“Oral Administration of Maternal Vaginal Microbes at Birth to Restore Gut Microbiome Development in Infants Born by Caesarean Section: A Pilot Randomised Placebo-controlled Trial” (2021), by Brooke C. Wilson, Éadaoin M. Butler, Celia P. Grigg et al.

By: Kelly Roberts

Published: 2025-06-03

In 2021, Brooke Wilson and colleagues published “Oral Administration of Maternal Vaginal Microbes at Birth to Restore Gut Microbiome Development in Infants Born by Caesarean Section: A Pilot Randomised Placebo-controlled Trial,” hereafter “Oral Administration,” in eBiomedicine. Previous researchers had established that neonates born via caesarean section, or c-section, the surgical delivery of an infant through an incision made in the mother’s abdomen, have different gut microbiomes from neonates delivered vaginally. They further hypothesized that such a difference may be because infants born by c-section do not receive exposure to their mother’s vaginal microbiome during delivery. Thus, Wilson and colleagues investigate whether oral vaginal seeding, or the process of transferring vaginal microbes to a newborn’s mouth, can restore the gut microbiome of newborns born by c-section. “Oral Administration” was one of the first articles to demonstrate that oral vaginal seeding is ineffective in altering the gut microbiome of newborns delivered by c-section and prompted other researchers to explore alternative research routes to enhancing the gut microbiome of newborns born by c-section.

Background

At the time of the article’s publication in 2021, the authors of “Oral Administration” all conducted research on bacterial microorganisms and maternal and neonatal health at various institutions worldwide. Wilson, the first author of the paper, researched the human gut microbiome at the Liggins Institute at the University of Auckland in Auckland, New Zealand. The Liggins Institute is a research center for fetal and child health. The corresponding author, Wayne S. Cutflield, was a professor and researcher who studied the role of the microbiome in health and disease at the Liggins Institute. The other authors were also affiliated with the Liggins Institute and other research centers in Auckland, as well as various institutions worldwide in Sweden, China, Italy, the United States, and the United Kingdom.

“Oral Administration” uses several technical terms associated with the body’s collection of microorganisms. They use the term microbiome to refer to the collection of microorganisms, including bacteria, fungi, and viruses, that live on and within a person's body, as determined by the presence of specific gene sequences that uniquely identify those organisms. The researchers also use the term microbiota to refer to collections of microbes that they transfer from the mother to the infant. Different areas of the body may have different microorganisms present, and researchers refer to the collection of microorganisms in one specific area of the human body as that area’s microbiome. Different microbiomes are present in various localized regions, and researchers classify them as such, including the gut, skin, respiratory, and vaginal microbiomes. The human gut microbiome stimulates the immune system, which protects a person against harmful microorganisms like viruses or bacteria that cause infection. The development of the immune system begins in utero, and birth method can affect its development.

Previous research has demonstrated that there is an association between c-section delivery and chronic inflammatory conditions, and many researchers believe that association may be gut-microbiome-mediated. Pregnant women typically deliver their child vaginally or, alternatively, via c-section. Newborns delivered vaginally receive exposure to the mother’s microbiome in the vagina, or the canal connecting the uterus, where an infant develops, and the outside of the body. Unlike those delivered vaginally, neonates delivered via c-section develop their microbiome from microbes on the mother’s skin and in the environment, rather than from the mother’s vaginal microbiome. However, the skin-derived microbiome leads to the development of a microbiome and subsequently an immune system that does not function as well as one that develops from vaginal microbes. Notably, individuals delivered by c-section are at greater risk for obesity, immune deficiencies, inflammatory bowel syndrome, and connective tissue disorders. In 2021, over thirty-two percent of live births in the United States were via c-section, meaning that nearly one-third of newborns born in the United States are at risk of decreased immune and metabolic function.

Due to the differences in microbiomes of infants delivered by c-section compared to those born vaginally, researchers have investigated whether vaginal seeding is effective at restoring the gut microbiome composition. Researchers can perform vaginal seeding dermally, through the skin, or orally, through the mouth. In 2016, Maria Dominguez-Bello, a researcher who studies bacteria and microorganisms in the United States, published one of the first studies of dermal vaginal seeding. In that article, the researchers investigated whether applying a mother’s vaginal microbiota to her newborn’s skin after a c-section birth would enhance the newborn’s microbiome and determined that the dermal vaginal seeding helped newborns delivered by c-section to develop skin and oral microbiomes that were more similar to the microbiomes of newborns delivered vaginally. Later, in 2021, another research team studied the long-term effects of vaginal seeding and obtained similar results. Due to the previous findings, Wilson and colleagues explored the effectiveness of oral vaginal seeding in “Oral Administration.”

