Babies delivered by caesarean section are slower to acquire certain types of “good bacteria” in their gut and have higher levels of potentially problematic bacteria than those born vaginally, researchers say.

A study of more than 100 babies showed that those born vaginally had a very different make-up of their gut microbiome (clusters of gut microbes), potentially making caesarean babies more prone to respiratory infections. The differences were found to reduce as the babies grew older.

Previous studies have suggested that the mode of delivery affects the newborn’s microbiome, but some said this might be because many mothers who have had caesarean sections require antibiotics.

The new research, which will be presented at the European Congress of Clinical Microbiology and Infectious Diseases in Amsterdam, backs up claims that it is specifically the mode of delivery that drives the differences.

The research involved the team collecting faeces at 10 points in the year from 46 babies born by caesarean section and 74 babies born vaginally, starting from their first faeces, and analysing its microbial makeup.

Crucially, the team says that antibiotics, if needed, were only given to mothers once the baby was delivered – meaning babies were not directly exposed to the antibiotics.

The results, based on analysis of stool both from the mothers and the babies, also showed that babies born by caesarean section were slower to acquire certain “good bacteria” that are important in digesting milk, and had higher levels of certain types of potentially harmful bacteria than those born vaginally.

“We feel that it is proved that mode of delivery is an important driver or modifier of the gut microbiome in young infants,” said Prof Debby Bogaert from the University of Edinburgh, who worked on the project with colleagues in the Netherlands.

She added that the conclusion was backed up by findings that antibiotics given to mothers after delivery did not appear to affect their own gut microbiome, and that differences in babies’ microbiomes were also seen in babies that were only bottle-fed, suggesting the effects were not down to babies receiving antibiotics through breast milk.

The team adds that babies with higher levels of the potentially harmful bacteria tended to have more respiratory infections within their first year.

That, said Bogaert, might help to explain why some studies suggest babies born by caesarean section have a greater risk of respiratory infections.

A second study to be presented at the conference looked at whether the microbes found in babies’ guts were linked to their chance of becoming overweight as they grew up.

The team of researchers from Finland collected faeces from 212 newborn babies, including the first stool passed after birth, which is thought to form when the baby is in the womb. The results show that the makeup of the microbiome within a baby’s first stool is linked to whether the child is overweight at three years of age.

Katja Korpela, one of the researchers involved in the study from the University of Oulu, said there could be many factors affecting the microbial makeup of a baby’s first stool, including the mother’s use of antibiotics during pregnancy and the living environment of the pregnant mother.

However, it is unclear whether the observed link is one of cause and effect, or whether the mode of delivery influences the results.

“The concept of foetal microbiome is very controversial and the colonisation process after birth is better understood than the colonisation process before birth,” said Korpela. But, she said, it was interesting that the microbiome formed before the birth was possibly linked to children’s later health.

Tim Spector, professor of genetic epidemiology at King’s College London and an expert on the human microbiome, said the studies extended what had previously been suspected about the importance of gut microbes early in life.

“One study has confirmed large cross-sectional studies about C-section causing immune problems later in life with an increased risk of infections and the other showing that the very first microbes of a baby, which often come from the mum, increase the risk of obesity,” he said. “We need to take gut health more seriously when dealing with babies if we are to improve their health later in life.”