Gut Health in Pregnancy: Why It Matters for Baby

As a naturopath, one of the most powerful things I get to support in my practice is the transition into parenthood—and one of the most fascinating (and often overlooked) parts of that journey is the role of the microbiome.

Put simply, the microbiome is the community of bacteria, viruses, and fungi that live in and on our bodies—especially in the gut. These microbes play a massive role in how our immune systems function, how we digest food, how we feel emotionally, and even how our brains develop.

But did you know that your baby’s microbiome begins developing before they even take their first breath? Let’s explore how your body helps shape your baby’s gut health, how that impacts their immunity, and most importantly—what you can do to support it at every step.

🌿 How Your Microbiome Becomes Your Baby’s

Throughout pregnancy, birth, and early postpartum, your body is preparing your baby not just for life outside the womb—but also for the foundational handoff of beneficial microbes that will help train their developing immune system.

This transfer begins:

• During vaginal birth, when baby is exposed to beneficial bacteria from your birth canal and gut.

• Through skin-to-skin contact in those first precious hours after birth.

• In breastmilk, which contains both live probiotics and prebiotics that help healthy bacteria grow.

• Even during pregnancy, via your bloodstream and placenta.
  

🧠 Cool Microbiome Fact: By the end of your baby’s first month of life, up to 50% of their gut bacteria comes directly from you—primarily through birth, breastfeeding, and close contact. This is a powerful, natural gift that helps train your baby’s immune system to know what’s friend vs. foe.

🌿 What Can Disrupt This Microbial Transfer?

Sometimes, birth and postpartum don’t go exactly as planned—and that’s okay. But it’s helpful to understand some common factors that can shift or delay microbiome development in infants:

• C-section births may limit baby’s exposure to vaginal and gut bacteria, instead introducing more skin and hospital microbes.

• Antibiotics during labour or after birth, while often necessary, can reduce the number and diversity of beneficial microbes passed on.

• Formula feeding, when used exclusively, may lack some of the living bacteria and unique sugars that help grow baby’s healthy gut flora.

  
  

None of these are “bad”—and they’re often life-saving tools. But they can influence how and when the baby’s microbiome develops, which is why postnatal support matters so much.

🌿 Why the Microbiome Matters for Baby’s Immune System

The gut is often called the “second brain,” but it’s also the first classroom for your baby’s immune system.

A diverse, well-balanced microbiome helps your baby:

• Build strong immune tolerance—reducing risk of allergies, eczema, and asthma.

• Digest food and absorb nutrients more effectively.

• Reduce inflammation and support healthy metabolism.

• Develop a more resilient nervous system and emotional balance.

  
  

🧠 Cool Microbiome Fact: The human body is home to trillions of microbes—in fact, we have more bacterial cells than human cells. These bacteria play key roles in regulating inflammation, mood, and immunity from the very beginning of life.

🌿 Microbes Are Social, Just Like Us

Here’s something amazing: we don’t just pass microbes to our babies—we share them with everyone we live with.

• Partners, siblings, pets, and even grandparents all contribute to the microbial environment your baby is exposed to.

• The home you live in becomes a shared microbial ecosystem—and this can either support or hinder your child’s developing microbiome.

• Studies show that babies who grow up in households with pets, outdoor play, and greater microbial diversity often have more robust immune systems and lower allergy risk.

  
  

🧠 Cool Microbiome Fact: Within days of living together, couples’ gut microbiomes start to resemble each other, and babies quickly adopt the microbial "fingerprint" of their home. You’re literally growing a community—on every level!

🌿 The Good News: There’s So Much You Can Do

Whether you’re preparing for birth or already caring for your baby, you are not powerless. Here are naturopathic ways to support a healthy microbial foundation for your baby—no matter how they entered the world:

If you’re still pregnant:

• Eat a fiber-rich, whole food diet to nourish your gut.

• Include fermented foods like yogurt, kefir, miso, and sauerkraut.

• Consider a high-quality probiotic if recommended by your practitioner.

• Limit unnecessary antibiotics and manage stress (your nervous system and gut health are deeply connected!).

During and after birth:

• Prioritize skin-to-skin contact as soon as possible.

• Breastfeed, if you choose and are able—every drop helps!

• Use gentle, microbiome-friendly products on baby’s skin.

• Let baby explore! (Yes, even the floor!) Exposure to the natural environment helps diversify their microbiome.

General Notes for supporting a healthy microbiome:

• Avoid food additives that disrupt gut health

  Limit emulsifiers, artificial sweeteners, and gums (like carrageenan, polysorbate 80, and xanthan gum), which may alter the gut lining and microbiota.

• Choose whole, minimally processed foods

  Highly processed foods often feed the “wrong” microbes and increase inflammation.

• Opt for filtered water

  Reduces exposure to chlorine, fluoride, and other chemicals that may affect gut balance.

• Avoid antibacterial soaps and hand sanitizers when not necessary

  These kill both harmful and beneficial microbes on the skin.

• Switch to gentle, microbiome-friendly skincare

  Fragrance-free, non-toxic products help protect your skin’s natural barrier and its microbes.

• Minimize synthetic fragrances in your home

  Perfumes, air fresheners, scented candles, and dryer sheets can disrupt your microbiome and hormone balance.

• Avoid harsh cleaning products

  Especially those labeled “antibacterial” or “disinfectant.” Choose natural alternatives like vinegar, castile soap, and essential oils.

• Prioritize sleep and stress reduction

  The gut and nervous system are deeply connected. Chronic stress and poor sleep reduce microbial diversity.

• Move your body regularly

  Exercise supports a healthy microbiome, immune system, and digestion.

• Surround yourself with connection

  Touch, affection, and close relationships influence your microbiome—and your baby’s too.

🌿 Not a Perfect Start? You Still Have Time

This is really important: there is no such thing as a “perfect” birth or a perfect microbiome. Life happens—birth plans change, antibiotics are needed, and feeding looks different for every family.

The good news? The microbiome is resilient and ever-changing.

Even if your baby had a rough start, you can continue to support and shape their gut health (and your own!) at every age through food, connection, nature, and mindful living.

🧠 Cool Microbiome Fact: The microbiome continues to develop throughout the first 1,000 days (from conception to age two)—and even beyond. That means there’s always time to make a difference.

🌿 In Closing

Your body is already doing incredible work—growing, nurturing, and preparing for one of life’s most profound transitions. Understanding the microbiome adds another beautiful layer to how we care for ourselves and our little ones, reminding us that so much of health begins with connection—to our bodies, our environment, and each other.

Whether your journey into parenthood goes exactly as planned or takes unexpected turns, remember: there are always ways to support and strengthen the foundation of health, for both you and your baby.

This isn't about perfection. It's about knowing that the small, everyday choices we make—what we eat, how we rest, who we surround ourselves with—can shape wellbeing in powerful, long-lasting ways. You're not alone on this journey. Trust your intuition, stay curious, and know that healing and growth are always possible—at any stage.

Written by Dr. Natalia Rey-Caughlin, Naturopathic Doctor.

Dr. Natalia supports women and families through all stages of the perinatal journey—blending evidence-based naturopathic care with compassionate, individualized support. With a special interest in gut health, hormones, and early life development, her work is rooted in the belief that informed, connected care can shape a healthier future for both parent and child.