Babies born by C-section have different gut bacteria

Babies born by caesarean section have a reduced level of “good” gut bacteria and an increased number of pathogens linked to hospital environments, according to research co-led by UCL that is the most comprehensive study of the baby microbiome to date.

In the study, published in the journal Nature, researchers analysed gut bacteria in stool samples taken from 596 babies born in British hospitals – 314 babies who had a vaginal birth, and 282 who were born by caesarean. They took samples four, seven and 21 days after birth and later in infancy and also analysed samples from 175 mothers to determine the origin of the gut bacteria. The samples were gathered as part of the Baby Biome Study, co-led by Dr Nigel Field (UCL Institute for Global Health).

Researchers concluded that babies born by C-section had a reduced number of “good” Bacteroides derived from their mothers and an increased number of opportunistic pathogens, including Enterococcus, Enterobacter and Klebsiella species.

The study provides evidence that the first colonisation of a newborn’s intestine with bacteria varies with different birth methods. Researchers concluded that the type of birth is a significant risk factor in how the gut microbiome from newborns to infancy will be composed.

Immediately after a natural birth, the intestines of infants are quickly colonised with microorganisms of the mothers, but also by microbes from the environment. For several years, researchers have suspected that childhood and later life diseases may be the result of disturbed first colonisation of the gut microbiome of newborns.

Researchers cultured more than 800 strains of bacteria and then analysed their entire genome (genome sequencing). As a result, they detected bacterial virulence factors and clinically relevant antimicrobial resistance in the caesarean section children in some opportunistic pathogens, which could make their carriers susceptible to infections with weakened immune systems.

It remains unclear where and how exactly colonisation with antimicrobial-resistant opportunistic pathogens occurs in those born by caesarean section and to what extent the hospital environment differs between natural and caesarean births.

The study cannot make any statements about concrete clinical consequences of the changed colonisation, but the authors call for prospective and long-term cohort studies that should also include infants from home births.

Senior author Dr Nigel Field (UCL Institute for Global Health) said: “Our study showed that as the babies grow and take in bacteria when they feed and from everything around them, their gut microbiomes become more similar to each other. After they have been weaned, the microbiome differences between babies born via caesarean and delivered vaginally have mainly evened out. We don’t yet know whether the initial differences we found will have any health implications.”

The study was a collaboration between researchers at UCL, the Wellcome Sanger Institute and the University of Birmingham.

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