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Learn Why It’s Important to Understand Gut Bacteria with Autism

February 19, 2024

Did you know that with over 90 trillion bacteria cells in our bodies we have more bacteria than human cells? This is something that is strange to think about but can have more impact on our health than we could have imagined.

Learn Why It's Important to Understand Gut Bacteria with Autism

One of the areas in our bodies where bacteria have a significant influence is in our gut. The bacteria in our gut is called our gut microbiome and is so important that it’s often time referred to as our “second brain.”

What’s interesting is that while studying the gut microbiome, we’ve discovered that children with autism and their first-degree relatives have different gut bacteria than their peers. With this discovery, there has been a theory developing called the autism gut bacteria theory.

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Probiotics and Autism

How Exactly Does Our Gut Bacteria Affect Us?

Our gut bacteria have a significant influence on what goes on with our nervous system. Our gut is linked with a network of neurons, called the enteric nervous system.

There is a direct line between our gut and our brain called the vagus nerve. You can consider it a highway that sends signals between the brain and the gut. Some of these signals are neurotransmitters, which are chemicals that affect our thinking and our mood.

Serotonin is a neurotransmitter where the majority of it is produced in the gut. Serotonin plays a key role in:

  • Sensory gating and processing
  • Behavior inhibition
  • Appetite
  • Aggression
  • Sleep
  • Mood
  • Brain development

These are all areas where children with autism differ from their neurotypical peers.

There have been many studies backing up the differences in serotonin levels in children with autism and those without. One study found that 30 percent of people with autism have abnormal blood levels of serotonin.

Autism and Leaky Gut

Another gut-related issue that affects children with autism is called leaky gut, which means having poor gut permeability.

In our guts, we have a lining that is supposed to keep bad things out and allow good things in. However, children with autism tend to have a poor gut lining, which can allow toxins into their blood.

So not only do those with autism have abnormal gut bacteria, but they are already at a disadvantage because their gut lining is leaky! It’s a very unfortunate combination, but the good news is that there are specific things we can do to promote healthy gut bacteria and repair gut lining.

There is Good News in the Autism Gut Bacteria Theory

This review of multiple studies on gut microbiome and autism showed that treating children with ASD from a microbiome angle is a promising avenue for treatment strategies.

On top of this, a study using mice that had their gut bacteria manipulated showed that using a strain of good bacteria fixed their leaky gut and reduced their autistic symptoms. Then by altering the microbes in their guts to match other mice who had autism brought the autistic symptoms right back.

What’s more is that Dr. Sanford Newmark, an integrative medicine doctor at UCSF who specializes in treating autistic children, says the majority of his clients see an improvement in autistic symptoms when changing their diets.

There are two strategies for improving your child’s gut bacteria and lining. To remove problematic foods and to add in foods and supplements that repair and nurture a healthy gut lining and microbiome.

Let’s start with which foods to remove.

Here’s What to Remove From Your Child’s Diet

The first food we’ll look to remove is gluten. You may have heard about gluten before, as it’s received a lot of publicity in the last few years on whether or not there is a need for healthy individuals to remove it from their diets.

However, for children with autism, the evidence is heavily pointed towards removing it from their diet.

One study found that a subset of autistic children showed heightened reactivity to gluten. When gluten is broken up into smaller pieces in your gut, these fragments cause the release of zonulin, which then tells the lining of your gut to become looser. This is particularly a problem for those with autism because of their already damaged gut lining.

The next food that can cause problems is casein. Casein is a protein found in dairy and has a very similar makeup to gluten. Autistic children who remove casein from their diets appear to do better than those who don’t.

To remove casein from your child’s diet, you’ll have to remove dairy. This can be difficult since dairy is typically a major part of people’s diets. However, the benefits your child could experience could make it worth at least a one-month experiment.

If you are worried about calcium intake from dairy for strong bones, dark leafy greens can actually fill that gap.

A report found that the stricter parents were with their children’s diets, the larger improvements they saw. Make sure you give 100% effort and try it for an extended period.

What to Add to Fix Your Child’s Gut

Now that you’ve found out what to remove from your child’s diet let’s look at what foods and supplements can be added to improve their diet. It is best to work with your child’s physician on adding these in, as they can help with proper dosing for your child.

As an upfront note, while supplementing is a great start, the real goal would be to make sure your child is getting as many vitamins and minerals from real whole foods as possible.

The first place you’ll want to start with when adding foods and supplements to your child’s diet is an effective therapeutic strength probiotic that will increase the number of good bacteria in your child’s gut.

There are many different species and strains of bacteria, so you’ll want one that has a wide variety and is highly concentrated. You’ll want to look for a probiotic that has at least 8 billion bacterial cells per gram.

