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Can Gut Bacteria Affect Symptoms of Autism?

By Casey Ames, Founder of Harkla

Have you heard about the autism gut bacteria theory before? If you haven’t, don’t worry. This article will cover everything you need to know about it, including what can be done to help your child’s autistic symptoms by improving their gut bacteria.

If you have heard of it before, then prepare to learn a little bit more. We pulled together all the studies we could find related to autism and gut bacteria to give the best breakdown of it as possible.

Before we dive into the research and how we can take advantage of this to help improve your child’s ASD symptoms, let’s explore exactly what our gut microbiome and lining are.

What is Our Gut Microbiome?

This may sound crazy, but we are all more bacteria than we are ourselves. With over 90 trillion bacteria cells living inside of us and on our skin, these little guys outnumber our human cells by ten to one. Now that is a little gross to think about, but at the same time it is super fascinating!

Our gut bacteria affects way more than you think it would. It is a diverse makeup of different strains of bacteria, where some are good, and some are bad. We don’t know what an “ideal gut bacteria” makeup is, but we do have an idea of what increasing and decreasing certain kinds do.

So how does our gut bacteria affect us?

With the recent discoveries in the last decade of our microbiome, the scientific community is coming to call our gut our “Second Brain” because of its major effects on our immune system, mood, thinking, hormone production, and much more. Seems like having a “gut instinct” may be more than just a common idiom.

There is a major network of neurons all along our intestinal lining, which is called the enteric nervous system. Enteric means “pertaining to the gut.”

Our nervous system has a direct line between the gut and the brain called the vagus nerve. This is like a highway that sends signals and neurotransmitters (chemicals that affect our thinking and mood) between the brain and the gut.

An example is serotonin and GABA. They are both neurotransmitters that affect mood and thinking and are partially produced in our gut. We will dive into serotonin more in a bit as there is research linking abnormal serotonin levels with autism.

Another condition of our gut lining that sees a lot of problems is called “Leaky Gut.”

Leaky gut is when our gut lining becomes less effective than it should be. This means toxins we eat and would just digest without a problem make it into our bloodstream. This isn’t good.

This information  is important for everyone, but why does it get special attention in this guide for children with autism? Well, it turns out that children and their first-degree relatives have unusual gut permeability, meaning they are more likely to have leaky gut. That’s the only study showing that the relatives of children with autism have abnormal gut permeability, but other studies confirm that children with ASD are more likely to have leaky gut than their non-ASD peers.

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 commensal bacterium B. Fragilis (a strain of good bacteria) fixed their leaky gut and reduced autistic syndrome. Then by altering the microbes in their guts to match other mice who had autism brought the autistic symptoms right back.

All these add up to show that your child’s gut bacteria can have a significant impact on their autistic symptoms.

What’s more is that Dr. Sanford Newmark, an integrative medicine doctor at UCSF who specializes in treating autistic children, says that when treating his clients through modifying their diets, 1/3 see great improvements and 1/3 see mild improvements. Those with gastrointestinal problems, like constipation, usually are the ones with the best results.

This means that if you work with your child’s physician to start implementing the protocols in this article, your child will most likely see some good improvements. But before we dive into the protocol, let’s take a look at another indirect way that fixing your child’s gut can have an effect on their ASD.

Serotonin and Autism 

I mentioned serotonin before, and how there are abnormal levels of it in children with autism. It’s become such a high correlation, that many people think it is a key link of why some children are autistic and others aren’t.

Personally, when looking at all of this research, I don’t think there is just one key link. I think there are many factors of why some children have autism. While one strategy may work wonders for one child, it may have minimal effect on another. This is why working with your doctor to create a personalized strategy for your child is very important.

With that said, serotonin is one factor that seems to have a big impact. Serotonin is a neurotransmitter that plays a key role in:

  • Sensory Gating and Processing
  • Behavior inhibition
  • Appetite
  • Aggression
  • Sleep
  • Mood
  • Brain Development

Do any of these sound like traits that your child has problems with? For most people this list is pretty evident.

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.

The reason we are talking about serotonin along side gut bacteria is because it is estimated that 90% of our serotonin is produced in our digestive tract. We can see how fixing the gut could be a big win for children with autism.

