Clinical implications of recent study exploring ‘microbial restoration procedure’ for caesarean-born infants

microbial restoration procedureMode of delivery is known to influence the microbiota composition of newborns. Vaginally-born infants develop a microbiota that resembles the mother’s vaginal bacterial community, while those born by caesarean section (c-section) have a microbiota that more closely resembles adult skin. C-section delivery—increasingly prevalent in many countries—is associated with a greater risk of obesity, asthma, allergies, and immune disorders, but it’s not known whether microbiota differences account for the increased risk.

A group of researchers from the USA and Puerto Rico recently conducted a pilot study on a technique aimed at ‘restoring’ the microbiota of caesarean-born infants. They studied eighteen infant-mother pairs: seven of the babies were delivered vaginally, and eleven by scheduled c-section. Of the c-section babies, four underwent the “microbial restoration procedure” and the others did not. The procedure involved incubation of sterile gauze in the vagina of the mother prior to the c-section; within the first two minutes of birth, each baby’s mouth, face, and body were swabbed with the gauze. Researchers sampled the anal, oral, and skin microbiota of the babies at six time points within the first month. Results were reported in Nature Medicine.

No adverse events were observed in this small cohort of c-section infants. Researchers found the bacterial communities in the gut, mouth, and skin of newborns who received the intervention were enriched in vaginal bacteria that were underrepresented in the infants who hadn’t received the intervention. For the infants who underwent microbial restoration, the similarity of their microbiomes to those of vaginally delivered infants was high in the oral and skin samples and lower in the anal samples. Since all the women breastfed, diet was not considered a confounding factor.

Authors concluded that the complement of vaginal microbes was partially restored at birth in infants who received this intervention. They speculated that full restoration of the vaginal microbiota was not achieved because of the antibiotics that accompany c-section procedures, or because of suboptimal bacterial transfer from vagina to gauze and from gauze to baby. They also noted that this preliminary data is not enough to justify implementation of the microbial restoration procedure on a large scale.

In a published comment on the paper, Alexander Khoruts wrote that the technique, “although clever in its simplicity, does seem to require optimization.”

GMFH editors reached for comment Dr. Allan Walker of Harvard Medical School (USA), who was not involved in the study. Says Walker, “This is a very preliminary publication… [that has found] the ability to transiently demonstrate the presence of vaginal bacteria in c-section babies exposed to maternal vaginal microbiota. No long term affects are provided, there is no evidence whatsoever that this does in fact affect the incidence of either immune mediated or metabolic disease.”

Walker also notes that vaginal birth is complex, as infants born in this way are exposed to their mothers’ intestinal microbiota as well as their mothers’ vaginal microbiota. The gut microbial communities of the mothers were not tracked in the recent study.

A news article from Imperial College London (UK) reported that patient requests for this ‘vaginal seeding’ procedure are growing, despite expert opinion that the technique is not ready for widespread use. In a recent BMJ editorial, Dr. Aubrey Cunnington and colleagues warned against implementing the procedure, arguing the small risk of harm is not justified unless there is clear evidence of benefit to the infant. The authors highlighted the possible risk of infant infection from exposure to vaginal bacteria such as group B streptococcus—a particular concern in countries where pregnant women are not routinely screened.

Researcher Rob Knight, who has publicly discussed carrying out this technique surreptitiously with his own daughter after her c-section birth, defended vaginal seeding in a recent opinion article in The Scientist, noting “the challenge of evidence-based parenting”.

Indeed, in Cunnington’s BMJ article he and co-authors acknowledge the vaginal seeding procedure is transparent and parents may decide to carry it out themselves. In these cases, they say, “…we should respect their autonomy but ensure that they are fully informed about the theoretical risks.” They advise keeping lines of communication open: if an infant becomes unwell, health professionals should not hesitate to ask about vaginal seeding and parents should not hesitate to mention they performed it.

Walker says there is much work to do before justifying the procedure clinically. He says, “At this point the only thing that could be suggested [is] further studies in larger numbers over a long period of time and that this should not be at the moment recommended routinely for c-section delivered infants.”


Cunnington AJ, et al. (2016) “Vaginal seeding” of infants born by caesarean section. BMJ, 352:i227 doi:

Dominguez-Bello MG, et al. (2016) Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine 22, 250–253 doi: 10.1038/nm.4039

Khoruts A. (2016) First microbial encounters. Nature Medicine 22, 231–232 doi:10.1038/nm.4042

Kristina Campbell
Kristina Campbell
Science writer Kristina Campbell (M.Sc.), from British Columbia (Canada), specializes in communicating about the gut microbiota, digestive health, and nutrition. Author of the best selling Well-Fed Microbiome Cookbook, her freelance work has appeared in publications around the world. Kristina joined the Gut Microbiota for Health publishing team in 2014.  Find her on: GoogleTwitter