Microbiome seeding – also called vaginal seeding – is the practice of wiping a caesarean-born baby’s mouth, face and/or skin with a cloth that has been in or near its mother’s vagina just prior to the caesarean.
The term ‘seeding’ just means to start off the baby’s collection of bacteria., so the idea is that bacteria from the mother’s vagina will be transferred to the baby.
This bacterial transfer happens naturally during a vaginal birth, and it is very beneficial. When babies are born in the traditional manner, the bacteria that they acquire from their mother’s birth canal help with the development of their metabolic and immune systems, and decreases their risk of disease.
But when a baby is born by caesarean instead of through the birth canal, this bacterial transfer doesn’t happen. Caesarean-born babies are thus disadvantaged because they do not get these good bacteria, which makes them more prone to disease, and poorer long-term outcomes.
Microbiome or vaginal seeding is a way of trying to undo that particular downside of having a caesarean birth.
In this blog post, I offer an overview of some of the research and thinking on this topic.
The origins of microbiome seeding
A seminal article evidenced that caesarean-born babies’ microbiomes were being ‘seeded’ by human skin bacteria from the operating room environment. One of the researchers on this team led the first pilot study that looked at maternal microbiome seeding (Dominguez-Bello et al 2016).
The results of this first study looked positive. Four babies were studied, and the results showed that their oral/skin (but not gut) microbiome had been partially restored compared to unseeded babies who had also been born by caesarean.
“Although the long-term health consequences of restoring the microbiota of C-section-delivered infants remain unclear, our results demonstrate that vaginal microbes can be partially restored at birth in C-section-delivered babies.” (Dominguez-Bello et al 2016).
The main downside of this study was obviously its size, and the fact that some babies were exposed to antibiotics, which could have affected the results. However, this study was important. It sparked widespread interest in microbial seeding interventions.
The debate begins
Almost as soon as microbiome seeding was proposed, women wanted to try it. It appears to have begun in Australia, but was quickly adopted by some women in the UK, and then around the world.
And almost as soon as women began to ask for this, doctors began to question its use, warning against it.
In the UK, a 2016 British Medical Journal podcast described it as “popular but unproven.”
At about the same time, the NHS website put up a warning that microbiome seeding wasn’t proven to be safe, however this was quietly removed a few months later. Despite making enquiries, I have been unable to find out why. At the time of writing, no information is listed on the NHS England website for those searching on this topic.
A year later, in 2017, another UK commentary raised some key questions, while an ACOG Committee Opinion cautioned against routine vaginal seeding due to infection risks. The Opinion writers were particularly concerned about undetected Group B Strep (GBS), and herpes simplex virus (HSV). Their statement noted that there was insufficient evidence for health benefits despite a theoretical rationale for the idea of microbial seeding.
Varied evidence, divided opinions
Since vaginal seeding began, it has been hotly debated, as is often the case with interventions that benefit women and families but which did not arise from within the obstetric paradigm. Much of the ‘how to’ information about seeding has been shared online and anecdotally, between women and families, and woman-centred caregivers.
In 2022, ACOG reaffirmed their view 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.”
This statement continues to influence hospital policies concerning the non-research use of microbiome seeding, in other countries as well as the USA. This is despite the fact that ACOG and other obstetric organisations support the use of several obstetric interventions in the same situation, that is where there is ‘insufficient evidence for health benefits.’
But it is also important to know that the evidence from other research studies has been as varied as the wider debates.
Let’s look at some of the later key studies and papers.
Wilson et al (2021)
This was another small trial, which had disappointing results, although the authors (Wilson et al 2021) did raise some ideas about why this might be, which could help inform future research.
The researchers tested oral administration of vaginal microbes to caesarean-born infants, which is somewhat different to what most families were (and still are) doing. They found no gut microbiome differences between seeded/unseeded groups at one to three months of age, but suggested that this could be because of the lack of multi-site exposure.
In order to explain this, I need to explain how people actually go about the seeding process.
How to do vaginal seeding
In simple terms, most people who undertake microbiome seeding use a sterile cloth (often muslin) or swab. A health professional who is supportive of seeding may agree to give parents a sterile swab in a sealed packet that they can open when needed. It’s also easy to buy these online, or from a pharmacy.
