Chat with us, powered by LiveChat

The Perfect Birth Won’t Guarantee Healthy Gut Flora for Baby

Healthy baby's gut flora actually begins BEFORE birth.

That moment when I saw a young pregnant mom in a bar drinking a beer (or two or three), long before I was a real food blogger, long before I was a mom myself, and even before I was of drinking age…I gaped in horror.

I knew nothing about prenatal nutrition, health, or growing a healthy baby, but even then, I knew enough to know that what mom does during pregnancy has a huge effect on her unborn baby, even for the rest of the child’s life.

When I did become pregnant myself, that began the journey of natural living that you find me on today, here at Kitchen Stewardship®. There’s something powerfully motivating about having another life wholly dependent on you for everything.

I learned quite quickly that not only does a baby’s womb experience drastically impact her development, but also that the actual birth process can leave lifelong marks. Not adult coneheads from being squeezed though the birth canal, no, rather that a baby’s microbiome or gut flora is seeded while going through the birth canal.

That knowledge guided our birth plan and fueled my fire for a natural birth, and in fact study after study demonstrates a link between more robust and healthy gut bacteria in vaginal births vs. C-sections.

Baby Gut Health at Birth…and Before

Healthy gut flora actually begins BEFORE birth for babies

I think we are at a time in history where it’s generally accepted – or mostly so and becoming more mainstream all the time – that quite a few parts of the birth process itself have both short and long-term impact on the child, most notably the development of healthy gut flora (source). The microbiome, our three trillion-plus microscopic co-dependents on this earthly journey, is the subject of much scientific interest, and I can’t wait to see what we continue to discover and understand about the symbiosis of human and bacterium.

So far we’ve proven that our gut flora do far more than just assist digestion:

  • comprises over 75% of our immune system, providing protection from infection
  • regulates metabolism (is often a key to weight loss like these women found)
  • has been linked to autoimmune disease (Crohn’s, Hashimoto’s), psychological imbalances (depression), autism, asthma and allergies
  • sources: 1, 2, 3, 4

We know it’s vital to our overall health, and we know it starts early, but contrary to the previously held “blank slate” or “sterile womb” understanding of the newborn gut, new studies are showing that in fact, we get to throwback to that basic knowledge that I had in the bar at age 19:

What a mother does during pregnancy has a huge effect on her unborn child.

Numerous studies (analyzed here) have shown the likelihood of the infant gut being seeded in the womb, not at birth for the first time.

Correlations include:

  • the placenta’s own lively microbiome, including some bacteria never seen before
  • bacteria directly found in intestinal tissue samples from surgery immediately after C-section births
  • bacteria in newborn meconium
  • cultures from previously-thought-to-be sterile amniotic fluid during pregnancy growing various good and bad bacteria

That amniotic fluid may have an impact on the term of the pregnancy itself as well as the health of the newborn’s gut, underscoring once again the vital importance of mother’s health during gestation.

Healthy Gut Flora Starts Before Birth in the Womb what mom eats and probiotics count

How to Promote Baby’s Healthy Gut Flora in the Womb

Studies are also showing that what a pregnant mom eats – particularly if she consumes probiotic foods like Lori showed us how to make on Monday – affect the unborn baby’s gut flora via her own gut and placenta. In face, just 14 days of a probiotic supplement improved the flora of babies born via C-section who were not inoculated with mom’s vaginal fluids.

Well Belly

So this is new: Mothers don’t only pass on their hair or eye color, shyness, or propensity toward chocolate. “It seems that maternal gut microbiota may be able to translocate to the baby/placenta via the blood stream (1; 2; 3; 4; 5). And the unique ecosystem of bacteria in the placenta may originate from bacteria in the mother’s mouth.” Mothers may even pass on the effects of stress to their unborn babies via bacteria (6; 7, 8).

How might the blood transfer mom’s microbiome to baby? Blood cells actually carry whole bacteria – and more of them and different types during pregnancy (9)! The bacteria are then found in infant feces, leading many to speculate that there must be a transfer in the womb. (source for above 2 paragraphs)

In other words, setting up your baby for a lifetime of better health beginning in the gut isn’t all about that perfect birth, or even getting probiotics started early (like these infant probiotics).

