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How to Avoid Negative Side Effects of a Gluten-Free Diet and Make the Most of Your Diet

by Lindsay Christensen, MS, CNS, LDN, A-CFHC

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Gluten-free diets are trending due to increasing awareness of gluten sensitivity and the myriad ways in which gluten can adversely impact health. As of 2017, 3.1 million people across the United States reported following a gluten-free diet. (1) After being confined to health food stores for decades, gluten-free foods can currently be found nearly anywhere, with mainstream supermarkets and fast-food joints alike offering gluten-free options. (2) In 2018, the gluten-free foods market was valued at $2.7 billion, and this figure is expected to double by 2025. (3)

negative side effects of gluten-free diet
A gluten-free diet that’s high in processed alternatives can cause negative health effects. iStock/Aja Koska

While simply eliminating gluten can be helpful for people with non-celiac gluten sensitivity (NCGS), and potentially lifesaving for those with celiac disease, gluten-free diets are not all created equal. Emerging research shows that the typical gluten-free diet is lacking in fiber, minerals, and other micronutrients. It may also be high in mycotoxins and heavy metals, toxins that detract from our health. Read on to learn about the potential pitfalls and negative effects of a gluten-free diet, and why whole, nutrient-dense foods should form the foundation of a healthy, sustainable gluten-free diet.

Are you experiencing negative side effects after adopting a gluten-free diet? Find out what could be causing them and learn more about a healthier way to eat gluten-free. #nutrition #wellness

Gluten-Free Diets Can Be Life-Changing, but They Are Not All Created Equal

A gluten-free diet requires the complete exclusion of gluten, a protein complex naturally found in:

  • Wheat
  • Barley
  • Rye
  • Spelt
  • Kamut

Due to its low cost and stabilizing, thickening, and flow-enhancing properties, gluten is also used as an additive in countless processed food products. In genetically susceptible individuals, gluten triggers an autoimmune reaction, damaging intestinal villi and extraintestinal tissues (celiac disease) or gut dysbiosis and a non-autoimmune systemic inflammatory response in NCGS.

As many people with celiac disease and NCGS will attest, a gluten-free diet can be life-changing, producing vast improvements in symptoms and health. Yet, while research clearly supports the health benefits of gluten-free diets for susceptible individuals, the scientific community has begun to question the nutritional profile of products people use to replace gluten-containing foods. (4) Research indicates that a gluten-free diet alone is insufficient for improving symptoms in a subset of people with celiac disease, suggesting that the typical gluten-free diet is not necessarily health-promoting. (5, 6) Unfortunately, many people new to the gluten-free diet try to replace their favorite gluten-containing foods with gluten-free alternatives, made with processed and refined flours. A gluten-free diet centered around these foods poses several health concerns and is not an ideal long-term solution. 

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Six Possible Negative Effects and Drawbacks of a Gluten-Free Diet

1. Gluten-Free Replacements Are a Significant Source of Acellular Carbs

Acellular carbohydrates are carbohydrate-containing foods that lack intact cells. The carbs in these foods have a high carbohydrate density and are recent additions to the human diet. Examples of acellular carbs include flour and flour-based products like gluten-free bread, bagels, cookies, cakes, etc. Cellular carbs, on the other hand, are carbohydrate-containing foods in their natural form with intact cells. These cells are made of dietary fiber, which slows down the digestion and absorption of the carbohydrate molecules, creating food with a low carbohydrate density. Examples of cellular carbs include sweet potatoes and whole fruit.

Research indicates that acellular carbohydrates promote the growth of inflammatory gut bacteria and have adverse effects on blood sugar control and satiety. (7) Unfortunately, many gluten-free foods are made with corn, rice, and other starchy gluten-free flours, and are thus rich in acellular carbs. (8) Consuming lots of foods made with gluten-free flour may, therefore, impair the gut microbiota and metabolic health.

Do Processed Gluten-Free Foods Trigger Fat Gain?

Interestingly, an increase in body mass index (BMI) is commonly observed in children with celiac disease after they switch to a gluten-free diet. The high acellular carb content of gluten-free replacement foods may explain this relationship. While increases in BMI on a gluten-free diet may be due to a compensatory increase in nutrient absorption facilitated by the removal of gluten, it may also reflect increased body fat caused by the consumption of starchy gluten-free replacement foods. (9)

To complicate matters further, it is equally possible that a gluten-free diet may help prevent diabetes and metabolic dysfunction by improving leptin resistance, improving insulin resistance, and increasing beta-cell volume, as suggested by research. When it comes to gluten-free diets, the devil is in the details; while a nutrient-dense gluten-free diet centered around whole foods can be health-promoting, a processed gluten-free diet may be detrimental to long-term health. (10)

2. Mycotoxins Can Be Found in Gluten-Free Diets

As I discussed in my article “Food for Mold Illness: What to Eat and What to Avoid,” grains are common dietary sources of mold and mycotoxins, secondary metabolites of mold that have harmful effects on human health. Corn is one of the most mycotoxin-contaminated foods in the human food supply, and a corn-based diet significantly increases mycotoxin exposure. (11) Heavy consumption of corn-based gluten-free foods may substantially increase your exposure to mycotoxins, with harmful health repercussions.

