Treatment Guide

Probiotics and Prebiotics can Improve Health of Celiacs

probiotics gluten celiacCeliac disease is a complex inherited digestive disorder that affects I in 100 persons worldwide. This condition involves a unique immune response within the digestive tract to gluten, a protein found in the grains of wheat, barley, rye and oats.  All persons with celiac disease, regardless of age, race or gender, are susceptible to intestinal damage when they eat food containing gluten or its derivatives. The treatment for celiac disease is a strict gluten-free diet that stops damage and allows recovery.  Probiotics and prebiotics should be incorporated into the diet to improve the quality and balance of intestinal bacteria that inhabit the colon.

Intestinal enzyme deficiencies, sugar intolerances and associated dysbiosis, or imbalance of intestinal microbes, called flora, appear commonly in persons with celiac disease.1  Research indicates that the metabolic activity of intestinal microbial flora in celiacs is different from the general population and that it is a genuine phenomenon of celiac disease not affected by either the diet, the inflammation, or the autoimmune status of the patient.2   The severity of disturbances in intestinal balance of flora was found to depend on the gravity of the patients’ state. 3

Celiac reactions work in the following way. Undigested fragments of gluten cause a “leaky gut syndrome” by relaxing the normally tight intercellular junctions that function to prevent large molecules from slipping through the lining.  Penetrating gluten fragments become bound by the intestinal enzyme tissue transglutaminase (tTG) to form a molecule that triggers the development of antibodies.  These antibodies then attack the altered gluten molecule within the lining.

The immune reaction within the gut lining causes inflammation and damage to the delicate  structures of the lining, leading to failure to digest and absorb nutrients.  Malabsorption leads to malnutrition that then brings about malfunction of any or all body systems, depending on the nutrients that are missing.

In this way hundreds of diverse health problems may develop from celiac disease.

Various microbial imbalances stem from the unnatural passage of undigested fat, carbohydrates and protein into the colon, poor gut motility, and certain nutrient deficiencies. 

Passage of unabsorbed nutrients into the colon results from pancreatic insufficiency, bile insufficiency and digestive enzyme deficiencies.

  1. Pancreatic insufficiency results in deficiency of pancreatic digestive enzymes lipase, amylase, and protease needed for the digestion of fat, carbohydrates, and protein.
  2. Bile insufficiency results in impaired secretion of bile by the liver, obstruction of the bile ducts and abnormal circulation of bile salts that impairs the digestion of fats.
  3. Deficiency of lactase, sucrase, maltase and proteases result in failure to finish the digestion of sugars and protein required for absorption. Undigested nutrients arriving in the colon cause excessive fermentation and drawing of water from the bloodstream into the colon.  These conditions produce symptoms such as abdominal pain, watery diarrhea, IBS-like symptoms, bloating, and gas. Pale foul-smelling stool that float or stick to the toilet bowl results from fat malabsorption.

Altered gut motility and low stomach acidity commonly found in celiac disease promote fermentation in the large bowel and also overgrowth of yeast and bacteria in the small bowel, both serious conditions.

The health and integrity of intestinal cells depends on adequate availability of niacin, zinc and vitamin A.  Deficiency of these nutrients sets the stage for inflammation, infection and diarrhea that worsen gut function and induce overpopulation by pathogens.

For these reasons, persons with celiac disease should learn about and properly use both probiotics and prebiotics to improve their overall health and specifically their intestinal health.  This is especially important if they continue to experience fatigue, weakness, achiness, depression, foggy thinking and digestive problems while maintaining a gluten-free diet.

Probiotic supplements and fermented foods, such as yogurt and unpasteurized apple cider vinegar, replace lost or reduced health-producing bacteria populations, such as lactobacillus and Bifidobacterium, in the colon.

Prebiotics, including flax, honey, greens (especially dandelion greens, but also spinach, collard greens, chard, kale, and mustard greens), berries, bananas, and other fruit, legumes (lentils, kidney beans, chickpeas, navy beans, white beans, black beans), will stimulate their growth.

Indeed, good health depends on good balance of intestinal bacteria.

Find out more about the role of Probiotics, causes of dysbiosis and how to correct it naturally at the Gluten Free Works Treatment Guide.


1. Tjellström B, Stenhammar L, Högberg L, Fälth-Magnusson K, Magnusson KE, Midtvedt T, Sundqvist T, Norin E. “Gut microflora associated characteristics in children with celiac disease.Scand J Gastroenterol. 2001 Feb;36(2):163-8.

