A new study has found that there are significant dissimilarities between babies born by caesarean-section (CS) and those born vaginally when it comes to a newborn’s microbiome.


Microbiome is the genetic material of all the microbes – bacteria, fungi, protozoa and viruses – that live in the gut or inside the human body. They play a key role in keeping us healthy.

The study, conducted by Wellcome Sanger Institute, University College London and the University of Birmingham, discovered that vaginally born babies had most of their gut bacteria from their mother, while babies born via cesarean did not.

The researcher found out that babies given birth to through C-section had more bacteria associated with hospitals in their guts and it disappeared by the time the babies are between 6 and 9 months old.


The study, published in the nature international journal of science, assessed how microbiome forms when a baby leaves the mother’s sterile womb and enters a world full of bugs.

To investigate the phenomenon, regular samples were taken from the nappies of nearly 600 babies for the first month of life, and some provided faecal samples for up to a year.

The researchers discovered that about 80 per cent of C-section-born babies had hospital-acquired bacteria in their guts when they were born, compared with 50 per cent of vaginally born babies.


They also noticed that the bacteria made up around 30 per cent of the total bacteria in C-section babies compared with just 10 per cent in babies born vaginally.

The study found that while vaginally born babies got most of their early bacteria from their mother, those born with caesarean had high levels of hospital bugs such as klebsiella and pseudomonas.

It also found that children born by caesarean are at higher risk of some disorders such as type 1 diabetes, allergies and asthma.

“This analysis demonstrates that the mode of delivery is a significant factor that affects the composition of the gut microbiota throughout the neonatal period, and into infancy,” the study stated.


“Matched large-scale culturing and whole-genome sequencing of over 800 bacterial strains from these babies identified virulence factors and clinically relevant antimicrobial resistance in opportunistic pathogens that may predispose individuals to opportunistic infections.”

According to the study, the process of child delivery influences the operations of the immune system, the body’s defence against infection.

“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 Nigel Field, a senior author of the study  and clinical associate professor at University College London.

Consequently, 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.


Alison Wright, a consultant obstetrician and vice president of The Royal College of Obstetricians and Gynaecologists, said the study should not discourage 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.

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