The breast milk of mothers with celiac disease is higher in mycotoxins than that of breastfeeding mothers without celiac disease; exposure of infants to mycotoxins in breastmilk is concerning, given the fact that many mycotoxins have genotoxic, endocrine-disrupting, and immunosuppressive effects. If breastfeeding women with celiac disease rely heavily on processed gluten-free foods in their diets, they may inadvertently expose their babies to high levels of harmful mycotoxins. (12)

If you’re feeling discouraged, please don’t! While corn is the most highly mycotoxin-contaminated grain, rice is the least, and it is also gluten-free. I simply recommend that, if you want to make rice a part of your gluten-free diet, you eat whole-grain rice rather than gluten-free foods made with rice flour, which is high in acellular carbs.

3. Gluten-Free Diets May Contain Heavy Metals

Heavy metals such as lead, mercury, cadmium, and arsenic are abundant in our environment due to industrial pollution. Unfortunately, these metals also end up in our food supply, accumulating more readily in some foods than others. One study published in the NFS Journal suggests that the consumption of gluten-free foods increases the risk of arsenic and mercury exposure because rice, a central component of gluten-free diets, readily absorbs arsenic and mercury from the soil. (13) Another study found that blood levels of lead, mercury, and cadmium are higher in people on gluten-free diets than gluten-containing diets, even after controlling for seafood intake. This finding suggests dietary items besides seafood contribute to the heavy metal body burden in gluten-free dieters. (14)

4. Gluten-Free Diets Can Be Nutrient-Poor

The nutritional status of individuals with celiac disease is already compromised at diagnosis, and affected individuals may suffer from low levels of: (15, 16, 17)

Shockingly, micronutrient insufficiencies and deficiencies have been found to persist for 10 years after the implementation of a gluten-free diet if concerted steps are not taken to enhance the nutrient density of the diet! (18)

A diet high in processed, gluten-free replacement foods is frequently nutrient-poor, and thus insufficient for correcting these deficiencies. While detractors argue that the lack of fortified whole grains is to blame for nutrient deficiencies in people on gluten-free diets, this argument is beside the point. There are many foods naturally free of gluten that people can eat to correct nutrient deficiencies—no fortified whole grains required. As I will discuss shortly, whole, nutrient-dense foods should form the foundation of a gluten-free diet.

5. Processed Gluten-Free Diets May Disrupt the Gut Microbiome

According to surveys, wheat constitutes one of the primary sources of prebiotics in the average standard American diet. (19) Removing wheat from the menu, without replacing it with gluten-free food sources of prebiotics, may starve beneficial gut bacteria and explain the adverse changes in the gut microbiota observed in some people on gluten-free diets, including decreases in Lactobacilli and increases in Enterobacter. (20) Gluten-free foods made with acellular carbs may also promote the growth of inflammatory gut bacteria. (21) While it is difficult to parse out cause and effect when it comes to gluten-free diets and the microbiota, I think we can all agree that a diet low in prebiotics is suboptimal for gut health.

Gums and emulsifiers are commonly used in gluten-free processed foods to mimic the functional and sensory attributes of gluten and to inhibit staling. (22, 23) However, several of these gums and emulsifiers have been found to disrupt the gut microbiota, inflame the gastrointestinal mucosa, and may hurt metabolic health. (24) This is just one more reason to eschew processed gluten-free foods, and opt for whole, nutrient-dense foods instead.

6. Gluten-Free Diets May Be Difficult to Adhere to

Last but not least, many people have trouble adhering to a gluten-free diet. Approximately 40 percent of children with celiac disease experience ongoing gluten exposure, even after commencing a gluten-free diet. (25) Compliance with a gluten-free diet also varies widely in adults with celiac disease. (26) I believe that viewing a gluten-free diet less as just the elimination of gluten, and more as a nutritional overhaul centered around whole foods, may improve adherence by inducing a shift in values and motivations for eating. When people requiring a gluten-free diet are shown all the delicious, naturally gluten-free foods they can eat, rather than directed toward a bunch of processed gluten-free alternatives, their enthusiasm for sticking with the diet may be enhanced. For people who must be on a strict gluten-free diet for health reasons, a nutritionist and a health coach can be invaluable assets for improving dietary compliance.

