Building Baby’s Microbiome

Author: Audrey Fleck - MS, RDN, LDN Publish Date: April 16, 2019

Confessions of a New(tritionist) Mom:

If you didn’t know, I recently became a mom for the first time in October of 2017 to a little boy named Wyatt. I will be writing a series of blog posts sharing my experiences and highlighting health and nutritionally relevant topics that may be considered when making your own personal health and nutrition choices.  

My natural birth I had wanted and planned for did not happen for me. Pretty much nothing went my way, but then everything went my way since my baby boy came out healthy. That’s really all that matters in the end. I ended up needing a C-section after a long labor and trying to deliver.  The nutritionist in me really wanted to avoid a C-section because of the benefits of vaginal birth on an infant’s developing gut microbiome.  Here’s more on why baby’s microbiome is so crucial to his/her health’s future and what you can do to support your baby’s flourishing gut bacteria.

It all starts in the gut…

Your gut microbiome refers to the community of microbes that inhabits your intestine, primarily in the colon.

Research on human and gut microbiome is continuing to evolve, but what we do know is that the composition of microbes in our gut may influence way more than just digestion.

Our microbiome helps to synthesize certain vitamins and can also play a role in regulating mood, reducing anxiety, and protecting us from infections and some cancers.  Research has started to connect the dots between certain types of “good bacteria” and reduced risk for obesity, diabetes, and gastrointestinal diseases.  Imbalanced gut bacteria has been linked to health issues such as asthma, autoimmunity, allergies, heart disease, obesity, and digestive illnesses.

The foundation of our gut microbiome that we inhabit really begins from our first few hours to days of life and can ultimately play a role in our health throughout our lifetime.

When do we develop our microbiome?

A baby’s microbiome begins to form in the womb, but after birth, the bacteria rapidly begin to “move in” and colonize the gut.  There are different factors that play a role in the bacterial composition of the gut; one important factor that may make a significant difference on the microbial gut balance, is how a baby is born.

Vaginal vs. Cesarean Delivery

Within the first few hours, to days of life, is when the foundation of a baby’s microbiome is formed.  During vaginal birth, a mother’s vaginal and fecal bacteria comes in contact with the baby during delivery.  It’s actually quite fascinating that weeks leading up to birth, the flora in the vaginal canal begin to change and flourish, getting ready to be shared with baby as he/she is being born.

The microbiome of Cesarean delivered babies tends to reflect the environment baby is born into and the bacterial composition of mother’s skin.  Infants born through Cesarean delivery tend to have less Bifidobacteria and Bacteroidetes.  Research has found that microbial diversity within the first year of life is also low in Cesarean born infants. A long hospital stay versus going home might even be worse for baby’s developing microbiome.

Vaginal seeding involves wiping vaginal fluid on the baby after a cesarean delivery.  I was aware of this concept, but never discussed it with my midwife, nor was it a part of our birth plan (unfortunately).  Looking back, it would have been now.  Vaginal seeding is not part of standard of care and is, in fact, not recommended (YET, in my opinion) because there have not been any long-term studies showing the benefit and/or risks.  In my research, women who are infected with streptococcus B or have sexually transmitted diseases should avoid vaginal seeding.

It may be worth having the conversation with your midwife or OB-GYN to see if it could be something incorporated into your birth plan, if needed.  Although studies are lacking, it makes very much sense as a practical way of delivering mother’s vaginal bacteria to a baby who has missed out because of a C-section.

Preparing Mom’s Microbiome Before Birth

As mentioned earlier, a baby’s gut microbiome starts to form within the womb. It was once thought that the placenta was sterile, but research now has shown that it is actually rich in bacteria that is transferred to the baby while in gestation.

During pregnancy, mom can aid baby’s microbiome by eating probiotic-rich foods such as fermented vegetables (like pickles and sauerkraut) and organic whole fat yogurt, kefir and aged cheese.  Prebiotic foods “feed” our bacteria to help them stay put and thrive, once seeded in the gut. Some prebiotic foods are asparagus, onions, garlic, Jerusalem artichokes, dandelion greens, and bananas.

Taking a probiotic may also be a wise choice.  Real Food for Pregnancy (RFP) by Lily Nichols, RDN, CDE (highly recommended book) references a study where expecting moms who took a multi-strain probiotic at 900 billion CFUs during the last 4 weeks of pregnancy, and continued while nursing, was protective against infant colic, regurgitation, and overall digestive discomfort. Another study RFP references, notes that women taking 20 billion CFUs of Lactobacillus rhamnosus during the last 4 weeks of pregnancy and during breastfeeding produced milk with double the levels of immunoprotective compounds.  Plus, in the same study, the rates of eczema in the first 2 years of life were only 15% compared to 47% in the group that did not have a mom taking probiotics.

