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Do you want to start feeling better?

Yes, Where Do I Start?

How to Restore Gut Health After a Celiac Disease or NCGS Diagnosis

Gut Protective Steps for When You Can’t Tolerate Gluten

Celiac disease is one of the most common autoimmune disorders worldwide. It’s estimated to affect approximately 3 million Americans, though less than a million of these cases get a proper diagnosis [1].

If you have celiac disease, it’s important to know that the only way to stop ongoing damage to your small intestine is to avoid gluten completely for the rest of your life [2]. 

However, once you’ve cut out gluten, further diet and lifestyle steps can help repair your gut and keep it healthy over the longer term. 

Unfortunately, symptoms can continue in people with celiac disease, even after they’ve taken pains to cut out gluten. Lasting symptoms may occur as a result of cross-contamination or accidentally eating hidden gluten. Other contributors can be coexisting gut issues, like small intestinal bacterial overgrowth (SIBO), irritable bowel syndrome (IBS), or inflammatory bowel disease (IBD, such as ulcerative colitis or Crohn’s disease) [3].

In this article, I’ll lead you through the five steps that speed up the gut-healing process for my clients with celiac disease. I’ll also explain how these gut-supportive steps can help people with non-celiac gluten sensitivity, since the two conditions have many similarities.

Before getting into the five steps, let’s compare and contrast these two conditions.

Celiac Disease vs. Gluten Sensitivity

When people with celiac disease eat gluten, their immune system responds by producing antibodies that attack the small intestine.

Specifically, the immune system damages the villi, which are the finger-like projections that absorb nutrients on the internal surface of the small intestine. The resulting inflammation and nutrient malabsorption can lead to a leaky gut, abdominal pain, gas, diarrhea, and constipation, plus a range of non-digestive system symptoms, including [4, 5]: 

  • Brain fog
  • Fatigue
  • Depression and anxiety
  • Headaches or migraines
  • Iron-deficiency anemia
  • Itchy, blistery skin rash (dermatitis herpetiformis)
  • Joint pain
  • Missed periods
  • Mouth ulcers and canker sores
  • Nausea and vomiting
  • Bone disorders (osteoporosis and osteomalacia)
  • Weight loss

In children, celiac disease can also hinder growth and delay puberty [5]. 

In the separate condition known as non-celiac gluten sensitivity (NCGS), symptoms also arise upon eating gluten. Although NCGS doesn’t show up as inflammation in a biopsy of the small intestine, and it’s not an autoimmune disease, it can still trigger a systemic immune response and intestinal damage [6].

People with gluten sensitivity tend to have mainly brain-associated symptoms, such as difficulty concentrating, fatigue, and depression. For example, in one study, people with NCGS largely reported headaches, brain fog, balance issues, and tingling [7].

Research has not actually confirmed that gluten is the culprit in NCGS, as it is in celiac disease. In fact, what many people think is NCGS could actually be other health conditions or situations that look like NCGS, including:

  • FODMAP (fermentable sugars in some foods) intolerance [8, 9, 10, 11]
  • SIBO [12, 13, 14]
  • IBS [8, 15]
  • Intestinal dysbiosis (imbalanced gut bugs) [8
  • IBD
  • [8, 15]
  • Diverticular disease [8]
  • Microscopic colitis [8]
  • Non-responsive celiac disease (when symptoms persist despite a strict gluten-free diet) [16]
  • The nocebo effect (like the placebo effect, but it occurs when you expect something to harm you, and you experience harm from it as a result) [9]. 
  • Alpha-amylase/trypsin inhibitors in wheat (non-gluten molecules that prevent enzymes from breaking down wheat) [9]

None of this is to suggest that some people without celiac disease don’t get symptoms from foods that contain gluten (or more likely wheat, barley, or rye, which have sugars that can provoke symptoms on their own). Those symptoms are real, but they may actually stem from something other than gluten. 

To see the main differences between celiac disease and NCGS, check out this table.

