It is not clear what impact the difference may have on children’s future health, and the findings should not deter women from having C-section births, the scientists leading the work said.
But the “baby biome” project — the world’s largest such study — had opened a window on a little-understood stage in the development of human immunity, they added.
The gut microbiome is a complex ecosystem of millions of microbes and is thought by scientists to be important for how the immune system develops.
Previous research has suggested that a lack of exposure to some microbes in early life is implicated in autoimmune diseases such as asthma, allergies and diabetes.
But scientists have not yet been able to work out how important the initial gut microbiome — or “baby biome” — is to future immunity and health, or how a baby’s microbiome develops, or what happens to it with different modes of birth.
In this research, published in the journal Nature, scientists from University College London, Wellcome Sanger Institute and Birmingham University used DNA sequencing to analyze more than 1,600 gut bacteria samples from 175 mothers and almost 600 babies.
In samples from mothers and from the babies at 4, 7 and 21 days old, the team found there was a significant difference between the two delivery methods — with vaginally delivered babies having many more health-associated bacteria from their mothers than babies born by Caesarean.
In place of some of the mothers’ bacteria, the C-section babies had more bacteria typically found in hospitals, the researchers said, and these bugs were also more likely to be drug-resistant.