Other Factors That Influence Infant’s Microbiome

After birth, infant diet (breastmilk vs. formula and transition to solid foods) all play the most important role in shaping the composition of bacteria. We’ll save this topic for another time. 

There’s more you can do to help baby’s microbiome…

If you had a C-section like me or a natural birth, there is definitely more you can do to help baby’s healthy gut bugs. 


Skin-to-skin contact is also crucial to your baby’s newly developing microbiome.  I was fortunate to deliver in a hospital which had a skin-to-skin policy advocating that mom and baby be allowed to have 2 hours of skin-to-skin contact immediately following birth.  Skin-to-skin means holding baby against your bare skin (on your chest/belly).  It’s basically a newborn cuddle session, while at the same time, your beneficial bacteria on your skin is being transferred to your baby.  Dad’s and siblings can do skin-to-skin as well.  Immediate skin-to-skin interaction helps to increase chances that breastfeeding gets initiated soon after birth. Skin-to-skin also increases oxytocin (the love hormone) supporting both mom and infant’s stress levels after birth.

Skin-to-skin with newborn Wyatt

Don’t bathe baby! Hold off!

We waited until the day we left the hospital to give Wyatt his first bath, which was day 4.  I would skip the hospital soap provided, or bring your own natural soap. We used the Attitude brand which received an A+ rating on the EWG Skin Deep Database.  If a second baby comes along for me, I will probably even skip the soap next time.  Bathing baby too quickly removes the vernix (immune protective white substance that coats baby), vaginal fluid, and newly “seeded” skin microbiome.


Listen, I get it that there are many reasons why a mom may be unsuccessful at breastfeeding and this is meant to not pass any judgment whatsoever. I had a lot of challenges in the beginning and really worried that it was not going to work out for me, so I get it when breastfeeding just doesn’t work out for whatever reason.  What I will say though, is breastfeeding IS the best thing you can do for your child’s growing needs and flourishing microbiome.  Breast milk contains beneficial bacteria as well as specific typescarbohydrates (not found in cow’s milk) that help to feed beneficial bacteria. Breast milk is superb to other mammalian milks (check out this article). Even the skin of the nipple contains beneficial bacteria that baby ingests.  A paragraph is not enough to justify how amazing breastfeeding is, and I will write more on this topic at a different time.  

Infant Probiotics

Giving your baby a probiotic may be an additional way to provide healthy bacteria to assist in forming that healthy and balanced microbiome.  To my knowledge, there are no standards of care on how much or when to give probiotics to infants, so I do recommended consulting with your baby’s pediatrician or dietitian-nutritionist who is knowledgeable on this topic.

Personally, I can share that we began to give Wyatt  multi-strain infant probiotic as soon as we incorporated a bottle of breast-milk into his routine, which was around 4 weeks. We started at a low dose (5 billion CFUs) and worked our way upwards close to 50 billion CFUs. He has been getting around this dose for the past 4-5 months on average of 4-5 days per week.  You can also sprinkle some probiotic on your nipples during feeding as another route of administration.

If 50 billion CFUs sounds like a lot, Wyatt’s pediatrician was even encouraging closer to 100 billion CFUs. We are lucky that she specializes in functional medicine and supports us more holistically.

Side Note – I truly recommend finding a pediatrician who wants to collaborate with you rather than strictly tell you what to do. Not all pediatricians know much about nutrition, or even this specific topic of the microbiome! If you cannot find a pediatrician who knows much beyond medicine, I highly recommend incorporating a functional dietitian-nutritionist into your child’s care to support you and growing baby.

Mom Needs Nurturing Too!

To be continued in my next post… stay tuned!


Real Food for Pregnancy by Lily Nichols RDN, CDE

This blog pro­vides gen­eral infor­ma­tion and dis­cus­sion about med­i­cine, health and related sub­jects.  The words and other con­tent pro­vided in this blog, and in any linked mate­ri­als, are not intended and should not be con­strued as med­ical advice. If the reader or any other per­son has a med­ical con­cern, he or she should con­sult with an appropriately-licensed physi­cian or other health care worker. The views expressed on this blog and web­site have no rela­tion to those of any academic or other institution with which the authors are affiliated.

About the Author

Audrey Fleck - MS, RDN, LDN

I’m Audrey Fleck, a dedicated dietitian with over a decade of experience, and the founder of Functional Origins, my private practice located in Bucks County, PA. With a strong educational background, including a BS in Nutrition and Dietetics and an MS in Human Nutrition and Functional Medicine, I specialize in providing an integrative and functional approach to healing, primarily tailored for women.