2. Murray IA, Smith JA, Coupland K, Ansell ID, Long RG. “Intestinal disaccharidase deficiency without villous atrophy may represent early celiac disease.” Am J Gastroenterol. 2005 Dec;100(12):2784-8

3. Kamilova AT, Akhmedov NN, Nurmatov BA. “Intestinal microbiocenosis in children with intestinal enzymopathy.” Zh Mikrobiol Epidemiol Immunobiol. 2001 May-Jun;(3):97-9.

Copyright © Cleo Libonati 2007.

Cleo Libonati is the author of “Recognizing Celiac Disease,” an encyclopedia of celiac disease that can be found here.  Libonati is President and CEO of Gluten Free Works, Inc. and co-founder of

[Editor’s Note: Article originally published June 20, 2010.]

About Cleo Libonati, RN, BSN

Cleo Libonati, RN, BSN is CEO and co-Founder of Gluten Free Works, Inc. and She is the author and publisher of the highly recommended celiac disease reference guide, Recognizing Celiac Disease.


  1. This is a very interesting article. I’ve read alot about pro and pre biotics and I’ve tried numerous types. I run into a problem when I take them – my symptoms seem to worsen to the point where I can’t go anywhere! I don’t understand this. I certainly do better with a low/no sugar diet, no potatoes, and low starch. I thought it was related to a systemic yeast infection. I am slowly coming to the conclusion that I simply need to limit my diet beyond gluten free and also include the other items that bother me.

  2. Hi Terri,

    I am the same. I am celiac and have also had h.pylori. I do best on low starch, no potatoes, no sugar. I can finally manage fruit again. Have you tried the Specific Carbohydrate diet? Also look at their list of allowed and forbidden foods – I found it exactly matched what I could digest. Good luck.

  3. I tried a cheap brand probiotic and I felt terrible instantly, all of my symptoms returned. I then tried a really good more expensive brand, a powder and that one agreed with me a lot more and made me feel better. I am mostly frustrated because I think i am the only Celiac patient who has not lost any weight once I went gluten free. I can’t seem to figure out what is going on and why my weight won’t budge even though my diet has changed dramatically. Maybe I should try to limit some potatoes and other carbs.

  4. Celiacs can often have additional food sensitivities…testing such as MRT can help pinpoint additional foods that are triggers for inflammation.

  5. Michelle r. Taylor

    Hello Theresa,
    Like the member above, you might try changing your probiotic brand, if you are taking a man made brand, it could be the reason your probiotic is giving you issues, you would probably benefit from taking a whole food probiotic that is more natural for you or take a powder formula that you mix in your food or liquids. I have digestive issues and have to eat just about an organic diet, my stomach is very sensitive to what I eat and probably the reason I have a celiac disorder. As far as foods that trigger inflammation, I know that tomatoes and potatoes are big triggers for inflammation such as arthritis, don’t know what the others could be, I would be interested in knowing what they are so I can stay away from them. I don’t eat tomatoes or potatoes cause I also follow a blood type diet and blood type A’s should sway away from both of those foods, something to do with the lectins in the food that aggravate A’s.
    Theresa, hope you find the right kind of probiotic for you, try consulting a licensed or certified natural nutritionist to help you out, to find the best one for you. If you are a blood type A, be sure to get one with a bifidus factor in it, best for A’s.
    Take care and keep us all in touch,
    Michelle r.

  6. I sure would like a follow up to this topic. I also cannot tolerate probiotics. Rumbling stomach, gas, bloating, headaches, fatty loose stools. I tolerate high fat low sugar organic yogurt (Activia also makes me sick). It also helps when I make room for things like fermented fruits, small amounts of bananas (I think these are what serves as prebiotics). I have gone gluten free this year due to suspected celiac. My physician says she can’t test for it if I’m off of gluten and I’m not willing to go back on. I also gained weight when I first stopped consuming gluten. I finally lost weight when I quit trying to recreate my favorite wheat items using GF grains. I had to limit grains, period. More recently, I’ve cut out most sugar. I pray I never start reacting to dairy; it’s my treat these days. I mostly eat meats, veggies, some fruits, dairy and protein powder.

  7. Yes, yes yes! I am coeliac, and regular suffer with bloating and wind. A naturopath recently recommended a probiotic supplement to me and I’m feeling better day by day. It has been 3 weeks now and there is a definite improvement.

    I also read about probiotics on this site which I was very impressed with – full of tips on bloating , but with a focus on natural health – which when sifting through all the junk on the net these days, is a breath of fresh air!

    Thanks for a useful article. Great to understand the science behind my symptoms.

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