Vibrant Functional Academy

Functional Medicine for Autism: The Role of Gut Health, Nutrition, and Toxins

Written by Nancy Guberti, M.S., C.N. | Apr 10, 2025 3:05:49 PM

Autism spectrum disorder (ASD) affects 1 in 36 children in the United States, a number that continues to climb.¹Globally, estimates suggest that approximately 1 in 100 children has autism.² This rising prevalence signals a pressing need to look beyond conventional behavioral therapies like applied behavioral analysis (ABA) when providing patient care.

Many individuals with ASD struggle with co-occurring health challenges, such as digestive issues, chronic inflammation, nutritional deficiencies, and metabolic imbalances, which can amplify cognitive and behavioral symptoms.³

A functional medicine approach offers a way forward by addressing these underlying physiological factors with personalized, science-backed strategies. 

In this article, we’ll explore functional medicine for autism, considering how the gut-brain connection, gut-adrenal connection, gut-immune link, nutritional imbalances, metabolic dysfunction, and environmental toxin exposures shape the disorder. We’ll dive into advanced functional lab testing from Vibrant Wellness and show you how these tools can guide tailored interventions to help produce better outcomes.  

Whether you’re a practitioner supporting ASD patients or a caregiver seeking answers, here’s how to unlock a new level of intervention. 

Table of Contents

Functional Medicine for Autism 

Environmental Toxins and Neurodevelopment 

Gut Health and ASD 

Case Study: Functional Medicine for Autism in Action 

Nutritional Deficiencies, Metabolic Function, & Micronutrient Testing 

A Vital Piece to the Treatment Puzzle 

Food Sensitivities and Behavior in Autism 

About the Author

 

Functional Medicine for Autism 

Traditional approaches for autism spectrum disorder focus on managing symptoms rather than understanding the complex underlying causes. Treatment typically involves medication and behavioral therapy. 

Recently, there has been a shift toward a more holistic approach—namely, functional medicine intervention.

Functional medicine works to unravel the complex web of factors involved in ASD by targeting root causes and uncovering biological imbalances that might exacerbate symptoms. Looking into genetic vulnerability, diet, specific nutritional deficiencies, and environmental influences can offer many pieces to the puzzle.

Research shows that individuals with ASD frequently experience a cluster of physiological issues: gut microbiome dysbiosis, neurotransmitter imbalances, inflammation, immune dysfunction, and exposure to environmental toxins.⁴

Why does this matter? Because addressing these factors can improve digestion, energy levels, cognition, mood, and behavior. For your patients, this could mean fewer meltdowns, better focus, lessened sensory issues, or even enhanced sleep, outcomes that behavioral therapy alone might not achieve. The key is personalization, and that’s where advanced lab testing becomes your power tool kit. 

Gut Health and ASD  

Let’s discuss the gut-brain axis, a complex two-way communication pathway linking the digestive system to the brain. In ASD, altered gut microbiota and metabolites (e.g., short-chain fatty acids, neurotransmitters) often interrupt this pathway, leading to brain function issues and contributing to associated GI and behavioral problems. 

Different studies suggest anywhere from 70% to 91% of individuals with ASD have gastrointestinal problems like constipation, diarrhea, or abdominal pain.⁵ These aren’t just side effects—they’re clues.

While ASD is characterized by communication impairments, social issues, and specific behaviors, there are several observed medical comorbidities, particularly gastrointestinal issues, that are of particular interest because they correlate with autism-related behavior.  

Studies of the gut microbiome and microbiota-gut-brain axis provide insight into the mechanism leading to the neurological disorder’s onset and possible treatments for autism.⁶ In fact, some studies have shown that stool samples from children with autism have different gut fungal communities than those from healthy neurotypical children.⁷

Imagine a patient with frequent tantrums, severe sensory issues, or poor focus. Could an overgrowth of harmful bacteria or yeast like Candida send inflammatory signals to their brain? Understanding the gut microbiome and the role of gut health in autism spectrum disorder can help you manage symptoms and their impact on behavior.  

The Vibrant WellnessGut Zoomer is one way to gain this insight. This test assesses:

  • Microbiome diversity: Gut dysbiosis (an imbalance in gut microbes) can lead to inflammation and potentially influence autism-related behaviors.  
  • Yeast and fungal imbalances: Candida overgrowth can fuel inflammation, behavior, and immune dysfunction.  
  • Intestinal permeability markers: A leaky gut lets toxins and proteins enter the bloodstream, triggering immune responses. 
  • Inflammatory markers: Elevated levels signal a gut-brain flare-up. 