If a cloth is used, this is often rolled up into a tampon shape to make insertion easier, and some people use a few drops of sterile water to help insert it.
The swab or cloth is put into the woman’s vagina about an hour before the caesarean will begin.
The cloth is removed just before the caesarean begins, and carefully placed into a sterile container or bag.
When the baby is born, the cloth is wiped over their face (while avoiding the eyes), mouth and hands, so that the bacteria are transferred onto the baby’s skin.
So hopefully Wilson et al (2021)‘s comment about multi-site exposure now makes sense. They were wiping cloths just on the babies’ mouths. So they couldn’t be sure if seeding didn’t work well in their trial because it just doesn’t work, or because the cloths weren’t wiped on enough parts of the babies’ bodies.
Song et al (2021)
Another study at that time was carried out in China.
Song et al (2021) showed that vaginal seeding increased Lactobacillus in skin/oral/gut niches. However, the beneficial effects had faded by the time the babies were three months old, which suggests that the effects were transient.
One useful finding from this study was that breastfed babies retained the seeded microbes for longer than babies fed with artificial milk. This is just one of the studies which has shown that the area is complex, and that we need to be broader in our thinking.
Liu et al (2022)
The next key study was also carried out in China by Liu et al (2022), and included 117 babies who were randomised to seeding or not-seeding.
Its results were also disappointing to those who had had high hopes for microbiota seeding.
“For infants born through cesarean delivery, vaginal seeding has no significant impacts on the gut microbiota, growth, or allergy risks during the first 2 years of life.” (Liu et al 2022).
On a positive note, this study reported no adverse events, and no infections in any of the babies in the study. This was positive evidence of relative safety for some and, although much larger numbers would be needed to evaluate the potential chance of problems that are more unusual, this is one of several studies that have specifically shown that there were no adverse effects to vaginal seeding.
Mueller et al (2023)
In a large randomised controlled trial, Mueller et al (2023) showed that vaginal seeding increased maternal strains of a beneficial bacteria called Lactobacillus crispatus in infant stool (poo). However, the researchers suggested that repeated doses might be needed in order to achieve lasting effects. Like many of their colleagues, they were intrigued by their results and called for further research to explore the complexity of this area:
“In a double-blind, randomized, placebo-controlled trial, we determined the effect of vaginal seeding on the skin and stool microbiota of elective C-section born neonates and found that vaginal seeding increased mother-to-neonate microbiota transmission and caused compositional changes and a reduction in the skin and stool microbiota diversity. The reduction of neonatal skin and stool microbiota diversity when maternal vaginal microbiota is provided is intriguing and highlights the need of larger randomized studies to determine the ecological mechanisms and effects of vaginal seeding on clinical outcomes.” (Mueller et al 2023).
This study again supports the idea that vaginal seeding is safe. There were, as with the previous studies, zero cases of infection in the babies who participated.
Other ways to get good bacteria to babies
Vaginal seeding isn’t the only way that caesarean-born babies might get the good bacteria that they miss getting by not being born vaginally.
This was considered by Bogaert et al (2023), who looked at how microbes are passed from mothers to their babies and how the baby’s collection of microbes (called the “microbiota”) develops over the first 30 days of life.
Bogaert et al (2023) studied 120 mothers and their babies, collecting samples at different times from six parts of the mother’s body and four parts of the baby’s body. These different parts of the body are referred to as “niches,” meaning specific areas like the mouth, skin, gut (stomach and intestines), and breastmilk. Each of these niches can host different types of microbes.
On average, just over half (58.5%) of the microbes found in babies could be traced back to their mother’s body. Microbes from different parts of the mother’s body helped to seed the baby’s microbiota in several areas.
The researchers also found that certain things about the baby and their environment influenced which microbes grew where. In babies born by caesarean, fewer microbes from their mother’s gut made it into their own gut, compared to babies born vaginally. However, caesarean-born babies received more microbes from their mother’s breastmilk, which might help make up for some of the difference.
Overall, the study suggests that even when one pathway of microbial transfer is affected (like during a caesarean), other routes – such as breastfeeding – can help ensure babies still receive important microbes from their mothers.
