How to Boost Your Child’s Gut Health

When you boost your child’s gut health by supporting the microbiome, you’re setting them up for a lifetime of wellness – plus fewer colds, less severe stomach bugs, and many more benefits as science shows how a healthy microbiome is crucial to overall wellness.

Here, you’ll find tips for helping to balance your child’s – and your own – microbiome for optimal health.

Happy girl with healthy microbiome

Gut Health for Kids

With more research developing on the importance of the microbiome, it’s becoming increasingly clear that a healthy immune system starts with a healthy gut. This is especially the case when it comes to your child’s gut health.

Some kids seem to get sick with every season change. Add in seasonal allergies, and it can seem like a losing battle to stay healthy. To support your child’s immune system, digestive system, and for fewer sore throats, ear aches and tummy upsets, you can take steps to keep their microbiome in balance.

The gut is often referred to as the “second brain” because of its connection with the nervous system. A regulated nervous system is important for your child to feel safe and it also can affect their behavior and mood.

Some germs (good bacteria, microbes, beneficial probiotics) are essential for health!

What is the Microbiome?

“Every human has a unique microbiome that houses nearly 100 trillion bacteria,” explains Dr. Felicia Stoler, registered dietitian nutritionist, exercise physiologist and expert consultant in nutrition and healthful living.

“They outnumber our human cells by a factor of ten to one. Different kinds of bacteria have different jobs within our bodies,” Dr. Stoler explains. “About 85 percent of them are beneficial probiotics. These good guys help kids produce vitamins, absorb nutrients, regulate their immune system, and may even influence their mood.”

The first few years of a child’s life are crucial for proper microbiome development (source). Although a baby’s gut is mostly sterile in the womb (the placenta does contain some microbes), the major microbial inoculation begins as the baby descends through the birth canal, picking up vaginal bacteria along the way. Breast milk also provides tons of microbes.

As a child begins to eat solid foods, their microbiome continues to evolve based upon dietary intake and environmental factors. By about age two, a toddler’s microbiome resembles that of an adult.

The Microbiome’s Impact on the Immune System

More than 80% of your immune system lives in the lining of your gut. When good bacteria are destroyed, the bad bacteria proliferate, which can lead to leaky gut and a variety of poor health conditions.

Just one round of antibiotics decreases gut microbiome diversity by at least 30%. The diversity of the microbiome is key for immunity, nutrient absorption, and effects on the brain and behavior.

The microbiome also plays a role in a number of diseases caused by a disturbance in the normal balance of microbes. Low diversity in the microbiome is associated with a number of chronic illnesses including obesity, insulin resistance, high cholesterol, inflammation, Crohn’s Disease, Diabetes (both Type 1 and Type 2,) colorectal cancer, ulcerative colitis, celiac disease, allergies, chronic fatigue syndrome, and polycystic ovary syndrome. (source)

A Balanced Microbiome Can Prevent Leaky Gut Syndrome

Leaky Gut Syndrome is essentially inflammation caused when the microscopic “holes” in our gut lining open up and become bigger allowing food, gluten and bad microbes into the bloodstream.

This immune response plus inflammation can, over long periods of time, contribute to depression, brain fog, ADHD and autism, rheumatoid arthritis and joint pain, IBS, celiac disease and other autoimmune disorders.

In children, leaky gut most often manifests as issues with the lungs, ears, nose, or skin. Inflammatory symptoms associated with leaky gut may include eczema, rashes, congestion, asthma, diarrhea, ear infections, constipation, and abdominal pain. In babies, it may show up as colic.

How to Boost Your Child’s Gut Health

For those of us who’ve had a child with eczema, asthma, or frequent ear infections, it might have taken us a little longer to realize their gut health could be a factor. In addition to building your child’s gut health and microbiome, these steps can also help keep the immune system strong.

You can implement most of these tips without your child knowing why. But as they get older, it’s important to talk to them about the choices you make. A Garden in Your Belly is an excellent children’s book that explains “the garden of microscopic flora growing inside the body.” It takes your child on a journey that explains the microbiome via watercolor illustrations that are informative (and not gross).

