 – Lactobacillus
2 – Bifidobacterium
3 – Bacteroides
4 – some species of Clostridium
These microorganisms possess microbial peptidases capable of degrading proline-rich sequences present in gluten peptides [9][10].
Some studies also suggest that specific strains of Bifidobacterium and Lactobacillus may reduce the formation of toxic gliadin peptides and modulate the immune response associated with gluten [11].

6. Bioactive peptides derived from gluten
A further little explored aspect concerns the possibility that microbial degradation of gluten produces peptides with biological activity. Proteomic analyses have shown that gluten digestion generates numerous peptide fragments with potential biological and immunological activity [7][12].
Enzymatic digestion of food proteins can in fact generate bioactive peptide fragments with different biological functions, including:
1 – modulation of inflammation
2 – protection of the intestinal mucosa
3 – antimicrobial activity.
Among these, the following have been described, for example:
1 – the peptide ω-gliadin ω(105-123) from einkorn, which in in vitro studies showed protective effects on the intestinal mucosa
2 – the peptide p10mer (QQPQDAVQPF) identified in some wheat varieties
These results suggest that gluten degradation could generate biologically active peptides. The physiological role of many of these peptides in humans remains still poorly clarified and represents an emerging field of research.

7. The central role of short-chain fatty acids
The gut microbiota performs numerous important metabolic functions, including the production of short-chain fatty acids (SCFAs):
1 – butyrate
2 – propionate
3 – acetate
These metabolites derive mainly from the fermentation of dietary fibers and perform fundamental functions:
1 – nourishment of intestinal epithelial cells
2 – strengthening of the mucosal barrier
3 – modulation of the immune system
4 – reduction of intestinal inflammatory processes.
For this reason, the intake of fermentable fibers is considered one of the most important dietary factors for maintaining the balance of the microbiota [6].

In-depth section
Can undigested gluten have an ecological role in the microbiota?

An aspect rarely discussed in the relationship between gluten and microbiota concerns the possible role of gluten peptides that are not completely digested. Since some gluten sequences resist enzymatic digestion, part of the protein fragments can reach the colon. Some microorganisms of the microbiota possess enzymes capable of further degrading these peptides. Among the most studied genera are:
1 – Lactobacillus
2 – Bifidobacterium
3 – some species of Clostridium
4 – Bacteroides
Here these peptides can be used as a metabolic substrate by some intestinal bacteria, thanks to the presence of specific microbial peptidases [9].

Adaptation of the microbiota to the diet
The gut microbiota is strongly influenced by the habitual diet of populations.
It has been demonstrated that:
1 – populations with a diet rich in plant fibers show microbiotas dominated by Prevotella
2 – Western populations show greater prevalence of Bacteroides
This demonstrates that the human microbiota can adapt to the food sources habitually consumed.
Since in Western countries the consumption of gluten-containing cereals has been very high for millennia, it is plausible that part of the human microbiota has also adapted to the presence of peptides derived from incomplete gluten digestion. If this hypothesis were correct, the complete elimination of gluten could modify the ecological balance of some bacterial populations. At present, however, this hypothesis has not yet been demonstrated and requires further studies.

Modifying the ecological balance of some bacterial populations:
The possible modification of the ecological balance of the gut microbiota could consist above all in changes in the composition and functions of the bacterial communities of the intestine:
1. Reduction of some bacteria “adapted” to gluten
If some intestinal microorganisms are capable of using peptides derived from gluten as a substrate, completely eliminating gluten could:
reduce the availability of this nutrient
decrease the growth of those bacteria that metabolize it.
2. Increase of other bacterial species
When a nutritional source changes, other bacterial species can become more competitive and increase in number. This can lead to a different proportion among the various bacterial groups.
3. Changes in the metabolic products of the microbiota
Intestinal bacteria produce substances that are important for the organism, such as:
short-chain fatty acids (SCFAs): acetate, propionate, butyrate
vitamins
metabolites that influence the immune system.
If bacterial species change, the quantity or type of metabolites produced may also change.
4. Possible effects on digestion and immunity
A different microbiota balance could theoretically influence:
the digestion of some nutrients
intestinal permeability
the intestinal immune response.

In summary
The modification of the biological balance could mean:
1 – change in the bacterial species present
2 – change in their proportions
3 – change in the metabolic substances produced by the microbiota.
However, as mentioned in the text, this hypothesis is still under study and there is no definitive evidence that the elimination of gluten significantly modifies the microbiota in healthy people.

Conclusion
Scientific evidence indicates that a gluten-free diet may modify the composition of the gut microbiota. However, it is still not clear whether such changes are mainly due to the reduction of fermentable fibers, to overall dietary modifications, to adaptations of the microbiota, or to the absence of gluten itself.

