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Those worried about the health impacts of Caesarean sections say babies born that way miss out on the health benefits of a natural birth. Now, as Alanna Collen writes in this week's Scrubbing Up, some experts are suggesting a simple swab could mean that doesn't have to be the case.

Shortly after his wife gave birth by emergency Caesarean section in 2012, US scientist Rob Knight waited for the midwives and doctors to leave the room, then rubbed his new baby daughter's little body with a swab coated in his wife's vaginal fluids.

Although medical staff might have questioned his motives, Knight had good reason to believe his actions were in his newborn's best interests.

As a scientist studying the impact of the body's microbes on health, Knight wanted to make sure his little one got off to a good start, and that meant seeding her skin and gut with the vaginal bacteria she would have encountered during a natural birth.

Birth by Caesarean is increasingly common worldwide. In Britain, one quarter of babies are born this way. In New York, it's more like half of babies. And in some hospitals in Rio de Janeiro, Brazil, rates of C-sections top 90%.

Until recently, the potential downsides of C-sections were thought to be limited. But experts including Prof Knight, who is based at the University of Colorado in Boulder, have identified one that could be key to a baby's health - the lack of exposure to the microbes they would come into contact with during a natural birth.

He is part of the so-called 'microbiome revolution' - the scientific recognition of the crucial role played by the body's microbes in promoting good health.

Microbial 'birthday suit'

Studies around the world are demonstrating an important link between disruption to the complex microbial communities living in and on the human body and many of the modern illnesses that have been on the rise in developed countries over the past 60 years.

Allergies, autoimmune diseases, and obesity, in particular, are now thought to have their roots in a disrupted gut microbiota.

Before his daughter was born, Prof Knight had been involved in several research studies into the impact of Caesarean sections on the colonisation of newborn babies with microbes during birth.

For babies born naturally, life begins with a microbial birthday suit made up of vaginal and faecal bacteria.

It seems disgusting, but this coating of microbes means a baby's body, both inside and out, is protected from harmful infections.

What's more, the guts are colonised by bacteria that help the baby to digest milk and educate its naive immune system as to what is harmful and what is not.

Babies born by C-section, on the other hand, start their lives with a coating of skin bacteria - from mum, dad and medical staff - as well as hospital nasties like Clostridium difficile (C.diff) and Pseudomonas.

They appear to be more prone to picking up infections in the first weeks of life. And, as children and adults, those delivered by C-section appear to be at increased risk of developing allergies and autoimmune diseases, and becoming overweight.

The question is, can we do anything to reduce these risks in babies born by C-section?

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Accompanied through history

By swabbing his own daughter, Prof Knight hoped so. But he was keen to find out whether the technique really did make a difference to the gut microbes of babies.

He teamed up with another microbiologist, Maria Gloria Dominguez-Bello at New York University, to set up a small trial at a hospital in Puerto Rico.

The technique was simple. Some of the mothers due to give birth by C-section had a piece of gauze inserted into the vagina one hour before surgery.

The microbe-laced gauze was removed and placed in a sterile pot just before the C-section was performed, and immediately after each baby had been delivered, its body was wiped with the gauze, beginning with the mouth, then the head, and then the rest of the body.

The results from this preliminary trial - now under peer-review - showed that babies who were exposed to their mother's microbes after delivery by C-section had gut microbes that were more similar to vaginally-delivered babies than the guts of C-section babies who had not been swabbed.

Prof Knight and Dr Dominguez Bello are now working on a larger trial, and are planning to follow the babies as they grow to see if vaginal swabbing reduces rates of allergies and autoimmunity.

Just as with a vaginal birth, there are concerns about transferring harmful microbes alongside the beneficial ones that must be considered.

But if these and other trials prove a success, we could see vaginal swabbing rolled out as a standard procedure to ensure future generations continue to receive the beneficial microbes that have accompanied humans throughout our history.