Celiac DiseaseNon-Celiac Gluten Sensitivity  
Positive celiac disease blood test
Inflammation visible on an intestinal biopsy
Immune reactivity and inflammation✅ (likely severe)✅ (very mild to severe)
Gluten proven to be the problem
All gluten must be removed

Now, let’s turn to the five main steps that can help to heal and protect your gut from the effects of gluten (or wheat) intolerance in whichever form you experience it. 

Step 1) A Gut-Restorative Diet

As well as being gluten (and wheat) -free, a gut-healing diet for people with celiac disease or non-celiac gluten sensitivity needs to be:

  • Nutrient-rich
  • Microbiome-friendly (helpful for healing a leaky gut) 

Nutrient richness is important to help offset the lower vitamin and mineral absorption that can occur in celiac disease patients and others who avoid gluten and have a limited diet.

Microbiome friendliness is important because the leaky gut that often occurs in celiac disease and other types of wheat and gluten intolerance is closely linked to changes in gut microbiota composition [17, 18]. Focusing on foods that can help balance the microbiome will help speed up the healing of a leaky gut.

It’s hard to specify which healthy diet will work best for getting the gluten-intolerant gut back in shape, but reducing processed food is always a good place to start.

Many of my clients do well and get better gut health with a gluten-free, whole-food Mediterranean-style or Paleo diet.

Both of these diets are rich in fruits, vegetables, and lean protein, and are well-tolerated by people who don’t have other food sensitivities. 

Both diets also include fermented foods, like sauerkraut, kimchi, kombucha, and yogurt, all of which are great sources of healthy bacteria for your gut.

For many people, it also works fine to include whole grains that aren’t wheat, rye, or barley, each of which contains gluten and problematic sugars called fructans. Options could include oats, rice, buckwheat noodles, and gluten-free bread. 

Just make sure the grains you buy are certified gluten-free, which means they haven’t been processed on equipment shared with wheat or gluten products.

The Low-FODMAP Diet

FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. These are types of sugars in certain foods that can cause symptoms in some people. A temporary low-FODMAP diet can improve gut health in celiac patients and NCGS patients alike. 

For example, some celiac patients still have symptoms on a gluten-free diet, perhaps as a result of IBS, SIBO, or some other cause of FODMAP intolerance. Many gluten-free products contain high amounts of FODMAPs, so those who are sensitive to them may get symptoms after eating, without knowing why. For these celiac patients, clinical research has shown that a gluten-free low-FODMAP diet can reduce their digestive symptoms and improve their mental health [19]. 

And some non-celiacs who think they’re sensitive to gluten may actually be reacting to the fructans (a type of FODMAP) rather than the gluten in wheat, barley, and rye products [10]. Similar to celiac patients, these non-celiacs who go gluten-free but still have symptoms may be eating gluten-free foods that are high in FODMAPs without realizing it. If that is the case, a low-FODMAP diet may help a lot.

One study investigated the effects of gluten in patients with non-celiac gluten sensitivity who had reduced their FODMAP intake. Although the researchers expected that removing gluten would minimize the patients’ symptoms, their symptoms remained. Instead, a low-FODMAP diet relieved their symptoms, suggesting that the real issue was probably FODMAPs rather than gluten [20]. 

In short, a temporary low-FODMAP diet can be particularly helpful for people who feel like they react to gluten but still have symptoms even when they only eat gluten-free foods. 

Typically, a low-FODMAP diet is a short-term elimination diet that allows the gut to rest. After several weeks, the goal is to reintroduce as many of the eliminated foods as possible.

No Gluten or Some Gluten?

If you have celiac disease, any level of gluten exposure can significantly set back your gut healing, so complete and thorough removal of dietary gluten is necessary.

However, for non-celiacs who are sensitive to gluten or wheat, there may be some leeway. After following a low-FODMAP diet for a while, it’s possible to reintroduce some wheat- or gluten-containing foods without symptoms. 

