An estimated 5% of kids across the globe have autoimmune diseases and this number is rapidly increasing. The prevalence of type 1 diabetes has increased 200–300% over the past several decades and roughly half of all type 1 diabetes cases in the U.S. occur in children. Moreover, a study of National Health and Nutrition Examination Survey (NHANES) data found an alarming 300% increase in the prevalence of antinuclear antibody (ANA—a common biomarker of autoimmunity) in adolescents between the years 1988 and 2012.

Autoimmune diseases are financially costly, significantly decrease quality of life, and predispose kids to serious health consequences like heart disease and depression. Traditional treatment options often include strong medications to suppress inflammation and symptoms. While nutrition is a mainstay of traditional treatment for celiac disease and type 1 diabetes, it may be an overlooked option for kids with other autoimmune disorders. A functional medicine approach places great emphasis on nutrition in pediatric autoimmune disorders as a way to target root causes and foster more complete healing.

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Understanding Pediatric Autoimmune Disorders

The innate and adaptive immune systems exist to protect the body from outside invaders like microbes (bacteria, viruses, parasites, and fungi), but to also help counteract environmental toxins and eliminate potentially cancerous cells. In people with autoimmune diseases, the immune system mistakenly creates antibodies to attack their cells and tissues. If this inflammatory process continues unchecked, serious damage can result.

Autoimmune disease development can occur at any stage of the life cycle. Diagnosis is usually challenging because symptoms are often non-specific, and they tend to wax and wane. Diagnosing autoimmunity in kids can be even more difficult because they may not yet have the vocabulary to express how they’re feeling. Kids with autoimmune diseases may experience the following symptoms:

• Unexplained, low-grade fever
• Fatigue
• Dizziness
• Weight loss
• Skin rashes or lesions
• Stiff joints
• Hair loss
• Brittle hair
• Dry eyes
• Dry mouth
• Feeling unwell

While there are nearly 100 different autoimmune diseases, common pediatric autoimmune disorders include type 1 diabetes, juvenile idiopathic arthritis, and celiac disease. 

Type 1 Diabetes

In type 1 diabetes, the immune system destroys pancreatic beta cells, which prevent the creation of insulin. Kids with type 1 diabetes must take insulin and manage diet and lifestyle factors to keep their blood sugar levels in a safe range. 

Juvenile Idiopathic Arthritis

Juvenile idiopathic arthritis, formerly known as juvenile rheumatoid arthritis, is a systemic autoimmune condition most often affecting the joints, but also the skin and lungs. Conventional treatment includes starting with non-steroidal anti-inflammatory drugs (NSAIDs) and may eventually progress to immunomodulatory medications, physical therapy, and surgery. 

Celiac Disease

Celiac disease results when the immune system attacks the gliadin protein in gluten-containing grains, resulting in damage to the small intestine lining, chronic inflammation, and malabsorption. Kids with celiac disease must follow a strict gluten-free diet. Corticosteroids are sometimes used but aren’t beneficial for the vast majority. 

While all of these autoimmune diseases lead to different symptoms and systemic effects, they all share the common underlying feature of gut dysfunction.

Gut Health and Its Connection to Autoimmunity 

For the most part, autoimmune diseases have remained a mystery. Genetics and environmental triggers are generally accepted as contributing factors, but on their own don’t always lead to autoimmune disease development. A third factor, increased intestinal permeability, is becoming more widely recognized as a crucial player in the development of autoimmune diseases. 

Gut health in autoimmune disorders must not be overlooked. 70–80% of the body’s immune cells reside in the small intestine likely to help manage the high antigenic load that comes along with food consumption. The delicate small intestine barrier is regulated by tight junctions, adherens junctions, and desmosomes. When the barrier is intact and functioning the way it should, needed nutrients and fluids can cross into the systemic circulation while potentially harmful microbes, toxins, and undigested food particles are kept out. In the case of autoimmunity, the zonulin family of proteins that regulate small intestine barrier tight junctions are upregulated. 

When zonulin levels are higher than they should be (most often by gliadin exposure or microbial dysbiosis), the tight junctions loosen allowing toxins, microbes, and undigested food particles to enter the systemic circulation. This increased permeability forces the immune system into overdrive where T regulatory cells and proinflammatory mediators are released resulting in high levels of inflammation. If normal gut barrier function isn’t restored, the assault on a child’s cells and tissues becomes continuous. Diet, as a main driver of inflammation, immune function, and dysbiosis, is a critical piece of the puzzle when it comes to restoring normal gut barrier function and reversing the symptoms of autoimmunity.

