by Stephanie Greunke, RD and Whole Mamas Program Manager.

The information in this post is for educational purposes only. It is not intended nor implied to be a substitute for professional medical advice. Always consult your healthcare provider to determine the appropriateness of the information for your own situation, or if you have any questions regarding conception, pregnancy, or your prenatal treatment plan. For more FAQ posts, click here. Have a question for our team? Click here to e-mail us.

At Whole Mamas, we acknowledge that the journey to motherhood can happen in a variety of ways. We want to acknowledge that birth doesn’t always go as planned, and you might not always get to control your baby’s environment in utero or in delivery! You may have adopted, you may have scheduled a cesarean or you may have had an emergency procedure.

Either way, the emotional and physical healing after delivery deserves recognition. A c-section is not the “easy way out” and I want to acknowledge you for doing what you needed to or what you felt was best at that time. Chelsea shared her experience navigating the mixed emotions post-cesarean delivery, and I’ve discussed the emotional and physical recovery several times with experts such as Jessie Mundell, and mamas (even Melissa Hartwig Urban!) on my podcast. I discussed this topic in a video that members of our Whole Mamas community can find here.

Not a member yet? Click here to join!

When we asked our community for questions on gut health, we received a large response from mamas who had a cesarean section, wanting to know how that would impact their baby’s overall health. Although not every baby will receive vaginal inoculation of beneficial bacteria, there are things you can do to set your little one (and yourself) up for success no matter how baby arrives!

Beneficial gut bacteria perform a wide variety of important functions such as producing vitamins, stimulating normal immune development, preventing growth of harmful bacteria, and maturing baby’s intestines and immune system. By taking steps to ensure the right types and balance of bacteria, we’re improving our baby’s mental and physical health. This has a wide range of implications that last a lifetime.

There’s an important “window of opportunity” during the first three years of life to expose baby’s gut to specific beneficial bacteria and minimize exposure to antibiotics to improve overall health. I will explore four elements that influence your baby’s gut health: 

  1. Mom’s microbiome
  2. Type of delivery 
  3. Type of feeding
  4. Environment

We know that you might not be able to control each of these elements exactly in the way that you would like to. That’s OKAY. Put your mind at ease by knowing that this post is full of suggestions, and anything you can do to promote healthy gut health will benefit your baby. The goal is not perfection in each category, but arming you with information that you can apply depending on your circumstance.

Mom’s microbiome

While it’s still controversial, there’s evidence to support that babies are exposed to beneficial bacteria while in utero. In fact, the placenta has its own microbiome and scientists have found evidence of bacteria in the amniotic fluid and meconium. This means you may have the ability to impact your baby’s gut health prior to delivery! Pregnant mamas, this means you can work toward a healthy diet and lifestyle behaviors that favor a healthy microbiome and transfer those benefits to baby.


  • Eat a whole foods diet that’s low in sugar and rich in fiber and fermented foods (probiotics!) before and during pregnancy 
  • Be mindful of exposure to antibiotics. In cases where an antibiotic is warranted, and your provider approves, use a probiotic a few hours away from the antibiotic.
  • Switch to more natural cleaning and skincare products for you and baby, if possible. Considering your options for soap, shampoo, wipes, diapers and even things like tampons, condoms, and lubrication.

Type of delivery

Research shows there are significant differences between the gut microbiota in vaginally delivered infants compared to those born by cesarean. However, by understanding what types of bacteria are present in vaginal vs. cesarean born babies, we can take thoughtful steps to modulate babies microbiome towards one that’s colonized with beneficial bacteria such as Lacobacilli and Bifidobacteria to mitigate some of the potential concerns.


  • Focus on maintaining a healthy microbiome as mentioned above. Some research shows that it may be possible to reduce risk of preterm birth or premature rupture of the membranes if mom has a healthy vaginal microbiota rich in Lactobacillus species and reduces her exposure to antibiotics. This can reduce your risk of interventions during delivery which may lead to an emergency c-section.
  • If a cesarean is scheduled, you can discuss the option for vaginal seeding with your provider. Vaginal seeding is the practice of inoculating a cotton gauze or swab with fluids (including beneficial bacteria) from a mother’s vagina prior to surgery. A minute or two post-delivery, that gauze or swab is quickly rubbed all over baby. The intent is to transfer mom’s vaginal flora to babies born via cesarean who haven’t received that exposure. Babies swabbed with mom’s vaginal flora are found to have similar bacteria colonies to vaginally delivered babies. Be aware that we still have a lot to learn about this practice. The American College of Obstetricians and Gynecologists has warned against the practice stating concerns over the potential risk of transferring pathogenic organisms from the mom to her baby. If you’re interested in vaginal seeding, work with your provider to test and rule out the potential transfer of pathogenic organisms like herpes simplex virus, cultures for Group B strep, Chlamydia, and gonorrhea. As always, make sure it’s appropriate for your context.