 

With these valuable insights, you can recommend tailored and targeted interventions, such as probiotics, nutraceuticals, and dietary modifications, to restore balance in the gut-brain pathway.  

Nutritional Deficiencies, Metabolic Function, & Micronutrient Testing 

Nutrition fuels brain function, so what we feed the body can positively or negatively impact the brain. Many children and adults with autism don’t eat healthy, balanced meals and instead tend to gravitate to the Standard American Diet (SAD), which is characterized by processed foods, refined carbohydrates, and other non-nutrient food products. In addition, restrictive eating patterns and sensory sensitivities often lead to imbalances in micronutrients like vitamins and minerals. For example, levels of vitamins B1, B6, B12, A, and D are usually low in these patients.⁸

This scenario leaves the brain cells unnourished. Nutrient imbalances, meanwhile, can disrupt the production of neurotransmitters, such as serotonin (which is essential for mood) and dopamine (which supports focus), and impair cognitive health.

The role of metabolic functioning is crucial, as altered metabolism, especially of amino acids like tryptophan and phenylalanine, may relate to neurotransmitter synthesis and signaling pathway disruptions. Short-chain fatty acid metabolism may contribute to ASD, and differences in energy metabolism in children with autism may involve altered mitochondrial function.⁹

Research highlights common deficiencies in ASD patients: 

  • B vitamins: Essential for methylation (a detox process) and neurotransmitter synthesis.³
  • Vitamin A:  Vulnerable toanemia, weak infection resistance, ocular symptoms, and the risk of death.⁸ 
  • Vitamin D: Essential for bone metabolism. Positive results from supplements reducedirritability and hyperactivity.
  • Magnesium: Calms the nervous system and supports sleep. Studies showed supplementation reduced hyperactivity and aggressiveness and improved school attention.
  • Omega-3 fatty acids: Reduces inflammation and bolsters brain cell communication. Studies indicated supplementation reduced irritability and hyperactivity.
  • Glutathione: Required for normal immune function, detoxification capacity, and redox-sensitive enzyme activity.
  • Iron: Essential cofactor for enzymes.¹⁰
  • Selenium: Crucial for thyroid function, preventing oxidative stress.¹⁰
  • Zinc: Critical for metabolism and immunity. Supplementation improved behavioral deficits.¹⁰

But how do you pinpoint what’s missing? Start with the Vibrant Wellness Organic Acids Test (OAT). The OAT is a foundational test used to evaluate ASD patients. It measures the following, offering a metabolic snapshot:  

  • Energy metabolism markers: Are mitochondria (the cell’s powerhouses) struggling? 
  • Neurotransmitter metabolites: Are dopamine or serotonin pathways imbalanced? 
  • Yeast and bacterial overgrowth markers: Toxins from these microbes can stress the brain. 
  • Oxidative stress levels: Too much stress damages cells and worsens symptoms. 

Pair this with the Vibrant WellnessMicronutrient Panel to get a more complete picture of deficiencies—like low zinc or vitamin D—impacting immune or neurological function. The Micronutrient Panel measures a wide range of vitamins, minerals, amino acids, fatty acids, antioxidants, and other key markers to provide a detailed picture of nutrient absorption and utilization at a cellular level.

From there, you can develop plans to deliver personalized nutrition for ASD patients. For example, substitute processed snacks for fatty fish (hello, omega-3s) or add a methylated B complex to support methylation. Insight beats guesswork every time. 

Food Sensitivities and Behavior in Autism  

Food can be a friend or foe in ASD. Specific proteins like gluten from wheat or casein from dairy can spark inflammation and behavioral flare-ups in sensitive individuals. How? A leaky gut lets these proteins seep into the bloodstream, triggering immune reactions that reach the brain. Studies link food sensitivities to increased irritability, aggression, and even self-injurious behavior in ASD.¹¹

Food sensitivity testing can cut through the noise. It identifies specific triggers—gluten, dairy, soy, or beyond—so you can create a diet that works for your patient. What I have seen in over 24 years of testing special needs children is excessive opioid activity linked to the peptides of gluten and casein. These peptides may become biologically active through binding with opioid receptors. The resulting excess of opioids may lead to the behaviors exhibited in autistic spectrum disorders.¹²

That’s where Vibrant Wellness’ Wheat and Dairy Zoomer tests are very insightful. TheWheat Zoomer Test comprehensively analyzes an individual’s immune response to wheat proteins and peptides. The Dairy Zoomer Test measures IgG and IgA antibody responses to various dairy proteins and their peptide fragments, such as casein and whey, and a broad panel of dairy-derived peptides.  