Gut Bacteria and Autism Remedies

The best way to begin to heal your child’s gut is to remove the foods that are causing it.

One of the main culprits is gluten. You may have heard about gluten before and how many health conscious people are eliminating it from their diets. People seem to go back and forth on this of whether it’s serious or not, but for autistic children, it is completely serious.

One study found that a subset of autistic children showed heightened reactivity to gluten. Children with ASD seem to already have different gut bacteria and poor gut lining, but are extra sensitive to gluten, and gluten actually hurts gut lining for everyone! This happens because when gluten is broken up into smaller pieces in your gut, these fragments cause the release of zonulin, which then tells your the lining of your gut to become looser.

So this all seems to be stacking up that children with ASD should not be eating gluten.

The next big food problem for autistic children is casein.

Casein has a very similar makeup to gluten and is thought to be one of the main problems people have when it comes to consuming dairy, along with lactose intolerance. When it comes to healthy adults, it was hard to find studies on if casein affects them or not, however it is the typical protocol for autistic children to remove casein from their diets. Those who do, appear to do better than those who don’t.

An easy way to figure this out is to have your son or daughter not eat casein, which means removing dairy. I would do that for a couple of months, then slowly start working in healthy dairy to see if your child can tolerate it.

If you are worried about calcium intake from dairy for strong bones, don’t worry. Dark leafy greens, which are highly recommended, are high in calcium. On top of that, calcium is only a factor of bone health. Vitamin D and exercise are just as important.

Some of the dairy you’d want to start with is full-fat fermented dairy from grass-fed cows, like kefir or Greek yogurt. Another option is the same style dairy but from goats, since their milk is easier to digest and contains less lactose and casein from the get-go.

When it comes to working dairy back into your child’s diet, what you can do is mix it with some water, then rub the mixture on the inside of your child’s wrist before they go to bed. If they are still sensitive to the food, there will be a small red irritation on the inside of their wrist when they wake up. If not, then it’s a good chance you can start to work it slowly in over time.

Now if you still want to cook with butter (and who doesn’t) but want to avoid casein, go with ghee. Ghee is just clarified butter, so it has none of the casein or lactose but is a great substitute.

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 a long period. As we mentioned with the mouse study above, even fixing your child’s gut bacteria doesn’t mean it can’t move back to being abnormal if you let it.

Other foods to remove for good are processed and refined carbohydrates, sugar, and vegetable and soy oils because they cause inflammation, which impairs your child’s ability to heal.

Another irritant you’ll want to watch out for is “anti-nutrients”. The two worst ones are lectins and phytates.

Lectins cause problems because they potently inhibit plasma membrane repairbind to insulin receptors, have been shown to attack the lining of insects, and bind to human intestinal lining.

They make it hard for your child’s body to repair itself and worsens their intestinal lining, which is already impaired.

Here’s a list of foods with the highest amount of lectins:

  • Grains (especially wheat)
  • Legumes (especially soy)
  • Nuts
  • Dairy
  • Nightshade plants
    • Eggplants
    • Tomatoes
    • Potatoes
    • Peppers

Phytates cause problems because they bind to vitamins and minerals which make them bio-unavailable. This means that vitamins and minerals that should be helping your child’s body are just passing through, unable to be used because of phytates.

Here’s a list of foods with phytates to avoid:

  • Legumes
  • Seeds
  • Nuts
  • Grains

These are foods that you’ll want to remove at the start when your child’s gut is still healing. I’d give it one to three months; then you can slowly start to work these in. Not all the time, but occasionally eating these types of foods should be ok.

The last thing to avoid isn’t for your child, it’s for you as a parent or guardian. If you decide to implement these diet changes as a family, I suggest to remove drinking alcohol as well. You can slowly work alcohol in after you follow the strict protocol for 30 days, but if you want to see the effects and truly heal your gut microbiome and lining, then avoid drinking while doing it.

What to add to repair 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.

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. This is easier with some vitamins and minerals than others, but something to work towards. If you’d like to research more what a diet would like that includes all these protocol, I’d recommend looking into the Paleo Diet.

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. This is a way to 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. Another thing you’ll want to look for is to make sure it’s very concentrated. The way to find this is to check to see how many bacterial cells there are per gram. You want a probiotic with at least 8 billion bacterial cells per gram.