Bio-Kult is often recommended, but many others on the market meet our needs. You can work with your physician to find a probiotic as well.

Not only do you want to supplement with probiotics but if you can get your child to start eating probiotic-rich foods, then that will help as well.

Some good probiotic rich food to start with are sauerkraut, kimchi, or kombucha. Many children with ASD are very picky eaters, which may make this stage a little tricky. The kombucha is a good place to start since you can find tasty ones in your local grocery store. A good brand is GT’s Kombucha because they don’t put in extra sugar.

Like I mentioned above, you’ll want to avoid all dairy for at least the first month. However, when it comes time to add them, yogurt and kefir are healthier dairy products that have good bacteria in them.

The next thing we’ll want to add is prebiotics. Prebiotics are what the probiotics eat. One way to supplement this is to add resistant starches to your child’s diet. They are called resistant starch because they are resistant to human digestion, which allows them to make it down to our gut bacteria.

Resistant starches to slowly work into your child’s diet are banana flour, plantain flour, and raw potato starch. Some foods that have resistant starches in them are sweet potatoes, carrots, asparagus, squash, and leafy greens.

Since your child might have leaky gut and abnormal gut bacteria, they then will have problems properly digesting food and absorbing vitamins and minerals. Adding some digestive enzymes to help break down food is the next step to improving your child’s digestion and support the repair of their leaky gut.

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The next thing we’ll want to supplement with is some Betaine HCL with Pepsin.

Betaine HCL with Pepsin is a supplemental version of stomach acid. People with abnormal gut flora almost always have low stomach acid. Stomach acid is critical for breaking down food to digest it, so supplementing with this should be a quick win for helping your child.

Another supplement to add is Essential Fatty Acids, also known as omega-3 and omega-6 fats, which are crucial to a range of functions in our body.

Omega-3 is typically what we lack. Vegetable oil has a ton of omega-6 in it, so we usually get too much of that. We want our ratio of omega-3 to omega-6 to be 1:1 or even 2:1, with omega-3 being more.

Omega-3 is made up of two different fats, EPA and DHA. DHA plays a bigger role in our cognitive development while EPA has been shown to affect our ability to control our mood more.

Supplementing with omega-3 has been shown to improve symptoms of aggression, ADHD, dyslexia, and autism while also lowering inflammation in the body. On top of that, omega-3 supplementation has been shown to increase cognitive function in even healthy individuals.

These are all great things and can help a child with ASD.

One of the best ways to supplement omega-3 is with cod liver oil.

And once again, don’t use vegetable oils, since they are high in omega-6 and throw off our ideal 1:1 ratio.

The following two vitamins are ones that children with ASD are typically low in. The first is vitamin A. This one will be one of the easier ones to get from whole foods since it’s high in sweet potatoes, carrots, dark leafy greens, and squash.

The next supplement is vitamin D. Vitamin D plays a massive role in our body, and it’s extremely hard to get from food. The best source is the sun, but most of us don’t get enough sun, and some of us live so far north that half of the year the sun isn’t strong enough to give us any vitamin D.

You can overdose on vitamin D, so make sure to get your child’s blood levels tested to find where they are.

Vitamin D plays a role in regulating our immune systems, our microbiome, our gut lining, and our serotonin levels.

One study even went as far as to say:

“Supplementing infants with vitamin D might be a safe and more effective strategy for reducing the risk of autism.”

Another study found the link between why low vitamin D affects autistic symptoms:

“Now, researchers show that serotonin, oxytocin, and vasopressin, three brain hormones that affect social behavior related to autism, are all activated by vitamin D hormone. Supplementation with vitamin D and tryptophan would be a practical and affordable solution to help prevent autism and possibly ameliorate some symptoms of the disorder.”

As you can start to see, vitamin D is critical to your child, as well any most individuals in the United States.

Another supplement you can look to add is collagen. Collagen is the connective tissue of most biological structures. It will help repair your child’s stomach and gut lining. You can supplement with a collagen powder like the Upgraded Collagen from Bulletproof, or you can make bone broth at home.

The last supplement to add is vitamin B12. This is another one most autistic children are low in. When looking to find a supplement for it, look for Methylcobalamin, as it’s considered the best.

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Probiotics and Autism


Working on improving your child’s diet can have a significant effect on their stereotypical autistic symptoms. While changing your child’s diet can be a challenging task, the rewards can completely be worth it.

Like we mentioned above, it’s best to work with your child’s physician to make any diet changes. Every child is different, so it’s best to get a personalized protocol through your child’s doctor.

If you’d like to research more into diets that promote healthy gut lining and bacteria, the GAPs or paleo diet are good places to start.

This article was featured in Issue 63 – Keeping Our Kids Safe

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