Is the Rise in Grain/Gluten Sensitivity and Celiac Disease Caused by Changes in the Human Microbiome?

tall-summer-grainsGrains are difficult for humans to digest, and consequently we see a whole range of health problems associated with the consumption of wheat, barley and other cereals. Proteins and other antinutrients found in grains seem to be especially problematic, and anecdotal reports suggest that a lot of people see significant health improvements when they exclude these components from their diet. There is a whole spectrum of gluten-related disorders, ranging from a fairly harmless form of gluten sensitivity, to full-blown celiac disease where the immune system attacks the body’s own tissues. More and more people seem to react adversely to the consumption of grains, and new research points to changes in the bacterial community of the intestine as a likely culprit.

Although cereal grains contain lectins, phytates and insoluble fibers that might cause digestive problems and disrupt normal gut physiology; gluten, a protein found in wheat and other grains, is often considered the biggest offender. Three main forms of gluten reactions have been identified: allergic (wheat allergy), autoimmune (celiac disease, dermatitis herpetiformis and gluten ataxia) and possibly immune-mediated (gluten sensitivity) (1). While gluten sensitivity or intolerance long has been considered a diagnoses unfounded in science, research has now made it clear that gluten sensitivity definitely exists and that gluten often causes gastrointestinal symptoms even in those without celiac disease (2).

Because of the “toxic” antinutrients, indigestible fibers, and insulinogenic effect, grains have received a lot of negative press in the ancestral health community the last couple of years. While these concerns are legitimate, new research shows that alterations in the gut microbiome might be why so many people have difficulty digesting grains properly.

Observations and trends suggesting a possible link

Changes in the microbiome correlates with a rapid rise in gluten-related disorders

It’s really only in the last couple of decades that hygiene, sanitation, more frequent use of antibiotics, bottle-feeding, caesarean section and other factors have led to rapid changes in the human microbiome. The majority of people living in industrialized countries are also eating a typical western diet rich in refined and processed foods, with little to no fermented foods and fermentable substrates. It’s likely that we’re now missing some of the germs we have co-evolved with as a species, and there is no doubt that the typical human microbiome of the 21st century is a far cry from the paleolithic microbiome of our ancestors.
In the last couple of decades the prevalence of celiac disease has increased significantly, and the prevalence of non-celiac gluten sensitivity seems to be on the rise as well.
The correlation between these rapid changes in the microbiome and the rise in gluten-related disorders doesn’t necessarily indicate causation, but it’s an interesting observation.

Few adverse effects from the consumption of grains prior to the last decades (?)

In the ancestral health community, grain consumption is often considered an important underlying cause of the rapid rise in chronic inflammatory diseases we see today. However, when looking at the trends for most diseases of civilization it becomes clear that the significant increases took place in the last hundred years, and especially in the last couple of decades. How is it then that grains have been a part of the human diet for 10000-12000 years, but it’s only lately that the consumption of whole grains seems to be problematic?
Yes, it could be that we have strayed away from traditional methods of preparing grains…
Yes, it could be that there have been significant changes to the grain itself…
Yes, it could be that we don’t have enough data and that grain consumption always has been linked to health problems…
…and it could also be because we tolerated grains better before the major shifts in the human microbiome took place.

Isolated traditional societies have maintained excellent health even with cereal grains as staple foods

Children raised on a grain-based diet in the Swiss Valley with excellent teeth

Children raised on a grain-based diet in the Swiss Valley. All in perfect health and with excellent teeth.

Dr. Weston A. Price dedicated large parts of his life to travelling the world and investigating the health of isolated traditional societies. He documented his work in his excellent book “Nutrition and Physical Degeneration”, and it’s still often considered one of the best books on nutrition and health. Dr. Price found that primitive people maintained excellent physical health as long as they stuck with their traditional diet and lifestyle, but their health quickly deteriorated if they moved to a different location and switched to a typical western diet high in sugar and refined foods.

