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Annalies Corse BMedSc, BHSc

On February 1st, 2016, a revolutionary study was published in the esteemed international medical journal, Nature Medicine. Published as a brief communication, the study “Partial restoration of the microbiota of caesarean-born infants via vaginal microbial transfer” was the first of its kind to attempt the physical transfer of maternal vaginal microbes to babies born via Caesarean sections.

At other times in history, the clinical outcomes of this study may have been inconsequential. However, medicine is at a tipping point regarding our view of human health and its place in the wider biological community. We are right in the centre of a shift in knowledge regarding the relationship of human health and the microbial populations existing in, on and around all living organisms. The term for the collective populations of bacteria, viruses, fungi, yeasts, parasites, helminths (worms) residing in and on the human body is known as the micro biome. For more than a decade, evidence for the mastery of the micro biome over human health has been building. Some conditions related to an altered human micro biome includes:

  • Obesity
  • Psychiatric pathologies
  • Allergy and atopy
  • Diabetes
  • Autoimmunity and immune disorders

With time and more research, it’s not unreasonable to believe many other conditions will be added to this growing list. We already know the micro biome is largely responsible for fundamental aspects of digestion, immunity and the biosynthesis of essential amino acids and specific micronutrients including the vitamin K group, vitamin B12 and B3.  Like vital organs such as the brain, heart or liver, it’s likely the composition and functionality of the human micro biome will be quantified and elucidated further by medical science, cementing the need for human health to revisit and re-establish our evolutionary biological relationship with microbes. Please see this MINDD article on the micro biome for further insights into the importance of your micro biome to your health.

It is well known that the mode of delivery impacts the micro biome of the infant. Babies born via caesarean section are colonised with skin and oral microbes, and often with bacteria from the surrounding hospital environment. Many studies show that the difference in micro biomes between vaginally delivered and C-section babies can persist to 12 months of age.

Important details regarding the study:

  • It was a pilot study. Though small, a pilot study examines the feasibility of conducting larger scale studies of the same kind.
  • 18 babies and their mothers were sampled; 7 were vaginal deliveries and 11 were scheduled C-section deliveries.
  • 4 of the 11 C-section infants received maternal vaginal fluids at birth, via a swabbing procedure designed by the research team.
  • No adverse effects were observed in the 4 infants who underwent this procedure.
  • Results revealed these 4 infants to have similar micro biomes to vaginally born infants in the study.
  • Full micro biome restoration did not take place. This is likely due to the procedure not being exactly replicable to a vaginal delivery, or the use of antibiotics after C-section.
  • Gut microbes were not tracked in this study. Vaginally delivered infants are also exposed to maternal gut microbes.

As with any procedure involving infants or clinical practice different to the norm, medicine offers counter points and cautions. It is a reality that micro birthing may not be a safe practice for an infant 100% of the time. The biggest risk to a new baby with micro birthing post C-section is the transference of maternal pathogens, resulting in infection for the baby. Mothers MUST be tested for negative for the following infectious microorganisms:

  • Human Immunodeficiency Virus (HIV)
  • Chlamydia trachomatis (opthalmia neonatorum)
  • Group B Streptococcus (most common cause of neonatal sepsis). Approximately 20-30% of pregnant women are positive for Group B. Streptococcus. Positive.
  • Herpes Simplex Virus (opthalmia neonatorum)
  • Neisseria gonorrhoea

In Australia, some women are screened for these infections, providing she accessed and attended ALL antenatal check-up. Swabs for identification of these microorganisms usually occurs at the 36 Week check-up

Clinically, the following observations must be established for the procedure to take place:

  • A vaginal pH level <4.5 1-2 hours before the procedure (higher vaginal pH levels often indicate infection)
  • Negative for signs and symptoms of vaginosis
  • Negative for signs and symptoms of viral infections

What to do for a C-section baby where this procedure may not be possible?