Role of Nutrition in Managing Autoimmune Disorders

Nutrition’s impact on autoimmune disease development, progression, and treatment is immense. As previously mentioned, a strict gluten-free diet is the only effective treatment for children with celiac disease and kids with type 1 diabetes must manage their carbohydrate intake, but nutrition can be used as a first-line therapy for pediatric autoimmunity across the board.

Altered immune system function often results in malnutrition, which impacts a child’s development and future health. Kids with inflammatory bowel disease are commonly deficient in vitamin D and iron, those with celiac disease struggle with vitamins D and B12, iron, calcium, magnesium, folic acid, and zinc, and kids with juvenile idiopathic arthritis tend to have lower levels of zinc, selenium, iron, and vitamin D. Additionally, the dietary pattern is closely tied to the underlying causes of autoimmunity like immune system dysfunction, uncontrolled inflammation, and gut permeability. Using strategies to optimize nutritional status, as well as address root causes allows providers to help their clients better manage autoimmune symptoms, possibly reduce the need for medications, and improve long-term outcomes.

A dietary pattern that’s high in ultra-processed foods (fast food, packaged snacks, sugar-sweetened beverages, sweets, and processed meats) promotes inflammation and immune system dysregulation through gut microbiome dysbiosis and increased intestinal permeability. Aside from being low in fiber and micronutrients, the Western dietary pattern is high in sugar, inflammatory fats; and potentially harmful additives and chemicals, all of which promote inflammation. People who follow a Western diet tend to have higher levels of inflammatory mediators like C-reactive protein (CRP) and interleukin-6 (IL-6).

An anti-inflammatory dietary pattern, on the other hand, reduces inflammatory biomarkers, provides adequate fiber for gut microbiome balance, and is full of nutrients to meet the demands of a growing child. One small study found kids and adolescents who followed an anti-inflammatory diet for juvenile idiopathic arthritis had less pain and morning stiffness, reduced inflammatory markers, better physical function, and higher fecal butyrate levels after four weeks on the diet.

Nutritional Interventions and Dietary Recommendations

Outside of a strict gluten-free diet for patients with celiac disease, there isn’t one perfect autoimmune diet. Rather, dietary interventions for autoimmune diseases in kids should be tailored to the child with the overall goal of optimizing gut health and nutritional status. It may be most helpful to initially implement the 5R protocol for gut healing to lower inflammation, reduce the immune system burden, and support microbial balance, and then work toward an anti-inflammatory meal plan for maintenance.

Remove

This initial phase aims to identify and remove anything that’s damaging the gut lining since an impaired intestinal barrier triggers the immune system. Food sensitivities in autoimmune diseases are common, so an elimination diet that restricts the nine major food allergens including wheat, eggs, soy, milk, fish, shellfish, sesame, tree nuts, and peanuts can provide valuable information about foods that could be contributing to symptoms, as well as give the gut lining time to heal. The remove phase also targets inflammatory ultra-processed foods, non-nutritive sweeteners, food dyes, and additives, environmental toxins, pathogens, and unmanaged stress.

Replace

Important digestive secretions may be compromised in autoimmune conditions, which can hinder a child’s ability to fully digest and absorb their food. This phase of the protocol involves replacing hydrochloric acid, pancreatic enzymes, and bile acids, if needed, to allow for more complete digestion. Providers may also tailor the meal plan and supplements to replace any nutrient deficiencies, like vitamin D and iron that have been identified.

Reinoculate

Microbial dysbiosis can trigger an upregulation of zonulin leading to increased intestinal permeability. The goal of the reinoculate phase is to restore gut microbial balance to support robust gut health, normal gut barrier function, and proper digestion. Studies on probiotics and autoimmunity have found improvements in both gastrointestinal symptoms and body-wide inflammation levels. Providers can use a combination of pre-and probiotic supplements, and tailor the meal plan to include daily fermented foods like sauerkraut, yogurt, kimchi, natto, and kefir.

Repair

In the repair phase, providers focus on further healing the gut barrier. Gut-healing supplement options may include l-glutamine, omega-3 fatty acids, and zinc carnosine.