Fecal transplants as an alternative
Although this blog post focuses on vaginal microbiome seeding, a number of researchers consider that fecal transplants may be a more effective alternative, so I want to mention this.
Korpela et al (2020) is a useful place to start if you re interested in finding out more.
Back to the safety debate
Some people (including myself) respond to those concerned about whether a baby might be infected with unwelcome bacteria by pointing out that the bacteria on the cloth is the same bacteria which the baby would have been born through if the caesarean section hadn’t taken place.
However, as is often the case, there are a few ‘buts’ here.
First, if a woman has an infection which may be potentially problematic for her baby, then this is definitely something that needs taking into account.
We do now have some evidence of safety from these studies, although I acknowledge that it would be even better if we had evidence of safety from larger studies as well.
However, a couple of colleagues whose opinion I respect have raised questions about whether, during the hour or so that the swab is in the vagina and then waiting in a sterile container until the baby is born, unwanted bacteria (such as GBS) may be able to outgrow the beneficial kinds of bacteria on the cloths used for seeding.
These are the same concerns that have been raised by doctors in some of the articles above, and they are valid.
However, it’s also true that we don’t have evidence of safety of many of the things that are done daily in maternity units.
In fact, we DO have evidence that some of these cause harm, and yet their practice continues.
So there is very much a double standard here.
Antibiotics
Another important point that needs to be considered relates to antibiotics.
That’s because (1) up to a third of labouring women get antibiotics in some areas, and (2) almost all women who are undergoing caesarean section are (because of the high chance of infection after caesarean section) routinely given antibiotics. So what effect does this have on their microbiome?
If we are going to target ways of helping babies acquire beneficial bacteria, then tackling the current overuse of antibiotics has to be a key issue.
This is what the authors of the 2017 review were saying. They called for more research, saying that we do not have evidence to support intervening in this way, and listed other things that we know can have a positive effect in this area. These things include avoiding caesarean section where not absolutely necessary, immediate skin-to-skin cuddling between mother and baby, breastfeeding for at least six months, and other factors such as good nutrition during pregnancy.
Other questions
These are not the only wider issues that we might benefit from considering.
Some midwives and birth workers raise questions about the way in which a vaginally born baby will also be born through fluid, which is a rather different environment for bacteria from a dry cloth. Does that make a difference? (We don’t know. No-one has researched this.)
Many people are concurrently asking what effect water birth and en caul birth (where the baby is born in its intact bag of waters) has on the microbiome, and we currently know very little about this. (There is a small discussion of this in my book Group B Strep Explained.) This is a side issue, because we’re talking about vaginally-born babies, but we know that the issues are complex, so it is useful to explore all angles.
A woman-centred analysis
In 2019, Amali Lokugamage and Sithira Pathberiya carefully navigated the difficult issues that have been raised by the rapid growth of interest in this area. They noted the increased calls from women wanting vaginal seeding to be a part of their caesarean alongside the way in which some professionals and several professional bodies are trying to prevent this from being an option because of the lack of evidence of the benefits or potential harms of vaginal seeding.
“In a global culture that is increasingly interested in ecological interventions, probiotics, ‘friendly bacteria’, microbiome preservation/restoration and long-term health, there is growing awareness of the idea of seeding the vaginal microbiome in the new born after caesarean section. It is postulated as a way of restoring helpful missing microbes and preventing long term non-communicable diseases of babies delivered by caesarean section. Currently, there is a deluge of evidence being published on the human microbiome, which can be challenging to digest and absorb by scientists, clinicians and patients. The specific evidence base around this technique is at its early stages.” (Lokugamage & Pathberiya 2019).
Lokugamage & Pathberiya (2019) point out that, “To unintentionally infer that the average human vagina is dangerous could provoke feminist consternation” (Lokugamage & Pathberiya 2019).
In addition, they offer useful guidelines for practice, based on careful, expert consideration of UK law.
Zhou et al (2023)
A randomised controlled trial published in 2023 showed more promising results than any of the previous studies (Zhou et al 2023).
It is noteworthy that this trial was also blinded, so that neither women nor their caregivers knew which babies had undergone seeding and which had been wiped with a sterile cloth.