  • Encourage and support breast-feeding, with extended breastfeeding beyond 12 months of age being ideal.
  • Unnecessary prescription of antibiotics in the prenatal, intrapartum and postnatal periods
  • Establishment of healthy maternal and paternal micro biomes pre-pregnancy (ideally in the pre-conception phase). There is mounting evidence that the uterine environment is not sterile, and maternal microbes can cross the placenta during pregnancy. Foetuses continually consume amniotic fluid orally, which is one potential source of their inoculation with maternal microbes.
  • Prescription and administration of probiotic microbes with the guidance of a health professional. Neonates and young infants have markedly different species of microbes in the gut as compared to adults, and the probiotic prescribed for the infant must reflect this
  • In arms infancy, baby-wearing, skin to skin contact are all sources of maternal microbe transfer, in addition to breast-feeding

There are a number of clinical considerations that may prevent the microbial seeding of C-section infants from occurring:

  • Maternal infections. Researchers who are ‘pro-seeding’ agree that vaginal seeding should not be performed if a mother tests positive for harmful vaginal pathogens
  • Willingness and knowledge of the obstetric and midwifery care team
  • Parents use of contaminated materials due to lack of formal procedure for this practice.
  • Minor injury to an infant would be rare and unintentional, however this point still requires careful consideration

Tip: Whilst vaginally delivered infants develop a microbial community in semblance with their mothers vaginal micro biome, this does not negate the need for mothers (and fathers) to ensure their own micro biome is as healthy as possible during the pre-conception phase. This ensures that a vaginally born infant (whose chances of receiving maternal for a are higher) receives more beneficial microbes in good numbers, and less opportunistic or pathogenic microbes. This MINDD article on gut health is a good introduction to this topic.

What may the future hold for micro birthing?

  • Medical professionals look for evidence when viewing treatments and interventions. This study reports on preliminary findings.
  • Evidence confirming that maternal vaginal microbes persist in C-section babies post infancy and into early childhood will be important to test for. Hopefully, more research groups will examine this.
  • Ideally, long-term effects should be tested, looking at C-section babies who receive vaginal and gut microbes, and following their health long-term. Fewer incidences of allergy, atopy, obesity, autoimmunity, etc. in these groups would be strong evidence that the procedures should become standard practice. Hopefully such studies will come to fruition.

Whilst micro birthing is not standard practice in any hospital in Australia or overseas, this does not override the sovereignty mothers have over attempting the practice for themselves. Additionally, discussion on ‘evidence-based parenting’ has been raised by members of the research team, who advocate for the procedure despite the lack of evidence to support its worth.

Theoretically, the procedure is not 100% risk free. It should not be performed if you have not been screened for STI’s or other localised vaginal infections. If you do go ahead and perform vaginal seeding with your baby, you must tell your baby’s healthcare provider.  This is especially the case if your baby becomes unwell or shows any signs of developing an infection, even after you leave hospital. C-sections do change the first microbial encounters of an infant, in ways medical science is beginning to appreciate. The simplicity of the procedure and what it offers babies delivered via C-section is incredibly promising. Ensure that like all matters regarding the health of your baby; uphold the lines of communication between you and your baby’s health care team.


  1. Dominguez-Bello, M. et al. (2016). Partial Restoration of the micro biota of caesarean-born infants via vaginal microbial transfer. Nature Medicine. 22, 250-253. Available at:
  2. Khoruts, A. (2016). First Microbial Encounters. 22, 231-232. Available at:
  3. Knight, R. and Gilbert, J. (2016) Opinion: A Mother’s Microbes. On Vaginal Seeding and the Challenge of Evidence Based Parenting. The Scientist. Available–A-Mother-s-Microbes/
  4. Thavagnanam, S. et al. (2007), A meta-analysis of the association between Caesarean section and childhood asthma. Clinical and Experimental Allergy. 38 (4): 629-633. Available at:;jsessionid=F04E2EAC29EA76D311E05B07D301E4F5.f03t03
  5. Dominguez-Bello, M. et al. (2010) Delivery mode shapes the acquisition and structure of the initial micro biota across multiple body habitats in humans. Proceedings of the National Academy of Science. 107: 26 (11971-11975). Available at:

Tags: Micro biome, Micro biota, Vaginal seeding, Micro birthing, Vaginal Delivery, Caesarean Section. Microbial Restoration.