Type of feeding

It’s been shown that breastfed infants are less likely to develop respiratory and gastrointestinal infections, allergies, and chronic diseases like diabetes, obesity and IBD. In addition to the beneficial bacteria found in milk, baby’s oral contact with the skin on mom’s nipple increase bacterial diversity and helps seed baby’s gut.

Researchers have found more than 700 species of microbes in breast milk, including colostrum! So even if you’re unable to breastfeed long term, know that some is better than none. The very first drops of breastmilk are rich in beneficial bacteria that have important implications for your baby’s immune system.

There are over 200 different types of oligosaccharides in breast milk that serve an important role in feeding beneficial Bifidobacterium strains in your baby’s gut which support brain development, immune functioning, and gut health!

Breastmilk and formula fed babies appear to have different gut flora. While formula doesn’t have as many protective benefits as breastmilk, formula companies are starting to acknowledge the importance of these beneficial bacteria and are working to modify their products to support an infant’s microbiome. Certain formula companies are now including probiotics, prebiotics, and non-digestible fibers, and choosing lactose instead of other sugars in attempts to more closely resemble the composition of breastmilk.

When baby starts solids, there’s another opportunity to expose your baby to a wide range of beneficial bacteria and diversify their microbiome. Breastmilk has a different microbial composition at six months than immediately postpartum. Introduction of solid foods, especially those higher in protein and fiber, shifts the infant gut microbiome towards one that begins to resemble an adult’s. 


  • Breastfeed for as long as you can or feel comfortable doing. 
  • Not able to breastfeed or exclusively breastfeed? Your baby is not doomed! Find a formula that works for your baby, ask your pediatrician about adding infant probiotic powder to the formula, and continue to work on your gut health to provide benefits through skin-to-skin exposure.
  • With your doctor’s approval, consider supplementing yourself and/or baby with probiotics, fish oil, and vitamin D to support immune function. Certain bacteria such as Lactobacillus, Bifidobacterium, and Bacteroides is delayed in infants born by C-section, so probiotics that include these strains may help reduce the incidence of allergy, atopic diseases, and immune concerns. If you’re breastfeeding, probiotics will be delivered to your breastmilk. You can also administer the probiotics directly to your baby by mixing the powder/drops into bottles or choosing a formula with probiotics. Some of the well-researched strains include L. rhamnosus, L. reuteri, B. infantis, and B. lactis. In some cases, babies do better with blends that are mostly B. infantis and only contain histamine-neutral or histamine-degrading strains of probiotics like this one. Prebiotics that feed beneficial bacteria, such as inulin derived from chicory root, can also be a helpful addition; however, caution that some babies are sensitive to prebiotic fibers.
  • Delay the introduction of solids until 6 months and choose healthy, whole first foods.


Skin-to-skin contact is a beautiful way to bond with your baby and expose baby to your microbiome. Microbes aren’t only found in the gut and vagina, they’re found all throughout your body — including your skin and your mouth. So while you, your family, and your partner are snuggling and kissing your little one, you’re also inoculating them with your bacteria.

And even your animals can help! Exposure to your pet’s microbes can diversify your little one’s gut, potentially reducing the risk of allergies and asthma by stimulating their immune system.


As you can see, there’s much more to gut health than the type of delivery. This is good news if you’ve had a cesarean section or are an adoptive mama concerned about your baby’s health. Remember that there’s a three year “window of opportunity” to optimize baby’s gut health, and you can take action starting today! Knowledge is power, and you’re doing great, mama! 

For more information on all of the topics covered here, find us on Instagram, Facebook, or join us in our Whole Mamas Pregnancy Program, where you can get questions answered by our team and an incredible group of encouraging, like-minded mamas.

Header Photo: Janko Ferlic

Stephanie Greunke is a registered dietitian with a master’s degree in nutrition who specializes in women’s health. She is a certified personal trainer and prenatal and postnatal corrective exercise specialist. Stephanie guides and supports women locally and globally through her web-based private practice,