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New research finds there are significant differences between babies born by cesarean and babies born vaginally when it comes to a newborn’s microbiome – the bacteria that colonize our gut and play a key role in keeping us healthy.

In the largest study of its kind, researchers found that vaginally born babies got most of their gut bacteria from their mother, while babies born via cesarean did not. Instead, they had more bacteria associated with hospitals in their guts. However, these difference had disappeared by the time the babies were weaned.

“We think it’s a critical moment in life. Babies are sterile in the womb and the moment they are born is a moment when the immune system has a huge number of bacteria it’s presented with. The hypothesis is that that moment of birth is a thermostatic moment that sets the immune system for future life,” said Dr. Nigel Field, a clinical associate professor at University College London, a senior author of the study that published in the journal Nature on Wednesday.

He said during a press conference that the more common bacteria found in C-section babies were called “opportunistic pathogens,” which can be carried by healthy people without causing any problem but “can cause disease when the immune system isn’t working properly or they get somewhere they shouldn’t, such as tissues or the blood stream.

“These difference largely even out over time, so by the time babies have weaned, about six to nine months, these differences have largely disappeared.

“We don’t know the long-term consequences so it’s important we now follow these findings up with further research to understand what the policy, clinical and microbiological implications are.

Previous research has shown babies born via C-section are at a slightly higher risk of immune-related conditions such as asthma, inflammatory bowel disease and other allergic conditions, Field said.

‘A cesarean is a life-saving procedure’

To understand more about the development of the microbiome, and how the method of birth affected this, researchers studied 1,679 samples of gut bacteria from nearly 600 healthy babies and 175 mothers.

Fecal samples were taken from babies age four, seven or 21 days old, who had been born in UK hospitals by vaginal delivery or cesarean. Some babies were also followed up later, up to age 1.

The study found that babies born via cesarean had more bacteria that are typically acquired in hospitals, and were more likely to have antimicrobial resistance. When the researchers isolated and sequenced the genomes of more than 800 bacteria, they found that they were the same as strains causing bloodstream infections in UK hospitals, a press statement said.

All women who have a cesarean in the UK are now offered antibiotics before the baby is born to help prevent the mother developing post-operative infections. This means that the baby also receives a dose of antibiotics via the placenta and the researchers said this could cause some of the microbiome differences seen between the two birth methods.

Dr. Alison Wright, a consultant obstetrician and vice president of The Royal College of Obstetricians and Gynaecologists, said the research should not stop women from having a C-section.

“In many cases, a cesarean is a life-saving procedure, and can be the right choice for a woman and her baby,” she said.

“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.”

Professor Andrew Shennan, a professor of obstetrics at King’s College London, agreed.

“Cesarean delivery results in fewer bacteria in the baby’s gut being like its mother’s. This is not known to be harmful and mothers who need a caesarean should not be alarmed. The further effects of this in long term health need to be evaluated,” he told the Science Media Centre in London.

Vaginal swabbing: No biological evidence

The study also cast doubt on the practice of vaginal seeding – swabbing the vagina and then wiping the fluids on the baby’s face or mouth. The aim of the procedure is to give the baby the bacteria it would have been exposed to during vaginal delivery and help kickstart a healthy gut microbiome.

But this new research suggests the practice, which is getting more popular among parents-to-be planning c-sections, isn’t grounded in evidence.

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Previous, smaller studies had suggested that vaginal bacteria were swallowed by the baby on its way down the birth canal.

“We didn’t see any evidence that those are the bacteria that colonize a baby’s guts. The bacteria that colonize a baby’s guts are the bacteria from the mother’s gut,” said Professor Peter Brocklehurst, the director of Birmingham Clinical Trials Unit at the University of Birmingham and principal investigator of the Baby Biome Study.

“The practice of vaginal seeding is quite a controversial one. [There’s] no professional group that supports that practice because it could potentially be harmful but here we are suggesting that we can find no biological evidence that it would be effective, anyway.”