If you have celiac disease or a non-celiac gluten sensitivity, and your symptoms haven’t improved with a gluten-free diet, you may benefit from taking probiotics. Probiotics have been shown to significantly improve the effectiveness of a gluten-free diet and reduce stubborn digestive symptoms of celiac disease.
Gut Microbiome and Celiac Disease

Celiac disease is an autoimmune disorder where the gluten proteins cause the immune system to activate and attack the walls of the small intestines. This results in intestinal permeability, or a reduced barrier between the gut and the rest of the body, lower production of enzymes that help digest food, and limited ability to absorb nutrients from your food. You can see this inflammation, the breakdown of the walls of the small intestines, in testing with a biopsy.
Non-celiac gluten sensitivity does not show inflammation to the small intestines on biopsy. However, people still get gastrointestinal and systemic inflammation symptoms after eating gluten. This may be because the inflammatory response is too low to test, but still high enough to cause symptoms.
The symptoms of celiac disease and non-celiac gluten sensitivity are similar but include various abdominal and non-digestive symptoms. Some symptoms include bloating, abdominal pain, diarrhea, joint pain, eczema, weight loss, or headaches.
Our gut microbiota is a beautiful and dynamic system, made up of millions of friendly bacteria which help keep invading pathogens at bay. However, the balance between friend and foe can be difficult to maintain. Excessive numbers of hostile bacteria can make the organism less tolerant to gluten. The worrying part is that, in genetically predisposed individuals, this can mean celiac disease. The theory goes that problems in the intestinal mucosa, such as increased permeability, can create conditions that favor nasty Gram-negative instead of helpful Gram-positive bacteria.
Symptoms of Celiac Disease
If you have celiac disease and accidentally eat something with gluten in it, you may have symptoms including:
- Abdominal pain
- Anemia
- Bloating or a feeling of fullness
- Bone or joint pain
- Constipation
- Diarrhea
- Gas
- Heartburn
- Itchy, blistery rash
- Headaches or fatigue
- Mouth ulcers
- Nausea
- Nervous system injury, including numb or tingling hands or feet, balance problems, or changes in awareness
- Pale poop, smells especially bad or floats
- Weight loss
Gluten-Free Probiotics
A much safer route for probiotics is eating fermented foods. Below is a list of gluten-free fermented food options.
- Kombucha
- Water Kefir
- Beet Kvass
- Lacto-fermented ginger ale and root beer
- Yogurt
- Milk kefir
- Buttermilk
- Cheese
- Sour cream
- Sauerkraut
- Fermented carrot sticks
- Cultured salsas
- Lacto-fermented dill pickles
How Probiotics Can Help People With Celiac Disease?
Thankfully, probiotics are safe to use if you have celiac disease or non-celiac gluten sensitivity because they do not contain gluten. Probiotics with a gluten-free diet are typically the most effective way to improve the gut microbiome and relieve gastrointestinal symptoms such as bloating, pain, and constipation or diarrhea. It is worth adding a daily probiotic into your routine with your gluten-free diet and seeing if it helps. You should then look for a healthcare professional who can help you look at any underlying issues that may be contributing to your symptoms and resolve any food intolerances, lack of digestive enzymes, histamine intolerance, or gut infections. If you are concerned you may have an underlying issue contributing to your symptoms, our clinic is ready to help you. You can fill out our patient request and we will get you started improving your gut health.
If you are gluten-free and still experiencing digestive symptoms, follow these three steps:
- Start taking probiotics, if you are not already doing so. Do this for a month and see if you improve. If not, move to step two.
- Keep taking probiotics and see if your symptoms improve. If they do improve, this is a good indication you may have a gut imbalance. If you do not improve, this is also an indication that you might have a gut imbalance or a parasite. In both cases, you should move on to step three.
- Work with a healthcare professional to check for gut infections, parasites, or any other condition that may be causing additional symptoms.
These steps should help you regain digestive balance or figure out if you have an additional underlying condition that needs to be addressed.