Gut Health for Children

Since most of our gut microbiome formation occurs between the ages of 0-3, then you might be wondering what you can do to promote optimal gut health in your children?

Given that the immune system is primarily located in the gut and that our microbiome can influence a lot of different health measures; one would think that you would want to optimize the environment at peak age rather than adulthood.

It also happens to be the most difficult age to introduce a variety of foods, go figure!

Despite babies and toddlers being a tough crowd, there are definitely some actions you can take as a parent to optimize your little one’s gut health! Don’t get discouraged.

Optimizing gut health in children

Let’s start from the beginning….

It all starts when you’re pregnant! A mother’s diet (which we already know) is important in determining the gut health of her baby. A high fat diet during pregnancy has been shown to negatively affect a baby’s gut microbiome (1).

Additionally, when you give birth, as the baby passes through the birth canal and out of the vagina, a whole host of beneficial microbes get passed on through the vaginal opening.  

Likewise, when breastfeeding, there are a lot of beneficial bacteria and antibodies passed on to your babies as well! Babies can get beneficial bacteria from both the milk and the skin around the nipple during breastfeeding (2). Human breastmilk contains HMO’s (Human Milk Oligosaccharides), which act as a prebiotic to help feed the intestinal bacteria of an infant (2).

Side Note: If you have had a C-section and decided to formula feed, then don’t worry. There are plenty of ways to optimize your child’s microbiome as they grow and formulas have also come a long way and mimic a mother’s breast milk in many ways. Skin to skin contact has been shown to help transfer some maternal bacteria (2).

What can negatively affect gut health in children??

Poor diet:

Sometimes it’s easier to grab fast food, I get it. And sometimes your kids are so picky that you have no choice but to throw chicken nuggets in the oven, I get that as well. However; sometimes we have to get creative. Don’t give up too quickly. Hiding fruits and vegetables is a good way to get your children to eat healthier foods. Further along in this post I provide some good snack options.

Antibiotic use:

Doctors, fortunately, are getting much better at regulating antibiotic use in children and adults. We all get sick, but it’s important to know when it’s the right time to use antibiotics versus when they are inappropriate. They are not useful in preventing/treating a VIRUS. Antibiotics should only be used for bacterial infections. Antibiotic use during pregnancy can also affect a fetus’ microbial exposure.  

Not Enough Fiber:

This is really important for all ages and comes full circle back to the importance of fruits and veggies! Oatmeal is also another great option for fiber if your children like it. Most of us are not getting enough fiber as it is, but it’s so important because that is what our gut microbes feed off of! Fiber is what provides the gut “prebiotics”, more specifically, indigestible fibers from plants. If your child struggles with fibrous foods, then introduce them slowly with plenty of fluid.


What are some things that optimize my child’s gut health?


This goes without saying, but proper nutrition can help. Probiotics, probiotics, and hydration all play a role in optimizing the gut environment. Below I’ve listed a bunch of snacks that are great for kids!

  • Yogurt : yogurt drinks, lactose free yogurt, frozen yogurt popsicles, frozen yogurt ice cream, Kefir drinks
  • Smoothies: another great way to hide veggies and fruits! You can also throw in some yogurt to make it creamy and more like a thick milkshake.
  • Apples with Peanut Butter
  • Baked Sweet Potato Fries 
  • Frozen Vegetable Blends in a Sauce (veggie tater tots, etc.)
  • 100% Fruit Juice 
  • Oatmeal with Berries 
  • Peanut Butter and Jam made with Crushed Raspberries (or homemade jam)

Exercise and hydration:

I don’t think I need to drive this one home since children usually get plenty of exercise. Keeping them hydrated is important. If they struggle with drinking water, then frozen popsicles or juices are an okay option. Watering the juices down will help reduce some of the sugar content in them without sacrificing the taste too much. 

Go easy on yourself:

Don’t stress too much about getting “all the right” foods into your children. It can be difficult and they can be very picky. At the end of the day all we can do is try. Gut health isn’t the only factor in determining a healthy lifestyle, it is just one player. Small wins add up! 

Be mindful of antibiotic use:

Sometimes antibiotics are absolutely necessary and unavoidable. But it isn’t uncommon for some people to think that antibiotics fix everything, which is not the case. Sometimes we have to let the virus ride out and allow them to build antibodies to strengthen our children’s immune systems.


Oh, as if we couldn’t love them anymore. Pets and playing outside in the dirt are great ways to boost your child’s immune system. Our immune system is directly tied to our gut health. So, try not to freak out too much next time your dog is excessively licking your child’s face. 

Gut health and the microbiome is still a newer science, but we are coming a long way with understanding its important role for children, as well as, adults.

For more information, you can find a blog post I did on gut inflammation and easy steps to take to optimize your own gut health!

Also, you can follow me on Instagram for more health, nutrition, and gut-related information. You can also sign up for my weekly newsletter below for more exclusive content!

Leave a comment below with any struggles or wins that you have with your own children and their eating habits!


hi there, i’m michelle

welcome to my little home on the internet! I'm a Registered Dietitian and am here to share with you evidenced based and realistic ways to better your health for the long haul. Here you'll learn ways to eat that are both practical and sustainable. Enjoy!

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