Article Contents

“Oral Administration” contains four sections. In the first section, “Introduction,” the authors explain that newborns born by c-section tend to have fewer bacterial strains in their gut microbiomes and decreased immune function due to lack of exposure to their mother’s vaginal microbiome. Thus, they state that they chose to focus their research on determining whether oral vaginal seeding could restore the gut microbiome in those newborns. Next, in “Methods,” the authors discuss that they recruited pregnant women and divided those women into groups based on whether they planned to deliver vaginally or via c-section. Then, they describe that they randomly split the neonates delivered by c-section into two groups and administered a placebo solution to one group and a solution of the mother’s vaginal microbiota to the other group. In the third section, “Results,” the authors explain that they took stool samples from the neonates delivered by c-section to analyze their gut microbiome compositions, and those findings demonstrated that vaginal seeding does not restore the gut microbiome of infants delivered by c-section. In the fourth and final section, “Discussion,” the authors explain that confounding variables, such as in utero exposure to antibiotics or the natural competition between gut bacterial strains, may complicate their study’s findings and also suggest that alternative therapies like probiotics or exposing neonates to the mother’s gut microbiome through fecal matter may have more success than vaginal seeding.

In “Introduction,” the authors explain that newborns born by c-section have different gut microbiome compositions than newborns born vaginally and propose that oral vaginal seeding may restore the gut microbiome of those neonates. Wilson and colleagues explain that previous researchers identified that neonates delivered via c-section had a reduced level of healthy gut bacteria and an increased susceptibility to metabolic and immune disorders than those delivered vaginally. Although previous researchers have not found evidence of a direct link between the two, the authors explain that there is an association between those differences in immune susceptibility and microbiome content, and as a result, researchers have been attempting to enhance the microbiomes of children delivered by c-section. The authors cite the 2016 study led by Dominguez-Bello and colleagues to support their hypothesis that oral vaginal seeding could lead to increased neonatal gut microbiome diversity in neonates born via c-section.

In “Methods,” Wilson and colleagues explain that they conducted a single-blinded, randomized, placebo-controlled study with neonates delivered via c-section to determine the effectiveness of oral vaginal seeding and compared those results to neonates delivered vaginally. First, the authors explain that they recruited pregnant women over eighteen years of age from three hospitals in Auckland, New Zealand, as participants. Wilson and colleagues outline that they excluded women who tested positive for pathogens, delivered preterm, had an emergency c-section, or birthed neonates who exhibited congenital abnormalities. Of those recruited to the study, only forty-seven were eligible to participate. Then, they state that they separated those eligible pregnant women into two groups, those planning on giving birth via c-section and those planning on giving birth vaginally, in order to compare the gut microbiomes of neonates from each delivery method and determine if oral vaginal seeding was effective. The research team reports that there were twenty-two women in the vaginal birth group and twenty-five women in the c-section group. The authors detail that they randomly assigned the neonates delivered by c-section to a treatment group and the parents of those neonates did not know which treatment their child received. For the newborns from the c-section group, they explain that they administered a placebo, or treatment with no therapeutic value, to thirteen neonates and the vaginal seeding treatment to the other twelve neonates to compare their results with the group receiving the treatment. Placebos serve as a control group and help researchers determine whether a treatment has any therapeutic effect.

After recruiting pregnant women to the study, the authors explain that they collected vaginal microbiota from women in the c-section group prior to delivery. In order to collect the vaginal microbiota, they detail that, prior to the c-section procedure, they inserted gauze into the vagina of those women for thirty minutes and removed the gauze before the surgery. After collection, the authors describe that they cut the gauze in half and rinsed one half of the gauze with five milliliters of sterile water to create a vaginal microbiota solution. They note that they used three milliliters of the vaginal microbiota solution for the vaginal seeding procedure and sent the remaining two milliliters of solution to the lab for analysis.

Following collection of the vaginal microbes of the mothers in the c-section group and subsequent newborn delivery, Wilson and her colleagues state that they administered the vaginal microbiota solution to the newborns in the vaginal seeding group and sterile water to the newborns in the placebo group. In order to deliver the required fluid, the authors report that they placed the neonate into a reclined position. Then, they explain that they administered three milliliters of the vaginal microbiota solution or water through a syringe into each newborn’s mouth, activating their swallowing reflex. The researchers describe that they gave the neonates the fluids of their assigned treatment group within twenty-four hours after birth and then monitored them for two hours.

At the end of “Methods,” Wilson and colleagues detail that they used genetic sequencing to analyze the mother’s vaginal microbiome and the neonate’s stool to determine if the newborns who received the microbiota solution had more diverse microbiomes that those who did not. Genetic sequencing allows the researchers to determine which strains of bacteria are present in the mother’s vaginal microbiome and the neonate’s gut microbiome. The authors explain that the parents collected fecal samples from the infants born by c-section and those born vaginally within the first twenty-four hours of life, then again at one month and three months of age. They note that they obtained the sample of vaginal microbiota prior to c-section delivery.

In “Results,” the authors explain that there were no significant differences between stool samples and gut microbiomes of infants born by c-section regardless of whether the researchers gave them the vaginal microbiota solution or the placebo solution. They mention that when they compared the group of newborns born vaginally to those born by c-section, their results matched those of previous studies, which had found that newborns born vaginally had higher levels of the bacteria genus Bacteroides. They explain that having higher levels of Bacteroides contributes to metabolic function as newborns born vaginally typically have better metabolic function due to the contributions of Bacteroides to various metabolic and microbial pathways. They note that twenty microbial pathways were more abundant in vaginally born infants than those delivered via c-section at one and three months of age. However, the authors also describe that they measured neonatal body composition, such as measurements of the length and weight of the head and abdomen, and found no significant differences in body composition between neonates who received the vaginal seeding procedure and those who did not. The authors conclude the results section by noting that no adverse medical effects occurred in the neonates as a result of the study.