It begins like everything else, with you. You and your placenta, that is.

Favorite Product Spotlight!

WellBelly is specially formulated for tiny tummies with only the easiest-to-digest probiotics, giving little ones exactly what they need and nothing more. It’s what we give Gabriel and have since he started eating. I bet moms needing a C-section could take it for a few weeks before too, to help seed their baby’s gut better (or maybe any pregnant mom should…?).

Thanks so much to Catherine Clinton, ND, who formulated the WellFuture products, for constantly pushing me to research and learn more and share it with you!

How to Give Birth to a Baby with Healthy Gut Flora


Genevieve from Mama Natural offers great week 2 week pregnancy updates. I wish I had these when I was pregnant!

I’m so happy to introduce you to Genevieve from Mama Natural. I loved her video series for years before I met her and I’m proud now that our families have become dear friends. She’s such a sweet, genuine woman!

Not only do I love her weekly pregnancy updates, but she is now offering a Natural Baby Care Course. I wish I had this with mine!

Imagine having access to a team of expert health professionals in your home, whenever you need them, as you raise your newborn.

  • A holistic pediatrician to give you tips on what to feed your baby.
  • A board certified lactation consultant to help you master breastfeeding.
  • And a firefighter / CPR instructor to make you aware and prepared.

This is a masterclass in everyday baby care. You’ll be supported for ALL the challenges that come up with baby in this program.

  • It’s easy to access. Watch the classes on your own schedule. No traveling across town after a long day at work.
  • It’s comfortable. Learn in the privacy of your own home—no sterile classrooms filled with rows of uncomfortable chairs. Simply curl up in your favorite spot and soak it all in.
  • It’s fast, but comprehensive. Other baby care courses speed through the most important topics to cover it all. We don’t do that. Instead, we unpack all of the issues that come up postpartum, but we do so in small chunks so you can squeeze the education into your busy life.
  • It’s affordable. Our course is priced lower than in-person classes and less than most online alternatives as well.

More of a book person? You must check out Genevieve’s week-by-week Guide to Pregnancy & Childbirth. It’s the natural answer to “What to Expect” and soooo comprehensive and beautiful!!

Other Pregnancy Posts at KS:



Unless otherwise credited, photos are owned by the author or used with a license from Canva or Deposit Photos.

5 thoughts on “The Perfect Birth Won’t Guarantee Healthy Gut Flora for Baby”

  1. it is ASTOUNDING all the ways the gut flora impacts our health. I actually read a study not long ago that showed that gut bacteria can influence BONE BUILDING! Who’d have thought?

    I’m curious about this seeding in the womb thing, though, because it wouldn’t seem that c-section babies and vaginally-birthed babies should have as great a difference in their flora if that’s the case. The Sonnenbergs, researchers specializing in the gut microbiome, found that c-section babies had gut flora that most greatly matched normal SKIN flora (which makes sense, given that’s what they would come into contact with first). Oddly enough, the vaginally-birthed babies had microbiomes that best matched their mothers’ GUT microbiomes, not their vaginal ones. So maybe there’s something in the normal vaginal microbiome that signals the bacteria regarding what to reproduce or not reproduce?

    The waterbirth question is a good one, too. All four of my births were waterbirths, so that’s a pretty relevant question for me. I have a hard time believing it makes a MAJOR difference, only because we know that just swishing our hands through a bowl of water, for instance, doesn’t cleanse them of bacteria — we have to work harder than that to wash it off. But it does seem that it could reduce the overall quantity of bacteria.

    1. I agree totally, Rachel – astounding! I think the c-section vs. vaginal birth impact on gut flora is still very evident and research-based, so it’s not that seeding in the womb precludes that or overrides it, but that it’s yet another part of the equation.


  2. Have you heard anything about water birth and how that affects the baby’s gut? I heard that having a water birth might “wipe away” some of the beneficial bacteria in the birth canal. Do you think there’s any truth to that?

    1. Hi Ellen,
      I did read something in all the research I was immersed in this week about that – no real research done but some theorize that it basically dilutes the bacterial transfer. 🙁 There is some proof that GBS is less likely to go to the baby in a water birth, so that would support the dilution theory. Kind of a bummer because I did a water birth last time!
      Good question – Katie

Leave a Comment

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.