A Functional Medicine Perspective On Autism Spectrum Disorder


Autism spectrum disorders (ASD) have skyrocketed over a short period of time. In 1970, an estimated 1 in 10,000 children were found to be autistic. In 1995 it was 1 in 500. In 2001 it became 1 in 250 and today, 1 in 36 children (1) are diagnosed as autistic and 1 in 45 adults in the U.S. have autism.

The reality is, genetics alone does not explain the epidemic growth of autism and other conditions like it. Our genetics haven’t changed in the last 40 years. Better diagnosis may explain part of the astronomic increase of autism, but only in part. In reality, the medical literature (2) is beginning to recognize autism as an autoimmune reaction against the brain. 


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What is autism?

Autism Spectrum Disorder is a neurodevelopmental condition that affects social interaction, communication skills, behavior, and often includes repetitive behaviors or restricted interests. It is referred to as a spectrum disorder because it can manifest in a wide range of ways and severity levels, hence the term "spectrum."

Individuals with autism may experience challenges in social situations, have difficulty with non-verbal communication cues (such as facial expressions, body language, or tone of voice), and display repetitive behaviors or highly focused interests. Some may also experience sensory sensitivities, finding certain stimuli (like loud noises or bright lights) overwhelming. Each person with autism is unique, with their own strengths and challenges, and may require different levels of support or accommodations to thrive.

It's important to note that autism is not a disease or an illness - it's a lifelong condition that is believed to have both genetic and environmental factors contributing to its development. Understanding these underlying factors can help us better support individuals with autism.

Autism and the gut-brain connection

Called the “second brain” in medical literature, your gut is home to around 80% of your immune system. We are only beginning to understand the communication lines between the gut and the brain - also referred to as the gut-brain axis - but every condition that has an immune component to it has been correlated to some dysfunction of the gut. 

Your gut microbiome is made up of trillions of bacteria and has been shown to be a key player in turning on and off genetic expression. Now you can see, with its implications in immune health and genetic expression, why the gut is at the center of some autism research.

In fact, a recent 2022 study published in Frontiers in Microbiology (3) found that children with autism didn’t have the same gut microbiome diversity that children without autism had. In another study (4) mice with autism-like symptoms had a similar lack of gut bacteria diversity.

The prevailing theory in the medical literature (5) is that an imbalanced microbiome and a weakened gut lining or “leaky gut” can cause an inflammatory immune response against the brain and cause a genetic predisposition to this condition to be turned on.

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Autism and genetic predispositions

Methylation, your biochemical reaction superhighway, happens more than 1 billion times every second in your body to keep you vitally healthy. Methylation protects our DNA, detoxes our body, and makes our brain and gut healthy.In short, if methylation is not working well, a lot can go wrong with your health.

There are many different genes that are responsible for making methylation happen but sometimes methylation gene mutations or variations can impair your body’s ability to methylate optimally.

One of those methylation genes is the MTHFR gene. MTHFR gene mutations don’t send all the instructions to make the important enzyme that converts the inactive B vitamin folic acid into the active methyl-folate. Some research estimates that those of us with MTHFR changes make up to 70% less methyl-folate!

So what does this have to do with autism? According to a 2020 study (6) people with the MTHFR C677T gene polymorphism had an increased risk of autism spectrum disorders. But that doesn’t necessarily mean that you have autism if you have one of these methylation gene variations. Ultimately, it’s epigenetic factors of the gut-brain axis that I mentioned before that can trigger the methylation gene changes that are already present.

Natural treatments for autism

Now it’s important to remember that there is no cure for autism. However, there are a lot of natural tools that can be implemented to care for the gut-brain connection, improve communication and sensory processing, and help those with autism thrive all around.

1. Get diagnostic testing

Comprehensive diagnostic testing will give insight into your particular health case to determine if there are any areas that require attention. Some of the labs that I run include:

Comprehensive Gut & Parasitology: This provides a look into the microbiome to assess for the presence of bacterial dysbiosis or parasites. I recommend a two or three day collection for the most accurate results.

Gut Permeability: This measures whether there has been damage to the gut lining (leaky gut syndrome) which can lead to inflammation of the gut and the brain.

Comprehensive Antibodies: This provides a detailed look at any inflammatory autoimmune responses against the brain, gut, and other systems in the body.

DNA Methylation Pathway Profile: This test looks at around 30 methylation SNPs (single nucleotide polymorphisms). By looking for DNA mutations that govern methylation, it gives us a personalized guide to what your unique genetic weaknesses and imbalances are so that they can be specifically addressed.