Many families and caregivers need test results to adhere to a diet change. For example, if dairy is a culprit, suggest swapping cow milk for coconut milk. Combine this with gut-healing strategies like bone broth and unsweetened coconut yogurt to tackle the root while easing symptoms. It’s a win-win. 

Hear from participants in Vibrant's landmark food sensitivity clinical trial:

Environmental Toxins and Neurodevelopment  

The world is a toxic place, and significant environmental and health challenges are potentially linked to toxic substances. “Forever chemicals” like PFAS and heavy metals are found in many products, while glyphosate, a widely used herbicide, has been detected in food. For individuals with ASD, the burden of toxins hits harder.  

Some kids with ASD have impaired detoxification pathways, sluggish liver function, or low glutathione (the body’s master antioxidant), making it challenging to clear heavy metals (lead, mercury, arsenic), pesticides, and endocrine-disrupting chemicals (like phthalates), which can derail brain development and behavior.¹³ 

Enter the Vibrant WellnessTotal Tox Burden Test. It identifies:

  • Heavy metals: Mercury from fish or lead from old pipes can build up in the brain; lead, mercury, arsenic, and cadmium, which occur naturally or through environmental contamination, can be found in certain foods. 
  • Glyphosate: The herbicide is found in various foods, including grains, beans, and processed foods, as well as in soil, water, and even air. 
  • Mycotoxins: Mycotoxins may delay and negatively influence the development of neurological, gastrointestinal, and inflammatory responses. Mold exposure can trigger neuroinflammation.¹⁴
  • Environmental chemicals: Phthalates from plastics disrupt hormones and development. Exposure to environmental chemicals during gestation is associated with different neurodevelopmental disorders and deficits in children.¹⁵

Once you know the toxic load, you can act with a nutraceutical plan. Boost glutathione with N-acetylcysteine (NAC) or sulfur-rich foods like broccoli. Support liver detox with milk thistle or a nutrient-packed green smoothie. These evidence-based steps help reduce the toxic burden safely.

Case Study: Functional Medicine for Autism in Action  

Meet Justin, a 7-year-old with ASD who struggled with meltdowns, constipation, bloated belly, sensory issues, and poor sleep. His parents were at their wits’ end, and conventional care wasn’t cutting it. This is where functional medicine for autism can step in.   

The following Vibrant Wellness tests showed potential connections between environmental toxins and neurodevelopment, as well as food sensitivities and behavior in autism:  

  • Gut Zoomer: Showed low microbiome diversity and Candida overgrowth. 
  • OAT: Revealed high oxidative stress, sluggish energy metabolism, and vitamin deficiencies.  

Tailored treatment included a dairy-casein-gluten-corn-free diet with low sugar, no artificial ingredients, and balanced whole-food meals. Nutraceutical protocol included probiotics for gut health; magnesium with P5P (B6), vitamin D, and methylated B complex to address deficiencies; NAC to boost detox; and homeopathic remedies for balancing neurotransmitters. Within three months, Justin’s constipation eased, his sleep improved, and his meltdowns decreased by more than half. His focus at school also sharpened. This wasn’t guesswork—Auit was biology, guided by data. 

As we dig deeper into functional medicine for autism, it’s clear that this approach could transform our understanding of ASD. By focusing on the wide range of factors affecting health, functional medicine sets the stage for more effective, customized treatments tailored to the specific needs of the individual.  

A Vital Piece to the Treatment Puzzle 

Behavioral and communication therapies, which are central to ASD treatment, fit seamlessly with functional medicine, as they aim to enhance daily functioning and quality of life for those on the autism spectrum. Beyond these established methods, functional medicine integrates alternative treatments and offers considerable potential to improve the well-being and capabilities of people with autism.

By targeting root causes and utilizing a variety of therapeutic techniques to address the connections between autism spectrum disorder and toxins, functional medicine aims to boost overall health and life quality, positioning it as a vital piece to the autism treatment puzzle. 

ASD is complicated, but its treatment is not out of our grasp. You can unlock improvements that behavioral therapy alone might miss by addressing gut health, nutrition, metabolic function, and detoxification. Tools like the Vibrant Wellness' advanced testing puts precision in your hands, letting you customize care for each patient. 

Ready to take your practice to the next level? Explore how Vibrant Wellness testing can transform outcomes for ASD and neurodevelopmental disorders. Your patients—and their families—deserve care that goes beneath the surface. 

About the Author

Nancy Guberti, M.S., C.N., is a functional medicine practitioner, medical educator, and founder ofTotal Wellness Empowerment Institute, offering accredited courses for Certified Autism Health Coach Training, Certified Master Health Coach Training, and Practitioner Mentorship. She specializes in empowering others to reach optimal wellness and success and has been featured on Shape, SheKnows, WorldLifestyle, Associated Press, and Huffington Post. Her book, Healthy Living Every Day: Total Wellness For Mind & Body, is available on Amazon. Connect with her on Instagram and LinkedIn. 