1. Feed Your Child Good-Bacteria-Friendly Foods

Offer a variety of healthy, real foods that are rich in minerals and fiber. Eating diverse foods that are as close to their natural state as possible offers the most microbiome benefits. Fruits, vegetables, and berries from your own garden or local farmer’s market haven’t traveled as long and are more likely to retain their nutrients and diversity.

Make sure your child also gets plenty of good quality protein, the building block for the antibodies that fight infection. Avocado, legumes, and eggs can be delicious, kid-friendly sources of protein. Plus beans are loaded with fiber.

Fermented foods such as kimchi and sauerkraut are loaded with probiotics. These can be a tough sell for kids at first, so you may want to start with fermented versions of the veggies your kids already like. Or go extremely basic with fermented ketchup or making your own yogurt.

Kefir and kombucha are also good choices. Kefir can really help with digestion. The active yeast, good bacteria, and excess digestive enzymes provide more nutritive value than yogurt by helping digest the foods you eat. (source)

2. Limit Sugar and Processed Foods

Eliminate gut-damaging foods whenever possible. Processed foods, conventional dairy, GMO foods, gluten, and sugar cause some level of gut damage for most people. Bad bacteria feed off of sugar, so the single most impactful way to heal your gut is to kick the sugar habit.

Sugar suppresses the immune system for several hours and feeds the bad bacteria in the intestinal tract. Of course, it’s hard to avoid sugar entirely. So when you know your child will have sweets, make sure they have a protein first to help offset the blood sugar spike and other imbalances.

3. Play Outside and Don’t Be Hyper-Vigilant About Dirt

Of course, we know that good hand washing is the best way to prevent the spread of germs. It’s not just the visible grime you should be worried about. A good scrubbing physically removes disease-causing germs. Just be careful about over-sanitizing.

There’s much to be said about good old-fashioned soap and water. I’m not a fan of antibacterial soaps because they kill the good bacteria as well as the bad. This is such a concern that some companies are now removing the antibacterial ingredients from their hand soaps. Try this DIY foaming hand soap you can make easily with Castile soap.

And speaking of dirt, get outside and play in the dirt with your kids! It’s one of the best ways to boost your child’s gut health and immune system. Whether it’s gardening or making mud pies, this is therapeutic as well as healthy. Shielding kids from dirt may weaken their immune systems.

The Farm Effect mentioned in the Amish study above is the corollary of the “Hygiene Hypothesis,” which states that a lack of early childhood exposure to infectious agents, microorganisms and parasites increases our susceptibility to allergic diseases by suppressing the natural development of our immune systems.

Outdoor play and time spent in nature are vastly beneficial to kids both physically and emotionally.

4. Avoid Unnecessary Antibiotics

With certain illnesses, you don’t need medical intervention. If a decongestant or home remedies do the trick, you may not need your doctor. There’s a movement in the medical profession to cut back on prescribing antibiotics. Or if you seek treatment from an naturopathic doctor or Chinese medicine practitioner, they can help you find natural ways of supporting the body back to wellness.

When the number of good bacteria in your intestinal tract is outnumbered by the bad you may experience gas, bloating, diarrhea, and even constipation. These symptoms can range from mild to quite severe. While just getting sick can result in decreased numbers of good probiotic bacteria, antibiotic use is one of the primary reasons that good bacteria gets wiped from our system

  • Don’t take an antibiotic for asthma symptoms, seasonal allergy symptoms, or viral infections like a cold, stomach virus, or the flu.
  • Keep antibiotic use to when it’s absolutely necessary and only to treat bacterial infections. This will help prevent antibiotic resistance.
  • Follow antibiotic prescription directions carefully. Don’t skip doses, double up on doses, or stop without finishing the cycle.

As it turns out, Mother Nature has provided foods that can reduce harmful bacteria in the body, lower inflammation, and build up protective bacteria. Oregano oil is an excellent choice because of its antiviral, antiparasitic, and antibacterial properties. Along with the probiotics and prebiotics above, add these foods into your family’s meals to boost your child’s gut health:

5. Use Probiotics After Antibiotics

If antibiotics are necessary, supplement with probiotics. Probiotic amounts in supplements are measured in CFUs (colony forming units). Make sure your child gets a minimum of 100 million CFUs per dose.