Whether you have celiac disease or gluten sensitivity, one way to help pave the way toward a more varied diet is to take probiotics. 

Step 2) Probiotics 

Probiotics work well alongside diet changes by promoting a healthy microbiome and speeding up gut healing.

For example, high-quality research shows that probiotics are consistently better than placebos at improving leaky gut, reducing inflammation, increasing beneficial bacteria, and correcting dysbiosis [21]. These are all prominent features of gluten intolerance and gluten sensitivity.

Probiotics are also an excellent treatment for IBS [22], which has many overlapping symptoms with NCGS.

Some studies have looked directly at the effects of probiotics in people with celiac disease:

  • A meta-analysis involving more than 5,000 participants with celiac disease showed that probiotics improved GI symptoms by an average of nearly 30% compared with a placebo [23].
  • In a systematic review of children with celiac disease, adding probiotics to a gluten-free diet reduced inflammatory markers in the body. Probiotics also changed their gut microbiomes to resemble those of healthy kids [24].
  • A randomized controlled trial found that a specific strain of probiotics (Bifidobacterium infantis) may be especially helpful for celiac patients with the worst symptoms [25].

Probiotics are likely also helpful for people with non-celiac gluten sensitivity, though the evidence is less abundant. For example, a small clinical trial showed that NCGS patients who ate a gluten-free diet while taking probiotics had fewer symptoms (like bloating, gas, diarrhea, abdominal pain, and constipation) after 3 months than they had at the beginning [26]. 

Now all we need are repeated randomized controlled trials to show that probiotics are better than a placebo for improving these symptoms in people with NCGS. 

Meanwhile, our experience at the clinic suggests that probiotics regularly improve symptoms in people with both celiac disease and NCGS.

Triple Therapy

At the clinic, we have the best results with a triple-therapy probiotic approach. It includes probiotics from these three categories:

  • Lactobacillus blended with Bifidobacterium
  • Saccharomyces boulardii (a type of beneficial fungus)
  • Soil-based probiotics

We see big improvements in digestive health across a number of health conditions when using probiotics from these three categories. It’s worth considering this approach if you’re still experiencing symptoms while on a strict gluten-free diet.

Step 3) Exercise 

Exercise brings many benefits that may improve gut health in people with celiac disease or gluten sensitivity. For example, higher levels of fitness are linked to a healthier more diverse microbiome [27], including bigger numbers of beneficial bacteria that produce short-chain fatty acids (SCFAs), like butyrate. SCFAs support healthy immune function, reduce inflammation, and provide us with energy [28, 29]. 

In terms of people with celiac disease, a pilot study looked at how a 12-week exercise and mental health support program would affect them. Half of the participants took part in high-intensity interval training (HIIT) with cognitive behavioral education, and the other half did neither. Only those who did HIIT and education experienced both a reduction in symptoms and improved quality of life [30]. 

A separate study of the participants’ gut microbiomes found that those who did HIIT and education had positive changes in resting heart rate and possibly beneficial shifts in gut microbiota, suggesting that HIIT is safe for celiac patients [31].

Unfortunately, we can’t tease out which was more helpful: the HIIT or the behavioral education, but a systematic review found HIIT was generally good for the gut microbiome [29]. Until we get more research on exercise for celiac patients, we won’t know which is the best type of exercise for healing the gut in people with celiac disease. Same goes for NCGS. 

That said, HIIT, may be worth a try, but it can also be taxing. For those who can’t or don’t want to do taxing workouts, moderate exercise can also support gut health [27]. 

A good rule of thumb for gut health is to do 3–5 sessions per week of some cardio and at least two days of strength training [29]. Strength training is especially important for supporting bone health, which can be compromised by nutritional deficiencies in celiac patients. Each exercise session should be 30–60 minutes of moderate-to-high intensity [29]. 

Step 4) Managing Stress

Maintaining a gluten-free diet can be mentally exhausting, leading to feelings of stress and anxiety. The good news? If you have step 3—exercise—checked off your list, you’re already doing a lot to manage your mental health. 

