In recent years, caesarean births have become increasingly common in Australia. In fact, according to the Australian Institute of Health and Welfare, more than one in three babies are now born via caesarean section. While C-sections are often medically necessary and lifesaving, research suggests they may also carry some long-term health considerations for babies. Studies have linked caesarean birth with a higher risk of conditions like obesity, allergies, and even certain neurodevelopmental issues—possibly because these babies miss out on early exposure to beneficial bacteria during vaginal birth.

So, is there a way to mimic that microbial exposure for babies born via C-section? That’s where the practice of vaginal seeding comes in.

What is vaginal seeding?

During a vaginal birth, babies are naturally exposed to the mother's microbiome as they pass through the birth canal. This contact helps colonise the baby’s skin, mouth, and gut with good bacteria that play an important role in shaping the immune system, digestion, and even brain development.

Babies born via C-section, however, are typically exposed to skin and environmental microbes instead, which may impact how their microbiome develops.

Vaginal seeding is a technique that aims to replicate the microbial exposure of vaginal birth. It involves placing a sterile gauze in the mother’s vagina before surgery. After the baby is delivered, the gauze is used to gently swab the newborn’s mouth, face, and body—essentially transferring the maternal bacteria to help kickstart the baby’s microbiome.

Does vaginal seeding actually work?

Studies suggest that vaginal seeding can shift a baby’s microbiome to more closely resemble that of a vaginally born baby. In a 2023 randomised controlled trial published in Cell Host & Microbe, researchers found that vaginal seeding successfully transferred maternal bacteria to the baby.

Even more intriguing, a 2024 study using a mouse model found that mice exposed to stool from vaginally seeded babies had lower levels of intra-abdominal fat—a type linked with metabolic concerns later in life. While these findings don’t yet confirm health outcomes in humans, they point to the potential long-term benefits of restoring microbial exposure.

What about other health outcomes?

Although the early results are promising, there’s still limited data on whether vaginal seeding can reduce rates of asthma, allergies, or obesity. One small clinical trial didn’t find differences in allergy or BMI outcomes between babies who received vaginal seeding and those who didn’t. However, several large-scale studies are currently underway to explore these outcomes more thoroughly.

Is vaginal seeding safe?

So far, clinical studies suggest that vaginal seeding is safe when carried out in a carefully controlled, medical environment. However, experts remain cautious. The main concern is the potential transmission of infections like Group B Streptococcus (GBS), herpes simplex virus (HSV), chlamydia, or HIV—conditions that can be very serious for newborns.

Because of these risks, vaginal seeding is not currently recommended for routine use in Australia. The Royal Australian and New Zealand College of Obstetricians and Gynaecologists (RANZCOG) has not issued specific guidelines, but international organisations such as the American College of Obstetricians and Gynecologists (ACOG) advise against performing vaginal seeding outside of a research setting.

Researchers recommend that families interested in vaginal seeding only do so under the guidance of a healthcare provider and as part of a clinical trial. DIY or unsupervised approaches are strongly discouraged due to infection risks.

What else are researchers exploring?

As science around the microbiome evolves, researchers are looking into other ways to support a healthy gut microbiome in C-section babies. These include:

In the future, scientists hope to create targeted microbial therapies—like a “starter kit” for the gut—to support newborns who miss out on vaginal microbial exposure.

In the meantime, there are well-established ways to support your baby’s microbiome:

The Bottom Line on Vaginal Seeding

Vaginal seeding is a fascinating concept that may help babies born via C-section get some of the early microbial exposure that vaginally born babies receive. While current evidence suggests it could support early immune and metabolic development, more research is needed before it can be safely recommended as standard practice.

For now, experts advise that vaginal seeding only be done within a clinical trial or research setting. As studies continue, this simple technique could one day become a powerful tool for supporting the long-term health of C-section babies.

 

***

REFERENCES

  • Air Pollution and Its Effects on Human Health: Advances in Air Pollution Research, International Journal of Environmental Research and Public Health, November 2020
  • Bacterial Metabolism of Host-Derived Nutrients Shapes the Gut Microbiota, Proceedings of the National Academy of Sciences, August 2010
  • Breaking the Silence: Antibiotic-Induced Changes to the Microbiota and Their Impact on Health, Cell, June 2014
  • Disruptions in the Gut Microbiome Contribute to Increased Susceptibility to Infection, mBio, May 2023
  • Effects of Early-Life Antibiotic Use on the Developing Microbiome, Cell Host & Microbe, May 2023
  • Functional Foods and Gut Microbiota: A Review on the Potential of Prebiotics and Probiotics, Microbial Ecology in Health and Disease, February 2024
  • Gut Microbiota Composition and Risk Factors in Pregnancy, American Journal of Obstetrics & Gynecology Maternal-Fetal Medicine, October 2022
  • Infant Gut Microbiota Development and Its Implications for Health, JAMA Pediatrics, February 2024
  • The Role of the Gut Microbiota in Metabolism, Cell, August 2020
  • The Vaginal Microbiota of Pregnant Women and Its Impact on the Newborn, Cell, November 2020
  • The Vaginal Microbiome and Preterm Birth, Cell Reports Medicine, September 2021
  • Mode of birth: Australia's mothers and babies, Australian Institute of Health and Welfare, accessed April 2025

View more posts tagged, health

Have questions about a Happiest Baby product? Our consultants would be happy to help! Submit your questions here.

Disclaimer: The information on our site is NOT medical advice for any specific person or condition. It is only meant as general information. If you have any medical questions and concerns about your child or yourself, please contact your health provider. Breastmilk is the best source of nutrition for babies. It is important that, in preparation for and during breastfeeding, mothers eat a healthy, balanced diet. Combined breast- and bottle-feeding in the first weeks of life may reduce the supply of a mother's breastmilk and reversing the decision not to breastfeed is difficult. If you do decide to use infant formula, you should follow instructions carefully.