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Health8 Ways to Help Baby Gut Health

8 Ways to Help Baby Gut Health

Motherly CollectiveMotherly Collective

In 2018 my first baby was born. The doctors had to perform a C-section due to her breech presentation. The procedure went without complications, but soon after starting solids, my daughter Charlize developed mild eczema and a sesame allergy. 

I started researching the effects of a C-section and discovered that a mother passes on her vaginal and gut bacteria to her baby through vaginal birth. The initial bacteria colonization lays the foundation for a child’s lifelong health. This process is called microbiome seeding.

My engineering background went into full effect. While combing through peer-reviewed scientific studies, I learned that babies born via C-section or exposed to antibiotics during labor may miss that essential bacteria

The key here is that 80% of your immune system lives in the gut and is dictated by which bacteria are or aren’t there. 

C-section babies may need more microbiome support

Unfortunately, microbiome seeding disruptions may have a downstream effect on immune development. Babies born via C-section tend to miss out on exposure to a mother’s gut and vaginal microbiome, which could protect their gut. 

And this matters. 

For example, research shows that C-section babies may have a higher risk of atopic march. This is a progression of allergy conditions that typically begins with eczema and can evolve into food allergies, asthma, hay fever and other chronic diseases. 

I also discovered that even with vaginal birth, a mom may not transfer essential bacteria for her baby’s gut health if she no longer has those protective bacteria herself, which may be a result of lifestyle or environment. So it is important to know if the mom needs extra support in the form of probiotics or lifestyle shifts before delivery as she passes on her gut and vaginal health to her baby. 

Related: 5 ways to protect your baby’s microbiome after birth

Fortunately, I learned there’s a way to restore gut imbalances in a baby in the first 1,000 days of their life. Studies show that if what’s known as the “C-section microbial signature” (the microbiome profile standard to babies born via C-section) is gone by one year of age, the baby’s risk for developing allergies is significantly reduced.

I equipped myself with further research and did all I could to support my daughter’s gut health. 

I opted for a vaginal swabbing procedure during the C-section. I breastfed for what some may consider a long time—18 months. I made homemade kefir and my own fermented vegetables. We spent time around pets and even visited local farms. 

Creating the first at-home baby gut health test

I had no way of knowing if all my efforts had the effect I was hoping for. A stool test for a child’s first 1,000 days didn’t exist. 

At that time, the only available gut tests used adult reference ranges which led to inaccurate results—and worse —suggestions not suitable for a baby. 

So I took matters into my own hands. One month after my second baby was born, I started a company called Tiny Health.

The goal of Tiny Health is simple: offer a test designed specifically for pregnant moms and babies during a child’s first 1,000 days. 

Related: Does my infant need baby vitamins? 

I began with a small, self-funded study with the help of a Scientific Advisor from Mayo Clinic. I had a cohort of nine mothers and started collecting their microbiome samples during pregnancy. After they gave birth, I took their babies’ stool samples at frequent intervals until their babies were 2. This data proved to be really impactful and actionable to parents, allowing them to detect any gut imbalances early on and make necessary changes.

After we raised our seed round in 2021, I worked with a team of microbiologists from John Hopkins, Cornell, USC and WashU to complete the proprietary bioinformatics pipeline and data science for our product. This resulted in us launching the first ever at-home baby gut health test that gives parents evidence-based insights and personalized nutrition, supplement and lifestyle recommendations. 

By providing transparency into what is in their baby’s gut, parents can take action sooner and get to the root cause of the baby’s gassiness, allergies and other chronic conditions. Ultimately, our mission is to improve the health outcomes of our future generation. We believe that our work will result in better data, research, diagnostics and microbiome therapeutics. 

Here are 8 ways to ensure your baby has the best gut health start in life 

1. Test your own microbiome first

Test your gut and vaginal microbiome during preconception or pregnancy to make sure you have the essential protective microbes to pass onto the baby during birth. 

2. If possible, plan for a vaginal birth

In the event of a C-section and if you have a healthy vaginal microbiome, consider a vaginal swabbing protocol.

3. Breastfeed for at least 6 months

If possible, try to exclusively or partially breastfeed your baby for at least six months to continue transferring beneficial microbes to your baby.

Related: Study: Babies gut bacteria is impacted by delivery method

4. Watch for symptoms

If your baby has the following symptoms, you may want to do a baby gut test to see if there may be potential gut imbalances that you can address: colicky, gassiness, sleep issues, eczema, food allergies, milk protein intolerance, constipation.

5. Not every baby needs infant probiotics

In fact, we do not recommend them for prolonged periods. If the baby has high levels of unfriendly bacteria, short doses of the right kind of missing strains can be highly effective. It’s important to know that not all probiotics are created equal. A baby gut health test can help you determine if your baby’s probiotics are working and when to stop.

6. Broaden their exposure

Small amounts of unfriendly bacteria are essential for immune system training in early life. We recommend exposing your baby to nature and animals and avoiding toxic household cleaners or antibacterial products. Babies in overly sanitized environments are more likely to develop allergies

7. Opt for plenty of nature play

Research has shown that picking a daycare that is more nature-based may lead to a more robust microbiome than one with artificial turf and fewer outdoor interactions.

8. Only use antibiotics if absolutely necessary

While antibiotics may be lifesaving, they have unintended effects on a child’s gut. Testing your baby’s microbiome before treatment gives you a baseline and insight on how to best restore their gut health afterward.

tiny health gut test kittiny health gut test kit

Bonus: Use code MOTHERLY20 to get $20 off any microbiome test from Tiny Health


Bager P, Wohlfahrt J, Westergaard T. Caesarean delivery and risk of atopy and allergic disesase: meta‐analyses. Clinical & Experimental Allergy. 2008 Apr;38(4):634-42. doi:10.1111/j.1365-2222.2008.02939.x

Olm MR, Dahan D, Carter MM, Merrill BD, Yu FB, Jain S, Meng X, Tripathi S, Wastyk H, Neff N, Holmes S. Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. Science. 2022 Jun 10;376(6598):1220-3.

Roslund MI, Puhakka R, Grönroos M, Nurminen N, Oikarinen S, Gazali AM, Cinek O, Kramná L, Siter N, Vari HK, Soininen L. Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children. Science advances. 2020 Oct 14;6(42):eaba2578.

Shao Y, Forster SC, Tsaliki E, et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature. 2019;574(7776):117-121. doi:10.1038/s41586-019-1560-1

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Vighi G, Marcucci F, Sensi L, Di Cara G, Frati F. Allergy and the gastrointestinal system. Clin Exp Immunol. 2008;153 Suppl 1(Suppl 1):3-6. doi:10.1111/j.1365-2249.2008.03713.xZhao Q, Elson CO. Adaptive immune education by gut microbiota antigens. Immunology. 2018;154(1):28-37. doi:10.1111/imm.12896

This story is a part of The Motherly Collective contributor network where we showcase the stories, experiences and advice from brands, writers and experts who want to share their perspective with our community. We believe that there is no single story of motherhood, and that every mother’s journey is unique. By amplifying each mother’s experience and offering expert-driven content, we can support, inform and inspire each other on this incredible journey. If you’re interested in contributing to The Motherly Collective please click here.

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