Microbiome seeding – what’s the evidence?

Microbiome seeding – also called vaginal seeding – is the practice of wiping a newborn baby’s mouth, face and/or skin with a cloth that has been held near its mother’s vagina during a caesarean.

The idea is that bacteria from the mother’s vagina will be transferred to the baby. This would happen naturally during a vaginal birth. But we know from research that babies who are born by caesarean are disadvantaged because they do not get these good bacteria. So it’s a way of trying to undo that particular downside of having a caesarean birth.

Early research in the form of a small pilot study looked positive.

“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).

But another small trial 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.

It’s clear we need more evidence.

In the meantime, vaginal seeding is hotly debated, as is often the case with interventions that benefit women and families and did not arise from within the obstetric paradigm.

So what do we know about this, and what are the issues?


The debate

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Since the practice of microbiome seeding began, most of the information about it has been passed between women and birth workers, often online. Conversely, a number of obstetric and health organisations have spoken out publicly against it.

But it’s interesting that, while some organisations have maintained a strong viewpoint, others are less dictatorial.

In 2022, for instance, the American College of Obstetricians and Gynecologists 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.” 

Microbiome seeding is also discouraged outside of a research study in at least one Australian state.

In the UK, a 2016 British Medical Journal podcast described vaginal seeding 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, but this was quietly removed a few month later. To the best of my knowledge, the RCOG doesn’t have a position paper that addresses it (but please tell me if I’m wrong and I will update this.) And women and birth workers tell me that whether or not it is supported varies according to the hospital and obstetrician.


The 2017 review

In 2017, a review of research on vaginal seeding written by Danish doctors and published in the British Journal of Obstetrics and Gynaecology. stated that the benefits of vaginal seeding “do not outweigh the risks”.

The alleged safety concerns attributed to the BJOG report need some analysis, however. Only one published study was included in the review, and this study only included four babies. It is impossible with such tiny numbers to draw any conclusions about the potential benefits or harms of any intervention.

One of the useful things that this study highlights is how difficult it can be to determine with confidence which bacteria are healthy and which are always, sometimes or occasionally harmful. We also think that many bacteria are ‘commensal’, which means that they neither harm nor help their human hosts, but our knowledge in this area is in its infancy and we would so often be far wiser to simply say that we do not know.


A small seeding rant

At this point in the debate, the things that were concerning me were manifold, and not least of these was the continued notion that we can make caesarean section almost as good as vaginal birth. Some people started using their support of seeding as a way to try to ‘sell’ elective caesareans, which seemed really inappropriate for so many reasons. I really do think that we need to make caesarean section as good as possible for the women and babies who truly need one, but we need to be very careful about thinking that we can improve on a process that we don’t even fully understand. There are deeper conversations to be had here, and they’re not going to happen in places where people can only write a sentence or two at a time. 

Happily that practice now seems to have stopped, perhaps because of the professional body statements.

But another disturbing element of this discussion are the heated debates about whether it is justifiable to expose the caesarean-born baby to the vaginal bacteria of his mother, with some proponents of this debate emphasising that this has not been proven to be safe.

Wednesday, Thursday, Friday, people!

It is indeed true that we don’t have evidence of safety.

But 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.

It’s not just about safety.

It’s about power.


Thinking it through

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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.

But, 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 is worth taking into account.

Second, a couple of colleagues whose opinion I respect have raised questions about whether, during the half hour or so that the swab might be in place, unwanted bacteria may be able to outgrow the beneficial kinds of bacteria on the cloths (usually swabs) used for seeding. We don’t know that either, which is just one reason why we need better research, and it’s a very fair question.

Another important point that needs to be considered is that (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?

And 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? Many people are already asking what effect waterbirth and en caul birth 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.)

So many questions.


A bit more on antibiotics

In fat, I want to pick up on the point about antibiotics.

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.

Which is, in a way, 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 6 months and other factors such as good nutrition during pregnancy.

The fact that the authors of this paper cite a lack of evidence as a reason to not recommend vaginal seeding is somewhat ironic, as – again – many of the practices that are used in maternity care are not based on good evidence. Let’s also not forget the vast quantities of antibiotics that are given to women and babies, often on a routine or population basis rather than in response to a particular concern.

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.


A woman centred analysis

In 2019, a really helpful paper was published. It looked at microbiome seeding and woman-centred care.

“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).

It was one of the most interesting, considered and balanced articles that I have read for a long time.

In it, Amali Lokugamage and Sithira Pathberiya carefully navigated the difficult issues that had been raised by the juxtaposition of the rapid growth in our knowledge of (and interest in) the microbiome coupled with, on the one hand, the call from women for vaginal seeding to be a part of their caesarean and, on the other, some professional’s and several professional bodies’ focus on trying to prevent this from being an option because of the lack of evidence of the benefits or potential harms of this.

The article is freely available so, as you can read it in full here, I won’t offer too much more of a summary. But it is well worth a read, not just because it does summarise the state of the evidence in a woman-centred way, but because the authors effectively highlight more of the complex but really important elements of this conversation.

For example, after detailing some of the published medical position statements on this topic, Lokugamage & Pathberiya (2019) also point out that the inference that vaginal bacteria could lead to unwanted infection is inappropriate given that, if the decision to have a caesarean is not made, this is how the baby would be born.

“To unintentionally infer that the average human vagina is dangerous could provoke feminist consternation” (Lokugamage & Pathberiya 2019).


There is much more to their article than this, though.

Lokugamage & Pathberiya (2019). also mention the need to discuss other elements of the evidence relating to caesarean section, antibiotic use (with a particular mention of group B strep prophylaxis) and the relationship between these and the microbiome.

In addition, they offer useful guidelines for practice, which are based on careful (and expert) consideration of UK law.


Where do we go from here?

There is, as Lokugamage & Pathberiya (2019) eloquently showed, much more we need to learn, 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.

It’s 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 truly know whether or not vaginal seeding is beneficial.


Lokugamage A & Pathberiya SDC (2019). The microbiome seeding debate – let’s frame it around women-centred care. Reproductive Health (2019) 16:91 https://doi.org/10.1186/s12978-019-0747-0

photo credit: sean dreilinger dark haired baby via photopin (license)

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