However, adding meditation and other relaxation techniques can add additional benefits.

For example, mindfulness meditation has been shown to help lower inflammation levels and modulate the immune system [32], which makes it a good idea for people with gluten sensitivities and celiac disease.

Some people also find the more meditative types of exercise particularly beneficial for  stress relief. In one study, an hour of hatha yoga a week for eight weeks improved perceived stress, fatigue, and quality of life while also reducing gut symptoms like abdominal pain and bloating [33].

This was in a group of participants with IBS , but similar results could be expected in those with celiac disease or other gluten intolerance.

Other proven methods of managing stress that can ultimately improve gut health include:

Spending time in nature: Several studies have found that spending time in natural settings, such as forests or parks, can help reduce anxiety, depression, and stress [34, 35].

Writing a journal: Research shows that journaling—writing down your thoughts and emotions—can help to reduce stress and improve health in people with health conditions [36]. 

Fostering social interactions: Having positive social connections with others can help buffer the negative effects of stress. Some of my patients find it helpful to seek out a local support group for gluten intolerance.

Getting better sleep: Some science-backed strategies for improving sleep include getting some outdoor light in the morning, reducing blue light exposure in the evening, maintaining consistent sleep and wake times, avoiding napping and caffeine in the afternoon, and not exercising too close to bedtime [37, 38].

Step 5) Additional Supplements

Probiotics are by far the most useful supplement for helping to heal your gut from celiac disease and non-celiac gluten sensitivity. But an A–Z type multivitamin and glutamine are two other supplements worth considering.


Some gluten-intolerant patients with slow-to-recover intestines or inadequate nutrition from restricting gluten [39] can benefit from extra micronutrients in a multivitamin supplement. 

A good quality multivitamin and mineral supplement comes with few downsides and is useful nutritional insurance for people with celiac disease.  


Based on client feedback and research data, glutamine (L-glutamine) is another gut-healing supplement that I sometimes suggest for people with celiac disease or gluten sensitivity. 

Glutamine (an amino acid) is a major energy source for the lining of the small intestine and may help it heal from celiac disease damage [40]. It also supports the integrity of tight cell junctions in the gut wall [41, 42] and may reduce inflammation [40]. 

What About Gluten Enzymes?

Supplements that contain gluten-digesting enzymes, such as latiglutenase (also known as ALV0030), are an attractive idea if they break down gluten and prevent symptoms from eating it. 

However, while gluten enzymes appear to be safe for people with celiac disease, the strongest available study found they were not effective for improving symptoms or intestinal health [43].

When it comes to the effects of gluten enzymes on NCGS, less research exists. One small randomized trial found that a gluten enzyme had no effect on abdominal pain, stool consistency, mental health, or quality of life in NCGS patients who reintroduced gluten [44]. 

Another RCT did show NCGS patients benefited from gluten enzymes, but the results are questionable because the study was only single-blinded, meaning the researchers knew who received enzymes and who received a placebo [45]. The study was also conducted by the company selling the enzymes.

The bottom line? Evidence to date suggests that gluten enzymes are probably not helpful for celiac disease or gluten sensitivity, though this conclusion might change as more data becomes available.

There’s Life Beyond Gluten Intolerance

Whether you’ve got celiac disease, non-celiac gluten sensitivity, or reactions to other components in gluten-containing products, you may have gut inflammation and damage as a result.

If you’re wondering how to heal your gut from celiac disease or NCGS, we at the clinic find it’s best to start with the diet. Then, adding in probiotics, exercise, stress relief, and other supplements can further the healing process.

If you have celiac disease, make sure to stay away from gluten and don’t rely on gluten enzymes to digest it.

If you are finding celiac disease, other food sensitivities, or autoimmune conditions too difficult to resolve alone, we can work through your issues with you—just reach out to one of our experienced health practitioners. If digging deeper into gut-healing therapies interests you, you may also benefit from reading my book, Healthy Gut, Healthy You.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.

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