Gluten Intolerance Results From a Lack of Gut Bacteria

Ian Spreadbury (PhD) hypothesize in his excellent scientific paper that acellular carbohydrates such as white bread is the primary cause of leptin resistance.I’ve previously highlighted the fact that gut dysbiosis sets the stage for grain-related disorders, and as the evidence is now piling up, I’m more convinced than ever that the gut microbiota is the key to preventing and treating non-celiac gluten sensitivity and possibly even celiac disease. The human cells in our body only produce the necessary enzymes to break down a minority of the nutrients we get from food, and we therefore rely on gut microbes to do the rest of the job. The gut microbiome – the aggregate of all the microbes and their genes found in the GI tract – encode 100-fold more unique genes than the human genome (1,2). This second genome in our body is the key to understanding food intolerance since it’s responsible for providing the enzymes needed to degrade non-starch polysaccharides, some proteins, and other compounds our human enzymes can’t do anything about.

What does the most recent research say?

In my previous article on gluten sensitivity and celiac disease I highlighted plenty of research indicating a link between gluten intolerance and microbiome diversity. Since that time, more studies have strengthened this relationship. One of the most interesting ones was published last week…

Diversity of the cultivable human gut microbiome involved in gluten metabolism: Isolation of microorganisms with potential interest for coeliac disease (3).

In conclusion, the human intestine exhibits a large variety of bacteria capable of utilising gluten proteins and peptides as nutrients. These bacteria could have an important role in gluten metabolism and could offer promising new treatment modalities for coeliac disease.

In another interesting article on gluten intolerance also published last week, Dr. Stefano Guandalini talks about the connection between the hygiene hypothesis, dysbiosis, and the rise of celiac disease. Even though his take on the hygiene hypothesis seems somewhat outdated, the article is definitely worth a read.

Food intolerance occurs when the microorganisms in the gut don’t possess the genes that are needed to break down the specific food ingredient

As we’re now seeing a widespread destruction of the human microbiome with western diets, modern hygiene, antibiotics, c-sections, and formula feeding in infancy, it’s no surprise that we’re also seeing a rapid rise in non-celiac gluten sensitivity, celiac disease, and other allergies and autoimmune disorders (4,5,6,7). Compared to our hunter-gatherer ancestors, we live in an extremely sterile environment. The urban western lifestyle doesn’t only alter the balance between healthy bacterial commuities and proinflammatory germs in the gut, but it also depletes the diversity of critters in our body. We’ve distanced ourselves from the vast microbial ecosystems found in soil, untreated water, and the rest of the environment, and our health pays the price.

Since a lot of people no longer harbor the necessary microbial genes to break down all of the food they eat, it’s no surprise that we’re seeing a steady rise in food intolerance.

Gluten sensitivity can be treated by introducing gluten-degrading microbes in the gut

To regain control of our microbiome and treat food intolerance we have to rewild our bodies. While the bacteria we ingest don’t necessarily take up root in the gut, they are able to transfer genes (horizontal gene transfer) to the bacteria living in gut biofilms. This is the reason why lactose intolerance can be treated with the right types of probiotic bacteria. Even if the probiotic bacteria aren’t able to colonize the gut, they transfer genes that are needed to produce lactose digesting enzymes. This gene exchange is part of the dynamic nature of the microbiome, and essentially means that new bacterial species with a somewhat different DNA are created all the time.

I want to make it clear that even though someone with the right set of gut bacteria is able to degrade gluten and other problematic components found in cereal grains, grain fiber is generally very hard on the digestive system. So, eating improperly prepared whole grains as a staple food is not a good idea even if you harbor gluten-degrading microbes.

I also want to make it clear that celiac disease is not a typical food intolerance. While the composition of the microbiome influences the susceptibility of getting celiac disease, it’s unclear whether manipulating the microbiome works as a treatment for celiac disease.


  1. How would you properly prepare your whole grains ? thx

  2. I really enjoy your articles! What is your recommendation for probiotics or speciific gut rebuilding foods?


    • Eirik Garnas says:

      Traditionally fermented foods such as kimchi are great for introducing beneficial bacteria. Onions, leeks, garlic, properly prepared legumes, and other plant foods provide fermentable substrates that boost good bacteria. I recommend that you read my articles on probiotics and prebiotics 🙂

  3. nochemicalcosmetics dotcom says:

    you are spot on, Elrik! there has been mounting evidence, for years, that balancing the gut bacteria is paramount to aid digestion, absorb nutrients and guard against food intolerance. Most people don’t realise that just drinking unfiltered tap water can alter the balance. Chemicals in the water are indiscriminate when it comes to billing off the bacteria, be they harmful or beneficial.

    • Eirik Garnas says:

      Yes, chemicals in drinking water could be more of a danger than we’ve previously realised. Some researchers are actually doing a pilot study on the effects of chlorinated water on the microbiome very soon, so will be interesting to see how that turns out.

      • sandra fraser says:

        Lack of bacteria in the gut is a direct result of overprescribing antibiotics and over-sterilising food, and the over-use of sell-by dates to me is a big concern. Because of this, a growing number of people are becoming unwell.

  4. “Gluten sensitivity can be treated by introducing gluten-degrading microbes in the gut” “horizontal gene transfer”… can you link to a study? You offer no proof on this point, just a description of how it works for lactose.

    • Eirik Garnas says:

      Hi Everphilski!

      Did you read through this post? And ?

      I’m not saying that eating a lot of foods containing gluten is good for you (I rarely eat grains myself). However, studies do show that several types of gut bacteria are capable of utilising gluten proteins and peptides as nutrients, suggesting that gluten sensitivity can be treated.

      While there are several studies which show that probiotics can be used in the treatment of lactose intolerance, I do agree that the data on gluten intolerance and probiotics is smaller. So I should probably have been more cautious with my claims on gluten intolerance instead of putting it in the same category as lactose.


  1. […] Two examples of this is lactose and gluten intolerance. Most people with lactose intolerance lack the allele (one of a number of alternative forms of the same gene) that produces the enzyme to degrade lactose, and lactose intolerance is therefore often considered a permanent condition. However, several types of bacteria, such as lactobacillus found in yogurt, are able to break down lactose. Even though these probiotics don’t necessarily take up root in the gastrointestinal tract, they are able to transfer lactose digesting genes to the bacteria living in gut biofilms through horizontal gene transfer. Since bacteria are able to degrade a wide range of food ingredients, it’s no surprise that studies show that lactose intolerance can be treated with probiotics and that a large variety of bacteria are capable of utilising gluten proteins and peptides as nutrients. […]

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