Rebalance

In this final phase, the maintenance meal plan and lifestyle strategies (like stress management, time in nature, physical activity, and healthy sleep) to maintain gut barrier integrity are implemented. Research has confirmed the intimate connection between diet and immune health, so an anti-inflammatory diet (like the Mediterranean diet) for children with autoimmunity is vital to their quality of life and long-term health outcomes. During the reintroduction phase, you’ll bring the eliminated foods back in to determine personal tolerance. Consider adding back one food item at a time and then monitoring symptoms over three days. If no symptoms occur, then keep the food in and move on to the next food. If your child reacts to the food, remove it from their meal plan and try to reintroduce it at a later time.

If your child has a known food allergy, it’s best to eliminate those foods indefinitely. For kids with celiac disease, a strict gluten-free diet is crucial, but gluten-free diets may also hold benefits for kids with other autoimmune disorders. Gliadin, a protein in gluten-containing grains, triggers the upregulation of zonulin, which can increase intestinal permeability triggering the immune system and the inflammatory cascade of events that follows. It may be helpful to continue to avoid gluten-containing grains (wheat, barley, and rye), but it’s important to discuss this with a healthcare provider.

Implementing Nutritional Plans in Pediatric Care

Significantly changing what they eat can be difficult for children. However, the process can be made easier by making family-centered dietary changes as opposed to creating an environment where kids with autoimmune diseases feel isolated. Parents and caregivers should speak with the child and their siblings (in an age-appropriate way) about the importance of nutrition and how it can impact the way they feel about their growing bodies and their future health. 

When implementing the 5R protocol, parents and caregivers may want to complete the elimination diet with their child. It's best to be positive about the process, avoid perfectionistic thinking, and educate them on each step, why it’s being done, and how long it will take. Using a wall calendar to mark off the days can be helpful. It may also be beneficial to explain that an elimination diet is temporary and they will likely be able to reintroduce many of the restricted foods fairly quickly.

Tips for implementing a maintenance anti-inflammatory meal plan for kids with autoimmune diseases include:

• Creating routine family meal times
• Adults modeling healthy food behaviors
• Keeping wholesome foods on hand at home
• Encouraging snacks like fruit, nuts, and vegetable sticks over chips and cookies
• Limiting restaurant food or take-out
• Helping kids pack their own anti-inflammatory lunch
• Replacing sweetened beverages with water
• Growing fruits and vegetables in a home garden
• Encouraging kids to ask questions about food and their body
• Avoiding fear-based tactics around food

Challenges and Considerations

Food has a tremendous impact on gut and total body health, but nutritional planning for children with autoimmune diseases can be challenging. Younger children may be hesitant to try new foods, older children and teens may be faced with peer pressure, and families may find anti-inflammatory eating less convenient and more expensive. Additionally, medication side effects can impact a child’s appetite and nutrient absorption. It's best to overcome dietary obstacles in autoimmunity by working with a functional medicine registered dietitian or nutritionist who can tailor the 5R protocol and maintenance meal plan based on the specific needs of the child and their family.

Parents and caregivers can overcome many of the challenges in nutritional management by getting kids and teens involved in menu planning and the cooking process. Many kids are eager to help plan meals and to learn how to cook their own food. It may be helpful to search for anti-inflammatory recipes online or purchase several kid-friendly anti-inflammatory cookbooks. Set aside time to sit down as a family to create a list of meals for the week, create a grocery list of needed items, and then shop for the ingredients so they’re readily available when it’s time to cook the meal. By getting kids involved in food choices and meal preparation, they’re empowered to take charge of their own health, gain confidence in their ability to follow an anti-inflammatory diet and learn valuable life skills for the future.

Additional tips include:

• Taking a family cooking class (online or in-person)
• Joining an autoimmune disease support group
• Giving a range of options when introducing new foods
• Trying new foods as a family
• Learning how to make anti-inflammatory versions of favorite foods
• Making menu planning and cooking fun
• Allowing children to be involved in their treatment planning and decision-making

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Nutrition for Pediatric Autoimmune Disorders: Final Thoughts

Autoimmune diseases are on the rise in kids. While genetics and environmental factors are known autoimmune triggers, increased intestinal permeability has emerged as an additional consideration. A functional medicine approach that restores normal gut barrier function with personalized, holistic strategies like the 5R protocol and an anti-inflammatory diet may reverse autoimmune disease symptoms, improve quality of life, reduce the need for medications, and improve long-term outcomes. While diet therapy is considered foundational for the treatment of type 1 diabetes and celiac disease, improving pediatric autoimmune health through nutrition should be a primary focus of treatment and research for all autoimmune conditions.