2. Heal your gut

Researchers found that by giving the “autistic” mice the beneficial probiotic bacteroides fragilis, they were less anxious and communicated more vocally - both common autism struggles. Many of my patients also see an improvement in autistic symptoms by addressing the gut. There are many tools that can be used to heal your gut including probiotic supplements, bone broth, dietary changes, and targeted supplements. For a complete guide to healing your gut, check out my article here.

3. Calm your brain

Because autism is also a condition that affects the brain, it is essential to support optimal brain health and calm any inflammation inside the brain. Foods like oysters and avocados are some of my favorite brain calming foods. For a complete guide to soothing neuroinflammation, check out my article here.

4. Uncover any food intolerances

Certain foods have been shown to perpetuate inflammation in both the gut and the brain. One study even showed that a gluten and dairy free diet can be beneficial (7) in improving some autism symptoms. Ultimately, it’s important to find out what foods trigger inflammation in your body and which foods your body loves. In addition to food intolerance labs, an elimination diet can help you uncover any underlying food intolerances that can exacerbate symptoms.

5. Support genetic weaknesses

Vitamin B12, in conjunction with other activated B vitamins such as methyl-folate help support optimal methylation pathways. There are many different, unique methylation genetic changes that can happen, so what works for one person may not for the next. Depending on the specific MTHFR polymorphisms at play, certain types of B12 may be better tolerated, which can support healthy methylation pathways. Working with a qualified practitioner can help determine if methyl B12, hydroxycobalamin B12, adenosynl B12, or cyano B12 is best for you.

7. Consider alternative therapies

Helminthic therapy - a process that involves swallowing a saline solution infused with mutualistic parasites, called helminths - has shown promise for improving symptoms of ASD. While this is not an FDA-approved treatment, it is being studied as a potential treatment for a range of autoimmune disorders, such as type 1 diabetes, Crohn’s disease, and multiple sclerosis - and yes, autism - with preliminary studies showing a lot of promise.

This is likely due to the fact that helminthic infections have the ability to decrease inflammation by suppressing Th1 and Th17 cells and increase T-regulatory cells. (8) Due to its connections with inflammation, studies have shown (9) that helminthic therapy was able to help improve the frequency of repetitive behavior in those with ASD.

In summary

With all this said, I in no way want to over simplify this complex condition. There is no easy answer to the multifaceted web of genetic and environmental factors that are at play with Autism Spectrum Disorders. Instead, I want to provide a starting point in understanding this complicated topic. As we continue to learn more about this condition, doctors, parents, support systems, and people with ASD, can implement the latest in clinical research to improve the lives of every single person living with this condition.

If you or someone you know is diagnosed with Autism Spectrum Disorder and you would like a functional medicine perspective on this condition, schedule a telehealth consultation today.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.

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  1. Autism Speaks "Autism Prevelance" Accessed December 2023. https://www.autismspeaks.org/autism-statistics-asd
  2. Brimberg, L et al. “Brain-reactive IgG correlates with autoimmunity in mothers of a child with an autism spectrum disorder.” Molecular psychiatry vol. 18,11 (2013): 1171-7. doi:10.1038/mp.2013.101
  3. Jones, Jacquelyn et al. “Changes to the Gut Microbiome in Young Children Showing Early Behavioral Signs of Autism.” Frontiers in microbiology vol. 13 905901. 28 Jul. 2022, doi:10.3389/fmicb.2022.905901
  4. Elaine Y. Hsiao, Sara W. McBride et. al. ""Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders" Cell Volume 155, Issue 7, P1451-1463, December 19, 2013. DOI:https://doi.org/10.1016/j.cell.2013.11.024
  5. Mulle, Jennifer G et al. “The gut microbiome: a new frontier in autism research.” Current psychiatry reports vol. 15,2 (2013): 337. doi:10.1007/s11920-012-0337-0
  6. Li, Yan et al. “Association between MTHFR C677T/A1298C and susceptibility to autism spectrum disorders: a meta-analysis.” BMC pediatrics vol. 20,1 449. 24 Sep. 2020, doi:10.1186/s12887-020-02330-3
  7. Whiteley, Paul et al. “Gluten- and casein-free dietary intervention for autism spectrum conditions.” Frontiers in human neuroscience vol. 6 344. 4 Jan. 2013, doi:10.3389/fnhum.2012.00344
  8. Kondĕlková, Katerina et al. “Regulatory T cells (TREG) and their roles in immune system with respect to immunopathological disorders.” Acta medica (Hradec Kralove) vol. 53,2 (2010): 73-7. doi:10.14712/18059694.2016.63
  9. Hollander, Eric et al. “Randomized crossover feasibility trial of helminthic Trichuris suis ova versus placebo for repetitive behaviors in adult autism spectrum disorder.” The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry vol. 21,4 (2020): 291-299. doi:10.1080/15622975.2018.1523561

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Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

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