References:

  1. Centers for Disease Control and Prevention. Autism Data & Research. CDC. Updated March 13, 2025. Accessed March 13, 2025. https://www.cdc.gov/autism/data-research/
  2. Zeidan J, et al. Global prevalence of autism: a systematic review update. Autism Research. 2022 May;15(5):778-790. doi: 10.1002/aur.2696. Epub 2022 Mar 3. PMID: 35238171; PMCID: PMC9310578.
  3. McElhanon BO, et al. Gastrointestinal symptoms in autism spectrum disorder: a meta-analysis. Pediatrics. 2014 May;133(5):872-83. doi: 10.1542/peds.2013-3995. PMID: 24777214.
  4. Vuong HE, Hsiao EY. Emerging roles for the gut microbiome in autism spectrum disorder. Biol Psychiatry. 2017 Mar 1;81(5):411-423. doi: 10.1016/j.biopsych.2016.08.024. Epub 2016 Aug 26. PMID: 27773355; PMCID: PMC5285286.
  5. Madra M, Ringel R, Margolis KG. Gastrointestinal issues and autism spectrum disorder. Child Adolesc Psychiatr Clin N Am. 2020;29(3):501-513. doi: 10.1016/j.chc.2020.02.005
  6. Bhardwaj G, et al. The hidden threat: environmental toxins and their effects on gut microbiota. Pathol Res Pract. 2024 Mar;255:155173. doi: 10.1016/j.prp.2024.155173. Epub 2024 Jan 28. PMID: 38364649.
  7. Herman A, Herman AP. Could Candida overgrowth be involved in the pathophysiology of autism? J Clin Med. 2022;11(2):442. doi: 10.3390/jcm11020442
  8. Robea MA, Luca AC, Ciobica A. Relationship between vitamin deficiencies and co-occurring symptoms in autism spectrum disorder. Medicina (Kaunas). 2020;56(5):245. Published 2020 May 20. doi: 10.3390/medicina56050245
  9. Al-Beltagi M, Saeed NK, Bediwy AS, Elbeltagi R. Metabolomic changes in children with autism. World J Clin Pediatr. 2024;13(2):92737. Published 2024 Jun 9. doi: 10.5409/wjcp.v13.i2.92737
  10. Kaczmarek KA, Dobrzyńska M, Drzymała-Czyż S. Iron, magnesium, zinc, and selenium — the most common elemental deficiencies in children with an autism spectrum disorder. Res Autism Spectr Disord. 2024;110:102288. doi: 10.1016/j.rasd.2023.102288
  11. Whiteley P, Shattock P, Knivsberg AM, et al. Gluten- and casein-free dietary intervention for autism spectrum conditions. Front Hum Neurosci. 2013;6:344. Published 2013 Jan 4. doi: 10.3389/fnhum.2012.00344
  12. Millward C, Ferriter M, Calver S, Connell-Jones G. Gluten- and casein-free diets for autistic spectrum disorder. Cochrane Database Syst Rev. 2008;(2):CD003498. Published 2008 Apr 16. doi: 10.1002/14651858.CD003498.pub3
  13. Rossignol DA, et al. Environmental toxicants and autism spectrum disorders: a systematic review. Transl Psychiatry. 2014;4:e360.
  14. Serkan Y, Beyazit U, Ayhan AB. Mycotoxin exposure and autism: a systematic review of the molecular mechanism. Curr Mol Pharmacol. 2021;14(5):853-859. doi: 10.2174/1874467213999200819145942
  15. Marí-Bauset S, Donat-Vargas C, Llópis-González A, et al. Endocrine disruptors and autism spectrum disorder in pregnancy: a review and evaluation of the quality of the epidemiological evidence. Children (Basel). 2018;5(12):157. Published 2018 Nov 23. doi: 10.3390/children5120157 

Regulatory Statement:

The information presented in case studies have been de-identified in accordance with the HIPAA Privacy protection.

The general wellness test intended uses relate to sustaining or offering general improvement to functions associated with a general state of health while making reference to diseases or conditions. This test has been laboratory developed and its performance characteristics determined by Vibrant America LLC and Vibrant Genomics, a CLIA-certified and CAP-accredited laboratory performing the test. The lab tests referenced have not been cleared or approved by the U.S. Food and Drug Administration (FDA). Although FDA does not currently clear or approve laboratory-developed tests in the U.S., certification of the laboratory is required under CLIA to ensure the quality and validity of the test