Healthy Gut, Healthy Child: 5 Risk Factors for Gut Dysfunction in Children

Did you know that a healthy gut is the key to a healthy brain?

If you read my last post, you learned about the human microbiome and its influence on our overall health (if you didn’t have a chance to read, click here).

Quick recap:

  • Our microbiome (the full collection of cells and genetic material of the different microbes that inhabit our bodies) has more of an influence on our overall health than our own genes.
  • Most of our trillions of microbes hang out in our gut and have many important jobs like: assisting in digestion, regulating our immune system and hormones, producing neurotransmitters and supporting detoxification.
  • The brain and the gut make up the “gut-brain axis” and are in constant communication about things that influence our health.
  • The quality of communication is dependent on having the right balance of “good” and “bad” microbes. More bad than good (gut dysbiosis) = communication breakdown = physical, mental and emotional health issues.
  • There is growing evidence of a link between gut health and neurological conditions such as SPD, ADHD and ASD.

Now that we’re up to speed on the importance of having a healthy gut, let’s dive into...

What causes an “unhealthy” gut in children?

First things first. If your child has an “unhealthy” gut, it is not your fault!

I repeat. It is not your fault!

Some of the factors I’m going to list will potentially stir up guilt (they did for me). If this happens, please let the guilt go as quickly as it came in. There is absolutely no judgment. You are all incredibly amazing moms and your kids are incredibly lucky to have you.

This information is meant to serve as just that- information. Our motto is, knowledge is power. The more informed we are, the better we can serve our kids.

The purpose of this post is to give you a better idea about whether your child’s gut is possibly playing a role in his cognitive, emotional and behavioral challenges.

The following is a list of five things that researchers have found to be risk factors for gut dysfunction in children:

(Note: If there are things on the list that apply to your child - there are for my boys - don’t panic. There are many things you can do to get your child’s gut in balance. I’ll fill you in on all of them next week… and remember, no judgment!).

1. Cesarean Sections

As babies travel through the birth canal, they take a giant gulp of their mother’s vaginal and rectal (I know, ew!) microbes. The bacteria they ingest move through the stomach and make their way to the lower and upper intestines where they set up shop.

This process sets the stage for the baby’s developing microbiome which has an enormous influence on his overall health and brain function.

Babies born via C-section (both my boys were) miss out on those beneficial birth canal microbes. Instead, their first microbial exposure is to those present in the hospital, which are not as beneficial nor protective and can set the stage for gut dysfunction.

Dr. Robynn Chutkan explains, “Lower levels of the protective microbes mean that babies born via C-section have higher rates of asthma, allergies, type 1 diabetes and other autoimmune conditions.”

Other consequences of missing out on the beneficial birth canal bacteria include an increased risk of digestive problems, ADHD, autism and obesity.

C-sections are responsible for saving millions of babies and mothers - there is nothing wrong with having one (again, both my boys were born via C-section). But, in the context of understanding whether your child’s gut is out of balance, it’s important to be aware that C-sections are a risk factor.

2. Baby Formula

Before you read this, please know there is absolutely no judgment about formula feeding. Remember, this is just information to help you determine whether your child’s gut might be playing a role in his developmental challenges.

Formula is the C-section of infant feeding. It’s a necessary, sometimes life-saving, intervention for many mothers and babies. But, much like missing out on the birth canal bacteria, babies who are formula fed miss out on many of the nutrients essential for creating a healthy microbiome.

Like C-section babies, those who are formula fed are at higher risk of asthma, allergies, digestive issues and autoimmune disorders.

Breastfeeding is shockingly challenging! After H was born, I remember thinking, Hey! Wait a minute! How come no one told me how ridiculously difficult this is?

I could write an entire book about my insanity-inducing breastfeeding experience with H. Under-supply, over-supply, latching difficulties, mastitis, thrush, colic, reflux, you name the issue, we had it and then some!

If, like me, you had a hell of a time breastfeeding, please do not beat yourself up or panic. Just make a mental note about its implications for gut health and use it as an empowering clue to better meet your child’s current needs.