The one that I’ve seen recommended quite a bit it Bio-Kult, however, 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’ll be great!

Some good probiotic rich food to start with are sauerkraut, kimchi (a fermented spicy vegetable medley), or kombucha (a probiotic drink). Now I know that many children with ASD also are very picky eaters, which may make this stage might be a little tricky. The kombucha is a good place to start since you can find tasty ones in your local grocery store. The brand I like 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 in is prebiotics. Prebiotics are what the probiotics eat! And yes, you do need to feed them. 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, where they can feed on it.

Some good resistant starches to slowly work into to 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.

Quick tip: Bake a sweet potato in the oven for about 30 minutes depending on size. Slice it in half, then add ghee and cinnamon to each side. It’s healthy and delicious. It tastes like it should be a dessert.

Now we’ll want to add some digestive enzymes to your child’s diet when they start to eat food. 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 enzymes to help breakdown food is a great step to help improve your child’s digestion and support the repair of their leaky gut.

The next thing we’ll want to supplement with is some Betaine HCL with Pepsin (you don’t have to know what these things are. You can take notes and bring them to your physician to help).

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 we’ll want to add is something that almost all Americans are lacking in unless you are eating a lot of fish. Essential Fatty Acids, which you may know to be omega-3 and omega-6 fats, are crucial to a range of functions in our body.

More specifically, omega-3 is what we lack. Vegetable oil has a ton of omega-6 in it, so we typically 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 for omega-3 is with cod liver oil. It is very bioavailable. I recommend the “Blue Ice High-Vitamin Fermented Cod Liver Oil” from Green Pasture Products.

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

The next supplement we’ll want to add is vitamin A. This one will be one of the easier ones to get from foods naturally, since it’s high in sweet potatoes, carrots, dark leafy greens, and squash. All foods that you can healthfully work into your child’s diet. This is a vitamin that most children with ASD seem to be low in.

Next is a big one. This is another supplement that almost all people could use since it’s estimated that up to 80% of people in the United States are deficient.

This supplement is vitamin D. Vitamin D plays a massive role in our body, and it’s extremely hard to get from food. As you may know, the best source is the sun, but since 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 even 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 systemsour microbiome, our gut lining, and our serotonin levels. This means vitamin D is critical for all of us. But like most of the things on our list, it seems that children with autism have an even lower amount of vitamin D than their peers.

One study even went as far as to say:

“The present study revealed that vitamin D deficiency was higher in autistic children compared to healthy children and 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. This means that adding it to your child’s diet will help repair their stomach and gut lining. You can supplement with a collagen powder like the Upgraded Collagen from Bulletproof, or you can create your own bone broth at home.

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

Now that we’ve covered what to remove and add to your child’s diet let’s look at a couple of activities you can start to do with them to jump start their healthy gut bacteria.

Add These Activities 

First and foremost, exercise is a great thing to add into your child’s life. Don’t think you need to sign them up for a gym membership, but rather just come up with something fun to do with them. It could be going on runs together, doing pushups in the backyard, or something simple like that.

In a study with mice, exercise was shown to improve their gut bacteria makeup.

To piggyback off of exercise, you should encourage your child to play outdoors and get dirty. It can be in the sun which would be good for their vitamin D levels, but also, getting dirty is good for their gut microbiome. We evolved to be primed for constant, low-level exposure to soil-based bacteria, so this kind of exposure can improve their gut bacteria.

The last activity is more something to avoid, and this should be on a case to case basis, but avoiding antibiotics when they are unnecessary is important. Antibiotics are great and have been a massive improvement for us as humans. However, I think we have a case of over prescribing them. As I’ve said before, make sure to work with your doctor on all of this. But if your doctor doesn’t find an antibiotic necessary when your child shows a hint of sickness, then I’d err on the side of not going with them.

Antibiotics completely wipe out our gut microbiome, hence the name ANTIbiotic.


There you have it! A massive article on autism and the microbiome. If you have any questions, please let us know in the comments! We’ll be happy to answer them.

Casey Ames is the founder of Harkla. Harkla is a company dedicated to making the highest quality products for those with special needs.