ION* Gut Support – ION isn’t a probiotic, but it offers many gut health benefits. It is designed to support the body’s production of beneficial enzymes through redox signaling (cellular communication).

It also protects the gut membrane from glyphosate and pesticide-laden food. It can help improve nutrient absorption and reduce inflammation. You can use code GREENCHILD to get a free travel size bottle (6 day supply) with your purchase of a 32 oz bottle.

Mary Ruth’s Organic Liquid Probiotics – organic, non-GMO and allergy free probiotic contains twelve probiotic strains in an enzyme-enriched substrate with water and a proprietary blend of 3 organic grasses.

Hyberbiotics PRO-Kids ENT – contains an oral probiotic strain called BLIS K12 that is specifically helpful for supporting the good bacteria that live in kids’ mouths and throats. This strain has been shown to benefit ear, nose, throat and upper respiratory health and should be taken in conjunction with a digestive formula.

Don’t be tempted by kid-friendly gummies with added sugars (or choose them only as a last resort). Look for an effective multi-strain kids’ probiotic formula that can withstand the stomach acid of the digestive tract, to ensure your kid gets a steady and potent dose of gut-friendly goodness.

Don’t stick to the same probiotic for long periods of time. Take a break or change brands so that you aren’t constantly seeding your child’s microbiome with the same strands.

How to Build Your Infant’s Microbiome

Many of us don’t know there’s an issue with our child’s gut health until they experience a health problem. If you’re a parent-to-be reading this – congratulations on starting early! There are some steps you can take to get your new baby’s gut health off to the best start.

1. Boost Your Own Microbiome During Pregnancy

Making sure your baby’s microbiome develops properly starts with nurturing your own gastrointestinal system during pregnancy. It’s not just your genes that will pass down to your growing baby, but also your microbes.

Microbiome seeding is generally regarded to start at birth (though new research is starting to propose that microbial transmission could occur in the womb via the placenta), through the vaginal canal, skin-to-skin contact, and breastfeeding.

Follow the same steps listed below for gut health for children, eat a variety of fresh whole foods, get plenty of foods that are rich in prebiotics (like garlic, onions, and bananas), avoid antibiotics unless absolutely necessary, grow a garden or find ways to get your hands in the dirt, and have meals or attend gatherings with other people. All of these steps help to diversify your microbiome.

Drinking tea is a relaxing way to support your microbiome. Tea is rich in polyphenols, a prebiotic substance that help to feed the healthy bugs in your gut. One note of caution – many tea bags are made with plastic. Learn how to avoid plastic in tea bags and find the brands that don’t use any plastic in their tea bags.

2. Take a Probiotic or Synbiotic

Our top recommendation for mothers (during pregnancy and beyond) is Seed’s Daily Synbiotic. Seed’s special 2-in-1 (prebiotic and probiotic) capsule and algae microsphere delivery system protect against stomach acid and safeguard viability through digestion.

Seed’s liquid prebiotic suspension acts as an additional barrier to oxygen, moisture, and heat (which bacteria are sensitive to).

3. Try to Have a Vaginal Birth

As mentioned above, a vaginal birth is ideal for boosting your child’s gut health right from the start. If you’re pregnant and already know you’ll require a C-section, talk with your OB about the option of vaginal seeding (or swabbing the baby after birth).

4. Breastfeed Your Baby for as Long as Possible

Breast milk is full of beneficial microbes and special nutrients that feed and nourish the probiotics so they can thrive. Researchers at Duke University Medical Center found that breast milk supports the growth of bacteria in the gastrointestinal tract that aid in the absorption of nutrients and boost immune system development.

Improve the Microbiome of Your Home

Just like your gut and your skin have their own microbiome, so does your home.

