The role of delivery method on the acquisition of a newborn’s gut microbiome has been an ongoing, controversial topic. Although vaginal and cesarean section deliveries have been previously shown to result in differences, the significance between the two in infancy, into childhood and beyond, has not been established.

A new study—the largest of its kind—has been published through the Baby Biome Study. The researchers from the Wellcome Sanger Institute, UCL, and the University of Birmingham found that babies born vaginally received most of their gut bacteria from their mother, while babies born through cesarean section are colonized less by bacteria found in their mothers and, instead, have more bacteria representative of the hospital environment.

The exact role of the baby’s gut bacteria is unclear and it isn’t known if these differences at birth will have any effect on later health.

The researchers found the differences in gut bacteria between vaginally born and cesarean delivered babies largely evened out by one year old, but large follow-up studies are needed to determine if the early differences influence health outcomes.

Published in Nature, in a paper titled, “Stunted microbiota and opportunistic pathogen colonization in cesarean-section birth“, this largest ever study of neonatal microbiomes also revealed that the microbiome of vaginally delivered newborns did not come from the mother’s vaginal bacteria, but from the mother’s gut. This calls into question the controversial practice of swabbing babies born via cesarean with mother’s vaginal bacteria. Understanding how the birth process impacts the baby’s microbiome will enable future research into bacterial therapies.

Researchers studied 1,679 samples of gut bacteria from nearly 600 healthy babies and 175 mothers. Fecal samples were taken from babies aged four, seven, or 21 days old, who had been born in U.K. hospitals by vaginal delivery or cesarean. Some babies were also followed up later, up to one year of age.

Trevor Lawley, PhD, a senior author on the paper and a group leader at the Wellcome Sanger Institute, said: “This is the largest genomic investigation of newborn babies’ microbiomes to date. We discovered that the mode of delivery had a great impact on the gut bacteria of newborn babies, with transmission of bacteria from mother to baby occurring during vaginal birth. Further understanding of which species of bacteria help create a healthy baby microbiome could enable us to create bacterial therapies.”

Previous limited studies had suggested that vaginal bacteria were swallowed by the baby on its way down the birth canal. However, this large-scale study found babies had very few of their mother’s vaginal bacteria in their guts, with no difference between babies born vaginally or by cesarean.

During birth, the baby will come into contact with bacteria from the mother’s gut. The study discovered it was the mother’s gut bacteria that made up much of the microbiome in the vaginally delivered babies. Babies born via cesarean had many fewer of these bacteria. This study, therefore, found no evidence to support controversial “vaginal swabbing” practices, which could transfer dangerous bacteria to the baby.

In place of some of the mother’s bacteria, the babies born via cesarean had more bacteria that are typically acquired in hospitals, and were more likely to have antimicrobial resistance. The researchers isolated, grew, and sequenced the genomes of more than 800 of these potentially pathogenic bacteria, confirming that they were the same as strains causing bloodstream infections in U.K. hospitals. Although these bacteria don’t usually cause disease while in the gut, they can cause infections if they get into the wrong place or if the immune system fails.

“Our study showed that as the babies grow and take in bacteria when they feed and from everything around them, their gut microbiomes become more similar to each other,” noted Nigel Field, PhD, a senior author on the paper. Field added, “After they have been weaned, the microbiome differences between babies born via cesarean and delivered vaginally have mainly evened out. We don’t yet know whether the initial differences we found will have any health implications.”

Alison Wright, MD, consultant obstetrician and vice president of the Royal College of Obstetricians and Gynaecologists asserted, “In many cases, a cesarean is a life-saving procedure, and can be the right choice for a woman and her baby. The exact role of the microbiome in the newborn and what factors can change it are still uncertain, so we don’t think this study should deter women from having a cesarean. This study shows that more research is required to improve our understanding of this important area.”

All women who have a cesarean are now offered antibiotics before the delivery to help prevent the mother developing postoperative infections, meaning that the baby also receives a dose of antibiotics via the placenta. This could also cause some of the microbiome differences seen between the two birth methods.

Principal investigator of the Baby Biome Study, Peter Brocklehurst, of the University of Birmingham, said, “The first weeks of life are a critical window of development of the baby’s immune system, but we know very little about it. We urgently need to follow up this study, looking at these babies as they grow to see if early differences in the microbiome lead to any health issues. Further studies will help us understand the role of gut bacteria in early life and could help us develop therapeutics to create a healthy microbiome.”

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