Babies born vaginally have different gut bacteria than those delivered by caesarean, new research suggests.


Scientists discovered that while vaginally born babies got most of their gut bacteria – microbiome – from their mother, babies born via caesarean did not.

Instead they had more bacteria associated with hospital environments in their guts.

Researchers from the Wellcome Sanger Institute, UCL, the University of Birmingham and their collaborators stress the exact role of the baby’s gut bacteria is unclear.

In the study published in Nature, they say it is unknown if these differences at birth will have any effect on later health.

We found significant differences between babies born by caesarean and babies born vaginally, but these babies were healthy when they took part in Baby Biome, and we don’t know what the long-term consequences are
Dr Nigel Field

Dr Nigel Field, Director of the Centre of Molecular Epidemiology and Translational Research at the Institute for Global Health at UCL, said: “Babies are sterile when they are in the womb.

“And the moment they are born is the moment when the immune system has a huge number of bacteria that is it presented with.

“And so the hypothesis is that that moment of birth might be a sort of thermostat moment which sets the immune system for future life.

“There is research showing that babies born by caesarean section have a slightly higher risk of immune-related conditions.

“They have a slightly higher risk of asthma, or inflammatory bowel disease and other allergic conditions.”

He added: “In summary, we found significant differences between babies born by caesarean and babies born vaginally, but these babies were healthy when they took part in Baby Biome, and we don’t know what the long-term consequences are.”

Read more about pregnancy:

The study, the largest ever 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.

Scientists say this calls into question the controversial practice of swabbing babies born via caesarean with mother’s vaginal bacteria.

Understanding how the birth process impacts on the baby’s microbiome will enable future research into bacterial therapies.

It is not fully understood how important the initial gut microbiome is to the baby’s immune system development and health, how a baby’s microbiome develops, or what happens to it with different modes of birth.

Researchers studied 1,679 samples of gut bacteria from 596 babies and 175 mothers.

Faecal samples were taken from babies aged four, seven or 21 days old, who had been born in UK hospitals by vaginal delivery or caesarean.

Some babies were also followed up later, up to one year of age.

Using DNA sequencing and genomics analysis, the researchers could see which bacteria were present and found there was a significant difference between the two delivery methods.

They discovered that vaginally delivered babies had many more health-associated bacteria from their mothers, than babies who were born by caesarean.

What is the microbiome?

Your gut microbiome is a vast community of trillions of bacteria and fungi that inhabit your gastrointestinal tract, and have a major influence on your metabolism, body weight, propensity to illness, immune system, appetite and mood.

These microbes mostly live in your lower intestine (the colon) and outnumber all the other cells in your body put together.

There are some organs we can live without, but we wouldn’t survive long without our gut microbes. Intriguingly, no two microbiomes are the same – we are all unique. And more than ever, we’re finding out just how important these microbes are.

According to research, the richer and more diverse the community of gut microbes are, the lower your risk of disease and allergies.

Find out more:

Scientists also found the differences in gut bacteria between vaginally born and caesarean 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.

Experts from the Royal College of Obstetricians and Gynaecologists say that these findings should not deter women from having a caesarean birth.

Dr Trevor Lawley, a senior author on the paper from 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.”

Principal Investigator of the Baby Biome Study, Professor 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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Alexander McNamaraOnline Editor, BBC Science Focus

Alexander is the former Online Editor at BBC Science Focus.