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What Is the Ideal Gluten-Free Diet? Whole, Nutrient-Dense Foods

Clearly, gluten-free diets centered around a bunch of processed replacement foods are not ideal for healing or long-term health. Interestingly, scientists have caught on to this issue, and several studies have been conducted to examine the effects of “the Gluten Contamination Elimination Diet (GCED)” on health, rather than the more conventional gluten-free diet.

The GCED focuses on the use of naturally gluten-free products rather than processed gluten-free food. It has been found useful for improving health in people with non-responsive celiac disease who did not have success with a standard gluten-free diet. (27) While this approach has been reserved for stubborn cases of celiac disease in the scientific literature, I think it is an ideal approach for anyone who needs to be gluten-free. 

Take a cue from the GCED and build your gluten-free diet out of whole, nutrient-dense foods. Get your carbohydrates from naturally gluten-free foods, such as:

  • Sweet potatoes
  • Winter squash
  • Plantains
  • Whole fruit

If you tolerate gluten-free grains and legumes, incorporate these in their whole-foods form, rather than as components of processed gluten-free foods.

Eat at least three to four servings of non-starchy vegetables per day, such as broccoli and cauliflower, and make sure you are getting enough bioavailable protein to support your activity level and metabolic health. Animal proteins are the best dietary source of iron and vitamin B12, micronutrients that are frequently deficient in individuals with celiac disease.

Finally, include plenty of healthy fats in your diet from:

  • Extra virgin olive oil
  • Olives
  • Avocados and avocado oil
  • Nuts
  • Seeds
  • Wild-caught seafood
  • Coconut
  • Full-fat dairy, if tolerated

Foods for Gut Healing on a Gluten-Free Diet

Make sure to include plenty of probiotics and prebiotics (foods that fuel the growth of probiotic bacteria) in your diet to counteract alterations in the gut microbiota induced by celiac disease and gluten sensitivity. Fermented foods rich in Lactobacillus and Bifidobacteria, such as sauerkraut and yogurt, may aid in gut healing in celiac disease and NCGS, and prebiotic fibers may enhance micronutrient absorption, helping to correct nutrient deficiencies. (28, 29, 30) Excellent gluten-free sources of prebiotics are:

  • Garlic
  • Onion
  • Green plantain and banana flour
  • Tiger nut
  • Artichoke
  • Asparagus
  • Chicory
  • Berries
  • Legumes (if tolerated)

Enjoy Gluten-Free Replacements as Treats, Rather Than Dietary Staples

Please note that while a whole-foods, nutrient-dense diet is the ideal template for those who need to avoid gluten, this doesn’t mean you can’t enjoy gluten-free bread, cookies, or other goodies now and then! I simply believe these items should be viewed as treats, rather than staples of your diet. If you have NCGS, as opposed to celiac disease, you may also be able to include gluten-containing treats in your diet every now and then, particularly once your gut has healed.

Limit the Cost of Going Gluten-Free by Eating Whole, Naturally Gluten-Free Foods

The good news is that when you center your gluten-free diet around whole foods rather than gluten-free replacements, your diet will be more nutritious and more affordable. Research shows that the cost of going gluten-free is high if you are trying to replace all your gluten-containing favorites with processed alternatives. By shopping the perimeter of your grocery stores and choosing whole, unprocessed foods that are naturally devoid of gluten, you can eat a diet that is healthier and more affordable. (31, 32, 33)

A gluten-free diet can have transformative effects on health, yet too many people are following a sub-optimal version of the diet, relying heavily on processed gluten-free foods. A diet comprised of whole, nutrient-dense, naturally gluten-free foods offers the perfect solution to the problems posed by a conventional gluten-free diet.

Lindsay Christensen professional photo
Lindsay Christensen, MS, CNS, LDN, A-CFHC

Lindsay Christensen is a research assistant and contributing writer for Chris Kresser. She has a B.S. in Biomedical Science and an M.S. in Human Nutrition and is a clinical nutritionist, freelance writer, and the newly minted author of The Lyme Disease 30-Day Meal Plan, a practical science-based guide on dietary and lifestyle changes that support recovery from Lyme disease. She currently sees clients through her nutrition consulting business, Ascent to Health, and has completed a 1,000-hour internship to obtain the Certified Nutrition Specialist (CNS) credential, a prestigious credential for nutrition professionals. Lindsay has also passed the Certified Ketogenic Nutrition Specialist exam developed by the American Nutrition Association earning her the CKNS credential.

When Lindsay is not writing and seeing clients, she can be found hiking, skiing, and trail running in the beautiful outdoor spaces surrounding her home in Broomfield, Colorado. You can learn more about Lindsay’s writing and nutrition consulting services at Ascent to Health, stay up-to-date on the latest nutrition science on her Facebook and Instagram accounts, and find her new book, The Lyme Disease 30-Day Meal Plan, on Amazon.


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