Vaginal Seeding, the Microbiome and Newborn Colonization

Sep 4, 2025

In your work as a childbirth educator, your clients may ask you about a childbirth practice called “vaginal seeding.” It’s also sometimes described as the “colonization” of newborns or “microbiome seeding.” While this practice isn’t yet recommended by organizations like the American College of Obstetricians and Gynecologists (ACOG), new parents are often interested in it, and may want to know more.
 
Here, we’ll take a close look at this practice, including the research behind it, what it involves, clinical guidelines, and how to talk to your clients about it.

The Theory Behind Vaginal Seeding and "Colonizing" Babies

When babies are born vaginally, they are naturally exposed to their mother’s vaginal microbiome, which refers to the bacteria, fungi, and other microbes found in the vagina. The microbes transferred from mother to baby are thought to play important roles in the immune system and metabolic programming of newborns. It’s thought that these benefits may extend beyond the baby years, and may offer lifelong health benefits.


When newborns are delivered by Cesarean section, they lose the opportunity to be colonized by their mother’s microbiome. There is some evidence that babies born by Cesarean section develop an increased risk for inflammatory and metabolic conditions, such as obesity, juvenile arthritis, inflammatory bowel disease, and immune issues. It’s been theorized that the lack of colonization by the vaginal microbiome may be a contributing factor.
 
It is important to note that the current results from studies on the health consequences of Cesarean vs. vaginal births are small and preliminary, include some inconsistencies and need to be verified by larger clinical trials.

How Does Vaginal Seeding Work?

Vaginal seeding is when babies born via Cesarean section are exposed to a sampling of their mother’s vaginal fluid shortly after birth. Typically, sterilized gauze is introduced into the vagina before the Cesarean. This gauze is then applied to the newborn’s mouth, face, and body after birth, in an attempt to mimic what happens during a vaginal birth.
 
The idea behind vaginal seeding is that it will colonize babies with their mother’s vaginal microbiome even when they are born via Cesarean, thereby offering them the health benefits associated with vaginal births.

Clinical Practice Standards

At this time, vaginal seeding is not recommended by major medical organizations. In 2017, ACOG reviewed the data on vaginal seeding and recommended that “vaginal seeding should not be performed outside the context of an institutional review board-approved research protocol until adequate data regarding the safety and benefit of the process become available.”

ACOG explained that while vaginal seeding is a compelling and potentially beneficial practice, it should not yet be widely implemented because:

  • More robust research is needed on its safety and benefits.
  • Vaginal seeding has the potential to transmit unwanted infections from babies to mothers, such as Group B Streptococcus, HIV, hepatitis B, hepatitis C, chlamydia, syphilis, herpes simplex virus (HSV), and human papillomavirus.

While not recommended across the board, ACOG has affirmed that vaginal seeding can continue to be performed within the context of research studies.

How to Discuss Newborn Colonization with Your Clients

Vaginal seeding is a trending topic in childbirth and your students may have questions and concerns about it. It’s good to be prepared to discuss it in a clear and responsible way. Here are some tips.

Share the Data

It’s important to arm your students with evidenced-based, up-to-date information about all aspects of childbirth. To that end, you can share the research out there on vaginal seeding, including potential benefits. Consider sharing the statement from ACOG, which includes some of the potential benefits of the practice, as well as a discussion comparing health outcomes of babies born vaginally vs. by Cesarean section.

Be Careful Not to Offer Medical Advice

Maybe you think vaginal seeding is a good idea, or maybe you think it’s not. Either way, you shouldn’t offer recommendations to your clients. Instead, you should offer resources and encourage them to educate themselves on the topic.

Encourage Clients to Discuss Vaginal Seeding with their Provider

Some clients will want to try vaginal seeding, in the event that they have a Cesarean birth. Encourage them to discuss this possibility with their healthcare provider before they give birth so they can put a plan in place for how to manage it.

Wendy Wisner, Freelance Writer and Lactation Consultant (IBCLC)

Sources

Committee Opinion No. 725: Vaginal Seeding. Obstet Gynecol. 2017 Nov;130(5):e274-e278. doi: 10.1097/AOG.0000000000002402. PMID: 29064974.
 
Hourigan SK, Dominguez-Bello MG, Mueller NT. Can maternal-child microbial seeding interventions improve the health of infants delivered by Cesarean section? Cell Host Microbe. 2022 May 11;30(5):607-611. doi: 10.1016/j.chom.2022.02.014. PMID: 35550663; PMCID: PMC9237654.

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