Vaginal Seeding After Cesarean: Is It Safe and Recommended for Your Baby?

As a doctor, I appreciate the indispensable, lifesaving contributions of western medicine – such as cesarean sections and antibiotics. They’re examples that, for many women, help avoid the largely preventable tragedy of maternal mortality, which according to the World Health Organization, remains unacceptably high in developing countries where access to procedures like cesareans and appropriate pharmaceuticals are too often limited, or entirely unavailable. And now, I do have a “but…” to add here (did you see it coming?), because as lifesaving and indispensable as some medical procedures can be, that doesn't mean they are not overused, and even when done appropriately, can have unintended consequences – sometimes wide-scale, long-term ones.

The Unintended Consequences Paradox

Antibiotic use and cesarean sections are prime examples of practices that while lifesaving when used appropriately, have both been widely overused in recent decades – and we're facing the consequences now. Antibiotic resistance as a result of antibiotic overprescribing has become one of the largest global public health problems we face, while overuse of cesarean section, which is associated with increased maternal infection, hemorrhage, and even death, has led even obstetric societies in the US to seek strategies for reducing what currently sits at a 34% national cesarean section rate. For the record, the World Health Organization (WHO) recommends an average of no more than 15% of births by cesarean section, for best maternal and neonatal outcomes.

One of the problems with cesareans (despite the very obvious fact that they are major surgery carrying risk of infection and requiring weeks of recovery…) is that babies are delivered abdominally, bypassing the bacteria-rich environment of the maternal birth canal. Whew, you might be thinking, well that sounds gross anyway. Actually, though, missing this exit ramp means that baby also misses skin and oral inoculation with important organisms, such as Lactobacillus and Bifidobacterium species, that lead to healthy immune system development, colonization of the baby’s own gut and skin flora that prevents infection, and that allows baby to also tolerate ingestion of mother’s milk. In fact, these organisms are sometimes referred to as ‘milk bacteria.” So why does this matter?

Babies, Birth, and Their Microbiome

Studies have demonstrated that babies born by cesarean have a greater lifetime risk of obesity, Type 1 diabetes, asthma and celiac disease, and it is thought that other diseases, including juvenile arthritis, inflammatory bowel disease, immune deficiencies, and perhaps additional conditions, are associated with this early perturbation of natural colonization of the infant with the maternal microbiome at the time of birth, early antibiotic exposure, or (yikes!) both. In other words, we've starting to uncover that vaginal birth possesses health advantages that cesareans miss out on.

Further, cesarean sections are accompanied by routine antibiotic administration to mom at the onset of the surgery to prevent infection – women undergoing cesarean section have a 5 to 20 times greater chance of getting an infection from birth compared with women who give birth vaginally. As research has been emerging on the importance of the human microbiome on our health, so too, has research emerged on the potentially deleterious impacts of early antibiotic exposure and cesarean section – which go hand-in-hand – on the long-term health of our children, including increased risk of obesity, alterations in the intestinal microbiome, increased risk of allergies, and more.

“But, Dr. Aviva, what if I don't (didn’t) have a choice but to birth by cesarean?”

Yeah, I hear you. It’s frustrating to hear this information and hard not to blame ourselves, because we live in a culture that blames the mom – as if we don’t do that enough to ourselves! The fact is, though, that sometimes cesareans are necessary. If you did birth by cesarean, out of necessity or not, learning about its effect on your baby's health isn't about judging the type of birth you had, mom judging, or mom shaming. It's about exploring possible solutions and letting go of judgment and guilt to focus on what really matters: how we can support our children's health and that of future generations, while also nurturing our own.

I know this probably sounds scary and, to be honest, slightly depressing, but I actually have some great news to share: researchers and microbiologists, such as Dr. Maria “Gloria” Dominguez-Bello, PhD, whom I had the pleasure of interviewing for my podcast, are exploring solutions to help increase the health outcomes for mothers and babies through a technique they named Vaginal Seeding, which can be used following a cesarean. I touched on the practice here in my article Protecting Baby’s Microbiome, and you can listen to the podcast on Natural MD Radio instead, here.

While research into the practice of vaginal seeding is new and in the early stages, it does hold great promise for the future health of our children. Curious about vaginal seeding and whether it is safe and recommended for you and your baby? Whether you're expecting yourself, or are a natural health practitioner wanting to help make recommendations on vaginal seeding for your clients, read on for what you need to know.

What is Vaginal Seeding?