“Here, we evaluated the effect of VMT [vaginal microbiome transfer] by exposing newborns to maternal vaginal fluids and assessing neurodevelopment, as well as the fecal microbiota and metabolome.
Sixty-eight cesarean-delivered infants were randomly assigned a VMT or saline gauze intervention immediately after delivery in a triple-blind manner.
Adverse events were not significantly different between the two groups.
Infant neurodevelopment, as measured by the Ages and Stages Questionnaire (ASQ-3) score at 6 months, was significantly higher with VMT than saline.
VMT significantly accelerated gut microbiota maturation and regulated levels of certain fecal metabolites and metabolic functions, including carbohydrate, energy, and amino acid metabolisms, within 42 days after birth.
Overall, VMT is likely safe and may partially normalize neurodevelopment and the fecal microbiome in cesarean-delivered infants.” (Zhou et al 2023).
Wang et al (2024)
A systematic review by Wang et al (2024) helped summarise the results of the studies that have been carried out in this area to date.
The researchers, “…summarize eight studies involving 558 cesarean section (CS)-born infants (274 exposed to vaginal seeding (VS), 284 not exposed) and 261 infants born vaginally to investigate the effect of VS on gut microbiome colonization and development in CS-born infants.” (Wang et al 2024).
They concluded that, “Current evidence indicates modest changes in the gut microbiome of CS-born infants following VS. However, further clinical studies are necessary to fully understand its impact on early-life health outcomes, particularly regarding potential microbiome alterations and associated health risks.” (Wang et al 2024).
Other key points from this review include that:
“Vaginal seeding facilitates partial restoration of key gut microbial communities in Cesarean-delivered infants [but] does not fully replicate natural microbial transfer at birth.” (Wang et al 2024).
This review also offers some evidence of safety.
None of the 512 infants in the included studies experienced any serious adverse events.
Hourigan, Mueller and Dominguez-Bello (2025)
The most recent (at the time of updating) paper on this topic was written by three medical researchers who have been involved in this debate for years.
Their paper summarises the research, much as I have done here, and they conclude by sharing that they, “…are excited to see evidence of partial restoration of the microbiome and improvement in neurodevelopment in offspring born by cesarean delivery receiving VS in RCTs and suggestions of metabolic health improvement from murine models.” (Hourigan et al 2025).
(By murine models, they mean studies carried out on mice.)
“We are optimistic we will see an improvement in cesarean delivery–associated inflammatory conditions from ongoing RCTs and that this simple, inexpensive intervention may become part of medical practice to improve the health of many.” (Hourigan et al 2025).
Again, they, “…urge mothers undergoing cesarean delivery to only consider VS in an approved clinical trial until there is robust evidence of efficacy and safety.” (Hourigan et al 2025).
While I understand their position and rationale here, I don’t suppose that this will be heeded.
Many women and families are well aware of the double standard which means that interventions preferred by women (such as water birth, holistic therapies and vaginal seeding) are consistently expected to meet a far higher threshold of efficacy and safety before their use is ‘allowed’ than those interventions preferred by the obstetric community.
Where do we go from here?
There is so much more we need to learn about this topic, but what is also really important here is the need to dance with the complexity of the conversation.
Because the question of whether vaginal seeding is beneficial and/or risk-laden isn’t a straightforward one.
Neither the proponents nor the detractors of this intervention currently have good evidence on which to base their claims or fears.
As a result, the information that women and families receive tends to be based on the beliefs of those who are talking about it.
And there is evidence that approaches such as breastfeeding and fecal transplants might be even more effective than vaginal seeding, so we need to make sure that we don’t become so focused on one possible intervention that we lose sight of the bigger picture.
It might feel tedious to always read the conclusion that more research is required, but in this case it really is the only thing that is going to help us move to a place where we know whether or not vaginal microbiome seeding is truly beneficial, or whether there are alternatives which will better solve this problem.
About the Author: Dr Sara Wickham is an author, speaker, and researcher specialising in pregnancy, birth and maternity care. Her work focuses on evidence-based, woman-centred information and informed decision-making, drawing on more than 30 years of midwifery knowledge and experience.
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