“More than sixty-three thousand species of fungi and a hundred and sixteen thousand species of bacteria” were found in one study’s swab of the interior door trim of forty homes in the Raleigh-Durham area. The results varied widely – especially if pets lived in the homes. Many beneficial species of bacteria were found, leading researchers to believe that our environmental microbiome works synergistically with us and may even help protect us from harmful bacteria.

You can improve your home’s microbiome by cleaning with mild, natural cleaning agents (no antibacterial cleaners), making sure there’s no mold growth, not wearing shoes inside to keep pesticides from disrupting the environment, and actively adding good bacteria with a product like Homebiotic spray, which is designed (and lab-tested) to reduce mold growth and improve the bacterial environment in a home.

The Skin Microbiome

The skin has its own microbiome. Just like in the gut, the skin protects against pathogens invading from the outside environment. When the healthy balance between the good and bacteria is upset, it can contribute to skin disorders and diseases.

“The same science that can heal our guts can also heal our skin and more,” explains Lindsey Moeller of Concur Microbiome Recovery. “A compromised skin microbiome, or skin dysbiosis, is a contributor to the most common skin issues. However, we are learning that our skin microbiome is not only directly responsible for skin health, but also plays a major role in our overall immunity and health by keeping pathogenic microbes at bay.”

“Our bodies are basically half human cells and half bacteria. So, when we don’t care for the natural bacteria on our bodies, we find a lot of disfunction. Maintaining a healthy skin microbiome means reducing or eliminating skin issues like acne, eczema, rosacea, psoriasis and common imbalance expression like oily, dry and sensitive skin.”

“Our microbiome changes seasonally based on climate, environment, age, hormones, ethnicity, etc. Using skincare that protects and supports the microbiome gives us the best chance to keep pathogenic bacteria from taking up residence in or on our bodies during those frequent changes. Not to mention the beauty benefits of having naturally soft, hydrated and glowing skin with far fewer skin issues.”

Topical probiotic sprays can help keep the ideal balance intact. Or go with the super budget-friendly option of DIY yogurt or kefir masks.

The short-term benefits of boosting your child’s gut health may include fewer upset stomachs, less skin sensitivities, and fewer allergies. Long-term, you’ll be helping to prepare their bodies for a lifetime of better wellness.

The Microbiome & Obesity

I also wanted to include this because I find it fascinating. Whether you’re concerned with childhood obesity or curious about how your gut health affects your own weight, these studies are worth noting.

In 2006, Jeffrey Gordon, a biologist at Washington University in St. Louis, reported that the microbiomes of obese mice had something in common. Compared with their lean counterparts, the heavier mice had fewer Bacteroides and more Firmicutes species in their guts.

Biochemical analyses showed that this ratio made the microbes better at “energy harvest”—essentially, extracting calories from food and passing it into the body. That is, even when mice ate the same amount and type of food, the bacterial populations meant that some developed metabolic problems, while others didn’t. Similar bacterial patterns have since been confirmed in obese humans. (source)

Gordon also found that the microbiome associated with obesity is transferable. In 2013, his lab took gut bacteria from pairs of human twins in which only one twin was obese, then fed the samples to mice. The mice given bacteria from the obese humans quickly gained weight. The others did not.

They essentially found that even with a transplant of those “good weight” microbes, if you don’t feed them properly, they’ll die off.


As always, you can take this information and start with baby steps. And speak with your health care provider before making any major changes.

There is solid research about the link between gut health and allergies and asthma. If you only implement a few of these steps, you can likely limit the severity and recurrence of at least some childhood illnesses.

Start by switching to soap and water instead of antibacterial soap. Buy kombucha or kefir at your local health food store and ease it into your day. Pretty soon, you might start making your own like I did. (Plus it’s very easy to sneak kefir into your child’s favorite yogurt!)

This article was originally published in 2017 and has been medically reviewed and updated.

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  1. Jessica L says:

    We’ve tried both Seed and Hiya for our kids. Big fans of Hiya — it’s just a better probiotic made specifically for kids. Huge recommendation.

  2. My kids are so picky with their food that it’s insanely difficult to give them probiotic rich foods. But this is my first time hearing about fermented ketchup! Definitely looking into that. I usually have to sprinkle probiotic onto their food to get them to eat it.