In the fourth section, “Discussion,” the authors explain that oral vaginal seeding is a largely untested procedure and not a viable method of restoring the gut microbiome in infants born by c-section. They reiterate that their study demonstrated that the oral administration of a solution of maternal vaginal microbiota suspended in water did not alter the structure or function of the gut microbiome in infants. The research team also states that their findings extend the results found by Dominguez-Bello and colleagues’ 2016 study, which demonstrated that dermal vaginal seeding did not completely restore the microbiomes of neonates delivered by c-section.

Although their research study demonstrated that vaginal seeding is not effective at restoring the microbiomes of neonates delivered by c-section, the research team notes that confounding variables, such as the administration of antibiotics to the pregnant mother prior to delivery, may have reduced the effectiveness of the maternal microbiota during the vaginal seeding process. They explain that all pregnant women in the c-section group received intrapartum antibiotic prophylaxis, or IAP, which is an antibiotic treatment administered preoperatively to the mother when the neonate is in utero to reduce neonatal infections and disease. According to Wilson and colleagues, the administration of IAP prior to c-section delivery exposes the newborn to antibiotics during a critical period of microbiome acquisition, which likely reduces the successful colonization of maternal microbes in the gut microbiota. Thus, they note that IAP could affect the ability of maternal microbes to seed the neonate’s gut microbiome.

The authors also discuss that another confounding variable may be that newborns born by c-section have competition between bacterial strains in their gut microbiome that could be reducing the abundance of healthy Bacteroides. They explain that compared to newborns born vaginally, newborns born by c-section have increased levels of the bacterial strains Haemophilus and Streptococcus, which researchers have found to negatively correlate with the abundance of Bacteroides. The authors suggest that the negative correlation could be due to competition between the strains, which occurs when two or more bacterial strains compete for the same resources. They advise future researchers to examine the interactions between those bacterial strains to determine if that competition affects neonatal microbiome content.

Then, Wilson and colleagues suggest potential alternative treatments to restore the microbiome of neonates delivered via c-section, beginning with their hypothesis that exposing infants born by c-section to their mother’s fecal microbiome may be more successful than vaginal seeding. They explain that Bacteroides are more common in the gut microbiome than the vaginal microbiome, thus, they propose that in order to restore Bacteroides content in neonates, it may be more beneficial to expose newborns to the maternal fecal microbiome. To support their idea, the authors reference a study published in 2020 by researchers in Finland who found that oral administration of breast milk containing small amounts of maternal fecal microbiota improved the abundance of Bacteroides in the neonatal gut microbiome during the first four weeks of life. However, they note that in that study, the prevalence of Bacteroides declined by twelve weeks of age, suggesting that the process has limitations and that researchers should study it further.

Wilson and colleagues conclude “Oral Administration” by suggesting that administering standardized probiotic formulation to infants following delivery may be a successful alternative therapy to restore the neonate’s microbiome. Probiotics are formulations of live microorganisms that can help balance the gut microbiota. According to the research team, probiotic therapy may aid in the restoration of gut microbiota in c-section newborns. They cite a 2018 study performed by researchers from various countries in Europe that examined the effects of probiotic therapy on 422 neonates. According the to the authors, that study demonstrated that the administration of probiotics had a strong overall impact on the microbiota composition. Finally, they mention that future research should focus on other interventions that can improve restoration and claim that once scientists better understand the development of the neonatal microbiome, other methods of restoration may become clear.

Impacts

According to Google Scholar, as of 2025, researchers have cited “Oral Administration” 104 times and other scholars have built on the work. For example, in 2022, researchers from Finland and the Netherlands published an article titled “Infant Gut Microbiota Restoration: State of the Art.” In that article, the researchers address Wilson and colleagues' suggestions about probiotic therapy, fecal microbial transplantation, and IAP antibiotics and conclude that future research should analyze and pursue those alternative treatments. Another article published in 2023 cited “Oral Administration” in its analysis of mother-to-infant microbial transmission. Those researchers argued that maternal fecal microbiota transplantation completely restored the gut microbiome of neonates delivered by c-section. They also found that the microbiota found in the mother’s breastmilk led to greater colonization of health-promoting bacteria in neonates delivered by c-section compared to those delivered vaginally and attribute that to the reduced diversity in the gut microbiome associated with neonates delivered by c-section. Thus, “Oral Administration” prompted further research on treatments to rehabilitate the gut microbiome of neonates delivered by c-section.

“Oral Administration” was one of the first articles analyzing the effectiveness of oral vaginal seeding. Although the authors conclude that oral vaginal seeding is ineffective at restoring the microbiomes of neonates delivered by c-section, the article suggests alternative therapies, such as probiotic treatment and maternal fecal transplantation, that other researchers have concluded demonstrate effective results.

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