Vaginal seeding, in very simple terms, means swabbing baby with vaginal fluids following a cesarean birth. These fluids are collected prior to birth: a sterile gauze is folded and inserted into the vagina and left to soak up beneficial vaginal microbiota for one hour.

Right at birth, the newborn is swabbed with the gauze, starting on the lips and the face and moving to the rest of the body for about fifteen seconds, before proceeding to standard newborn examination.

In a landmark but very small pilot study conducted by Dominguez-Bello et al, the microbiome of infants in whom vaginal seeding was done post C-section resembled that of vaginally delivered infants.

The procedure is quite simple, but there are important guidelines to follow to avoid potential health risks, which I'm covering below, and importantly, this is not yet recommended as a ‘self-help’ practice at this time. Further, while the pilot study on vaginal seeding did show partial restoration of the baby’s microbiome, we don’t yet know whether the partial restitution of these naturally occurring organisms will have a long-term impact on babies’ health – long-term studies are needed to determine this.

Are There Risks Associated With Vaginal Seeding?

The concept of vaginal seeding is gaining speed in the press, and many moms wonder: is the practice right for me, and more importantly, is it safe for my baby?

So far, as pointed out by the American College of Obstetricians and Gynecologists (ACOG), there's been a single pilot study in which only four infants underwent seeding, with no long-term follow up. What's more, the pilot study in question involved only women who were not carriers of group B streptococci, had no signs of bacterial vaginosis (BV), and had a vaginal pH of less than 4.5. In other words, we don't have solid data yet on the possible risks associated with vaginal seeding in the general public.

The question is, then: could the potential benefits of vaginal seeding still outweigh the possible risks despite the early stage of research?

The main concern with vaginal seeding is the spreading of undiagnosed infections in the mother (Group B Strep, chlamydia, gonorrhea, human papilloma virus, group A streptococci, and herpes simplex virus, among others), which could result in (serious!) neonatal infection otherwise avoided through cesarean.

In my opinion, concurred by Dr. Dominguez-Bello, the practice of vaginal seeding – with proper testing beforehand for infections in mom and supervision by a qualified birth practitioner such as a CNM, OB, or Family Physician – is likely quite safe and simply exposes baby to what she or he would have been exposed to any had the birth occurred vaginally. That being said, I agree with Dr. Dominguez-Bello and other physicians, midwives, and scientists who recommend waiting until more evidence is available before commonly practicing vaginal seeding, and all agree that pregnant women should be tested for GBS, HIV, Hepatitis B & C, and VDRL, and should be negative for genital HSV before proceeding with it. Several large studies are underway now.

Is Vaginal Seeding Ready for Primetime?

While vaginal seeding might not be ready for primetime just yet, it does reflect a really interesting and promising shift in our collective mindset regarding birth and the importance of the microbiome on children's health. Mothers are waking up to the fact that their children's health is suffering, and that it's time we do something about it. Widespread allergies, food intolerances, eczema, asthma, autoimmune diseases, obesity, diabetes… I've certainly seen the rise in health concerns in children in the last decades, both as a midwife, a herbalist, as a doctor, and as a mom and grandma.

So, until more research is completed and vaginal seeding becomes standard practice, what can we do to support a healthy microbiome right from the start? Here are some of my recommendations below.

What Else Can We Do to Support Baby's Health and Microbiome After Birth?

Avoid unnecessary cesareans
One of the best ways to support your baby's microbiome right from the start is to avoid unnecessary cesarean. This includes allowing for more time for labor to progress in the active phase, along with working with a midwife and doula (read more about why here) and of course, educating yourself about birth (start here, and here). Listen to my Natural MD Radio podcast episode with Neel Shah, MD, to learn more about unnecessary cesareans and how you can avoid one.

Consider vaginal seeding if appropriate, safe, and accessible
Work with your health care provider to arrange for vaginal seeding post-cesarean after thorough testing for possible hidden infections.

Practice attachment parenting
Starting at birth with skin-to-skin contact, continuing with breastfeeding ideally through the first year of life with no solids until at least 6 months or baby’s shows social readiness for food (reaches out for foods you’re eating and wants to put things in her/his mouth), and extending lots of cuddles with skin-to-skin and co-sleeping, encourages transfer of beneficial bacteria to baby and gets us closer to what nature intended.