The gut microbiota is a complex ecosystem whose stability depends above all on the availability of fermentable fibers and plant polysaccharides. At the same time, gluten is a protein partially resistant to digestion and its degradation can generate numerous peptide fragments that reach the intestine and can be further metabolized by the microbiota.

In addition to the possible ecological role of these peptides as substrates for some bacterial populations, gluten digestion can also generate bioactive peptides with potential biological effects, including modulation of inflammation, protection of the intestinal mucosa and antimicrobial activity. The physiological role of many of these peptide fragments in humans, however, remains still poorly clarified.

The gut microbiota is a complex ecosystem that depends above all on the availability of fermentable fibers and plant polysaccharides. At the same time, the possible role of peptides derived from incomplete gluten digestion represents a field of research that is still little explored. Better understanding these interactions will be fundamental to clarify the relationship between gluten, diet and gut microbiota health and to evaluate whether peptides derived from gluten may play a functional role in the intestinal ecosystem.

Scientific bibliography
[1] De Palma G. et al.
Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects
British Journal of Nutrition, 2009
DOI: 10.1017/S0007114509993533
Abstract – key points
study on healthy adults following a gluten-free diet
reduction in Bifidobacterium and Lactobacillus
increase in Enterobacteriaceae and E. coli
reduction in the intake of fermentable polysaccharides.

[2] Golfetto L. et al.
Lower bifidobacteria counts in adult patients with celiac disease
BMC Gastroenterology, 2014
DOI: 10.1186/1471-230X-14-86
Key points
reduced abundance of Bifidobacterium in celiac patients
persistent alterations of the microbiota even with a gluten-free diet.

[3] Bonder MJ. et al.
The influence of a short-term gluten-free diet on the human gut microbiome
Genome Medicine, 2016
DOI: 10.1186/s13073-016-0295-y
Key points
the gluten-free diet modifies the composition of the microbiota
variations observed especially in fermenting bacteria.

[4] Kaliciak I. et al.
Influence of gluten-free diet on gut microbiota composition in patients with coeliac disease: a systematic review
Nutrients, 2022
DOI: 10.3390/nu14102083
Key points
systematic review of studies on microbiota and celiac disease
the microbiota in treated celiac patients often remains altered.

[5] Hansen LBS. et al.
A low-gluten diet induces changes in the intestinal microbiome
Nature Communications, 2018
DOI: 10.1038/s41467-018-07019-x
Key points
randomized study on healthy adults
a low-gluten diet modifies the microbiota and intestinal fermentation.

[6] Sanz Y.
Effects of a gluten-free diet on gut microbiota and immune function
Gut Microbes, 2010
Key points
diet is one of the main factors that modulate the microbiota
complex carbohydrates represent a key energy substrate.

[7] Prandi B. et al.
Peptides from gluten digestion: comparison between old and modern wheat varieties
Food Chemistry, 2017
DOI: 10.1016/j.foodchem.2016.12.120
Key points
identification of numerous peptides derived from gluten digestion.

[8] Gianfrani C. et al.
Gliadin peptides resistant to gastrointestinal digestion
Journal of Immunology Research
Key points
some gluten peptides resist digestion
they interact with the intestinal immune system.

[9] Sanchiz A. et al.
Microbial peptidases: key players in reducing gluten immunogenicity
Applied Sciences, 2025
Key points
microbial enzymes degrade gluten peptides.

[10] Mamone G. et al.
Analytical and functional approaches to assess gluten immunogenicity
Frontiers in Nutrition, 2023
Key points
analysis of gluten proteins and derived peptides.

[11] Pecora F. et al.
Gut microbiota in celiac disease
Frontiers in Immunology, 2020
Key points
Bifidobacterium and Lactobacillus modulate the response to gluten.

Glossary
1. Metabolic substrate
It is the molecule that is used in a metabolic reaction to produce energy or to be transformed.
Examples:
glucose
fatty acids
amino acids
Practical example:
Glucose is a metabolic substrate of glycolysis, because it is degraded to produce ATP.

2. Enzymatic substrate
It is the specific molecule on which an enzyme acts.
Each enzyme recognizes a specific substrate (like a key in a lock).
Example:
lactase enzyme
substrate: lactose
The enzyme transforms the substrate into products.

3. Metabolite
It is any molecule that participates in metabolism, so it can be:
a substrate
a product
a reaction intermediate
Example in glycolysis:
glucose → glucose-6-phosphate → fructose-6-phosphate
These intermediate molecules are metabolites.