Among the primitive cultures Dr. Price visited were the people in the Lötschental Valley in Switzerland and the Scottish and Gaelic living in the Outer Hebrides. Both of these societies relied heavily on grains, but still maintained excellent health. If the antinutrients, indigestible fibers and high-carbohydrate content of grains are so bad, why where these people so healthy?
Most of the primitive cultures who ate a lot of grains usually soaked, sprouted or fermented the cereals, and this made the grains healthier and easier to digest. Besides using these traditional preparation methods, it’s also likely that a healthy microbiome (e.g., unaffected by antibiotics, exposure to dirt) made them able to tolerate grains much better than most people do today.

Scientific research suggesting a link

Food intolerance is a sign that gut flora lacks the genes/enzymes needed to digest a food component.
Lactose intolerance is one example of a food intolerance that can be treated by altering the bacterial communities in the gut, and it seems that most food sensitivities are caused by a lack of bacteria that provide the genes needed to fully digest the food component.

Celiac disease is associated with alterations in the gut microbiome
An excellent article in the New York Times highlights research showing that breastfeeding, gut flora diversity and the presence of Bifidobacteria and Lactobacilli influence the susceptibility of getting celiac disease.

Identification of Rothia bacteria as gluten-degrading natural colonizers of the upper gastro-intestinal tract.
“While the human digestive enzyme system lacks the capacity to cleave immunogenic gluten, such activities are naturally present in the oral microbial enzyme repertoire. The identified bacteria may be exploited for physiologic degradation of harmful gluten peptides.” (3)

Differences of Small Intestinal Bacteria Populations in Adults and Children with/without celiac disease: effect of Age, Gluten Diet and Disease
Patients with celiac disease have different bacterial composition of the gut compared to healthy individuals. (4)

Role of intestinal bacteria in gliadin-induced changes in intestinal mucosa: study in germ-free rats.
“Our results suggest that the composition of the intestinal microbiota affects the permeability of the intestinal mucosa and, consequently, could be involved in the early stages of CD pathogenesis.” (5)

Bifidobacterium strains suppress in vitro the pro-inflammatory milieu triggered by the large intestinal microbiota of coeliac patients.
“The intestinal microbiota of CD patients could contribute to the Th1 pro-inflammatory milieu characteristic of the disease, while B. longum ES1 and B. bifidum ES2 could reverse these deleterious effects.” (6)

Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children.
“In CD patients, reduced IgA-coated bacteria is associated with intestinal dysbiosis, which altogether provide new insights into the possible relationships between the gut microbiota and the host defences in this disorder.” (7)

Are grains healthy?

Although someone with the right types of bacteria tolerate grains fairly well, it doesn’t necessarily mean that grains should be a large part of that person’s diet. Grains still contain antinutrients and plenty of indigestible fiber that might promote leaky gut and chronic low-level inflammation, and some data suggest that grain consumption promotes unfavourable changes to the gut microbiota. A grain-based diet also means less room for grass-fed meats, fish, eggs, vegetables, fruits and other nutrient rich whole foods.

If you do want to eat grains on a regular basis you should look into traditional preparation methods in order to make the grains easier to digest, as well as including prebiotics and beneficial bacteria from for example fermented foods such as cultured vegetables, kombucha, cultured juices and yogurt in your diet.


  1. […] The first agricultural revolution is sometimes blamed for introducing harmful food into the human diet, and proponents of the paleo diet often claim that our genetics haven’t changed much since the paleolithic era and that we therefore haven’t had enough time to adapt to “neolithic foods”. This premise is highly debated among scientists, and we have also learned that although our human genome changes fairly slowly, the “second” genome in our body – the human microbiome – can be altered fairly rapidly. Micro-organisms in our body provide metabolic functions that stretch far beyond the capabilities of the human host and can adapt to break down a wide range of food ingredients. Both lactose intolerance and gluten sensitivity are often classified as permanent conditions, but the fact is that bacteria in the gut can provide the needed enzymes to break down lactose and are also able to degrade harmful gluten peptides. […]

  2. […] Recent discoveries have shown that some microbes produce enzymes that degrade gluten (13,14,15) and phytic acid (16) – two of the most cited reasons for avoiding cereal grains. I believe […]

  3. […] recientes han demostrado que algunos microbios producen enzimas que degradan el gluten (13,14,15) y el ácido fítico (16) – dos de las razones más citadas para evitar el consumo de cereales. […]

  4. […] Rise in Gluten Sensitivity & Microbiome […]


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