Use a probiotic
While not all practitioners agree on the value of using probiotics in infants, preliminary research suggests that giving probiotics to babies born via cesarean could lead to health benefits later in life. While researchers haven't yet confirmed whether boosting a healthy baby's gut with beneficial bacteria could lead to lower incidence of disease, the hope is that supporting diversity of bacteria may help fight conditions like allergies and autoimmune diseases. Probiotics are a perfect example of a process that offers little risk and many possible health benefits, so I encourage moms to both take them during pregnancy and breastfeeding, and give them directly to baby.

Get dirty
As your child is able to sit up and play, encourage your child to “get dirty” in clean, natural outdoor spaces – while we have come to culturally equate ‘dirt’ with ‘unclean’ we’ve also missed out on important exposures to soil microbiota that also inoculate us and prime a health immune system. Playing outdoors, having pets, and being exposed to natural environments have all been associated with reduced rates of allergies, asthma, and eczema.

Take care of you, too!
A healthy mama is at the core of supporting the health of your baby's microbiome, so remember to also restore your own microbiome after a cesarean (or if you’ve had antibiotics in labor for GBS or any other reason) with probiotic rich foods such as fermented vegetables and yogurt, and give yourself time to recover, allowing for self-care and rest.

You’re a powerhouse mom for reading this article! Have questions? I’d love to hear your thoughts in the comments below.



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American College of Obstetricians and Gynecologists. Vaginal seeding. Committee Opinion No. 725. Obstet Gynecol 2017:130:e274–8.

Arrieta MC, Stiemsma LT, Dimitriu PA, Thorson L, Russell S, Yurist-Doutsch S, et al. Early infancy microbial and metabolic alterations affect risk of childhood asthma. Sci Transl Med 2015;7:307ra152.

Bokulich, N, Chung J, Battaglia,T et al. Antibiotics, birth mode, and diet shape microbiome
maturation during early life. Science and Translational Medicine. 15 June 2016. Vol 8 Issue 343 343ra82

Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med 2016;22:250–3.

Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A 2010;107:11971–5.

Gaffin JM, Kanchongkittiphon W, Phipatanakul W. Perinatal and early childhood environmental factors influencing allergic asthma immunopathogenesis. Int Immunopharmacol 2014;22:21–30.

Moya-Perez A, Luczynski, P, Borre Y et al. Intervention strategies for cesarean section–
induced alterations in the microbiota-gut-brain axis. Nutrition Reviews. Vol. 75(4):225–240 225

Mueller NT, ,Whyatt R, Hoepn L. Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. Int J Obes (Lond). 2015 April ; 39(4): 665–670.

Neu, J. Dysbiosis in the Neonatal Period: Role of Cesarean Section. Nestle Nutr Inst Workshop Ser. 2017;88:57-66.

Pannaraj PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, et al. Association between breast milk bacterial communities and establishment and development of the infant gut microbiome. JAMA Pediatr 2017;171:647–54.

Renz-Polster H, David MR, Buist AS, Vollmer WM, O’Connor EA, Frazier EA, et al. Caesarean section delivery and the risk of allergic disorders in childhood. Clin Exp Allergy 2005;35:1466–72.

Rutayisire E, Huang K, Liu Y, Tao F. The mode of delivery affects the diversity and colonization pattern of the gut microbiota during the first year of infants’ life: a systematic review. BMC Gastroenterol 2016;16:86,016-0498-0.

Salminen S, Gibson GR, McCartney AL, Isolauri E. Influence of mode of delivery on gut microbiota composition in seven year old children. Gut 2004;53:1388–9. ⇦

Sevelsted A, Stokholm J, Bonnelykke K, Bisgaard H. Cesarean section and chronic immune disorders. Pediatrics 2015;135:e92–8.

Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, Murray SE, et al. Innate immunity and asthma risk in Amish and Hutterite farm children. N Engl J Med 2016;375:411–21.

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Hi dear Aviva, thank you so so so much for this article. I already felt how important this is but did not dare to look in to it.. fearing to encounter what I had missed out on (as I was an almost 2 month early c-section baby myself) and knowing I could potentially never restore that.. I was a bit hesitant to read up on it. But your article is so clear and beautifully written with good research.. Thank you so much!! Will definitely pass this on in my work as a doula <3

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Yaffi Lvova, RDN

Thank you for this information. I had my three children by cesarean, first twins as an emergency c-section and then a repeat fro a single. I was all prepared for vaginal seeding, and m medical team was on board, but then group B strep got in the way! I do hope there is more research and this is able to be a benefit for the general population. I'm sharing to Baby Bloom Nutrition!