A new study from the University of British Columbia challenges the long-held belief that a baby’s gut microbiome is primarily shaped by the mother’s vaginal microbiome, while also providing fresh insight into the variables that influence its development.

When babies are born, their intestines are a nearly sterile environment. But that soon changes as a baby’s digestive tract is home to trillions of microbial cells during their early development. The gut microbiome is an important part of overall health and changes early in life are associated with negative health outcomes later in life, including asthma and obesity.
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It has long been hypothesized that the mode of birth and exposure of newborns to the mother’s vaginal microbiome during labor greatly affects the development of the child’s gut microbiome. This has given rise to practices such as vaginal insemination, which aims to expose babies born via C-section to the microbiome of the mother’s vagina.
A new study published this week in Frontiers in Cellular and Infection Microbiology examined this interaction. The findings showed that, contrary to popular belief, the composition of a mother’s vaginal microbiome does not significantly affect the microbiome development of her baby.
“We show that the composition of the maternal vaginal microbiome does not substantially influence the infant’s fecal microbiome early in life,” said Dr. Deborah Money said. “Exposure to the maternal vaginal microbiota during vaginal birth establishes the infant’s fecal microbiome, suggesting that there is no justification for vaginal insemination as a practice.”
Researchers say that many other factors are more effective in shaping a baby’s gut microbiome.
“Through this study and other follow-up work, we were able to show that the transfer of vaginal bacteria to the infant gut is limited, and that the maternal vaginal microbiome is not a major contributor to the bacterial community that develops in the gut after birth,” said Scott Dos Santos, Ph.D. of the University of Saskatchewan. candidate and first author of the study. “In contrast, exposure to other maternal sources such as breast milk and the environment play a much larger role.”
The study is part of the Maternal Microbiome Legacy Project, a collaboration between researchers at UBC, the University of Saskatchewan and the Women’s Health Research Institute at the BC Women’s Hospital and Health Centre. The project recruited more than 600 Canadian women who planned to deliver vaginally and via C-section, making it one of the largest mother-infant cohort studies to date.
Participants were recruited from three hospitals across BC – BC Women’s Hospital, Surrey Memorial Hospital and University Hospital of Northern BC. Maternal vaginal swabs were collected before delivery, and stool samples from infants were collected within 72 hours of birth, as well as at 10 days and three months after birth.
The scientists found that regardless of birth mode and exposure to the maternal microbiome, the composition of the mother’s vaginal microbiome did not predict the composition of the baby’s stool microbiome 10 days or three months after birth.
One of the study’s co-authors, UBC PhD student Zahra Pakzad, is conducting further work to analyze the breast milk microbiome and better understand its relationship with the gut microbiome of infants.
“We had the opportunity to interact with hundreds of our participants on their postpartum experiences with breastfeeding and formula feeding, which inspired us to understand the breast milk microbiome,” Pakzad said. “If we find that this microbiome is an important contributor to infant gut microbiome development, it could help in the development of better infant probiotics and formulas.”
The scientists found statistically significant differences in microbiome composition by mode of delivery. To investigate how these could be explained, they looked at clinical factors.
“Differences between infants’ stool microbiome composition by mode of delivery in early life appear to be primarily influenced by exposure to antibiotics around the time of birth,” Dr Money said. “This is something we hope to see more of. It’s important that we understand other factors that affect the development of the gut microbiome, including breastfeeding and antibiotic exposure, because the microbiome has such a big impact on a child’s overall health.”
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