3. Antibiotics

We’ve got a theme going here… like C-sections and formula-feeding, antibiotics, aka “a marvel of modern medicine,” are often necessary and have saved millions of lives.

I’m going to pause here for a moment and vent. Why do so many helpful medical interventions have to come with a cost? (Shaking fists in the air.)

Here’s the deal with antibiotics. If you have a troublesome bug wreaking havoc on your system, antibiotics are your ally; they’ll get in there quick and get the bad guy.

The problem? They don’t discriminate between “good” and “bad” bacteria. Taking them is equivalent to setting off a bomb in your gut- they kill everything, the good and the bad bugs.

Stanford researchers Erica and Justin Sonnenburg explain, “the one course of antibiotics per year that the average American child is prescribed could permanently change that child’s microbiota and affect his long term health.”

Bottom line: If you were prescribed antibiotics during pregnancy (I was during my second pregnancy) or postpartum (I was after my first pregnancy) and/or your child has taken them during infancy or toddlerhood, he (like my boys) will be at higher risk for gut dysfunction.

Reminder- gut dysfunction can be reversed, so don’t panic!

4. Stress

Though it’s still not clear exactly how or why this happens, research has shown that a stressful episode can disrupt a person’s microbiota.

Examples of microbiota disrupting stressful episodes in early childhood are:

  • Traumatic birth
  • Maternal separation
  • Maternal depression
  • Feeding issues
  • Surgery
  • Illness
  • Poor attachment
  • Loss of a loved one

My older son had a traumatic birth and was separated from me for an hour after he was born. During infancy, he had feeding issues, an infected umbilical cord, difficulty sleeping (putting it mildly) and colic (read: screamed nonstop for months). I didn’t have postpartum depression, but I was highly anxious both during my pregnancy and my first few years of motherhood.

There’s no doubt that H experienced stress as a result of these experiences. Rather than feel guilty and blame myself (been there, done that!), I choose to view this information as one more puzzle piece in his developmental picture.

5. The Standard American Diet

Every bite of food we eat influences our microbiome.

Functional medicine doctor Mark Hyman says, “Every bite you take is a powerful opportunity to create health or promote disease.”

He explains that food “talks” to our DNA and has the power to switch the genes that lead to health or disease on or off.

Unfortunately, most of us, including our children, are eating more of the foods that turn on disease and not enough of the foods that turn it off.

The Standard American Diet (SAD), made up of processed foods full of dangerous chemicals, hormone and antibiotic injected animal products, and pesticide-laden crops, is contributing and exacerbating gut dysbiosis in millions of adults and children.

Here is a list of common microbiome offenders:

  • Sugar
  • Processed foods
  • Gluten
  • Soy
  • Corn
  • Dairy
  • GMOs
  • Artificial sweeteners
  • Tap water
  • Non-organic, non-grass fed meat and poultry
  • Farm raised fish
  • High fructose corn syrup

Children who have diets high in any of these offenders will be at higher risk for gut dysbiosis, especially if they have any of the other risk factors.

Before you get too overwhelmed, let’s go over a few things:

  1. If your child has signs of gut dysbiosis, it is not your fault.
  2. Gut dysbiosis is fixable.
  3. You are an amazing parent and your child is lucky to have you.

Repeat after me: Knowledge is power! Now you have more information to determine whether or not your child’s gut is in need of some good old fashioned TLC.

If it is, I’ve got you covered. Next week, I’m going to give you a step-by-step plan to get your child’s microbiome back in balance.

Here are a few resources to give you a jump-start...


The Good Gut

Healthy Food, Healthy Gut, Healthy Child

The Microbiome Solution


The Dr.’s Farmacy

The Model Health Show

Revolution Health Radio

If you have any thoughts or questions, leave them below. The Sensory Mom community and I would love to hear from you.


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Hi! I'm Cameron, mom of two incredible, "differently-wired" boys who have sensory processing challenges, wife of a nerdy surfer, mindfulness practitioner and Parenting Coach with master's degrees in education and psychology.