Babies born by caesarean section have different gut bacteria to those delivered vaginally, the most comprehensive study to date on the baby microbiome has found.

The study showed that babies born vaginally pick up most of their initial dose of bacteria from their mother, while C-section babies have more bugs linked to hospital environments, including strains that demonstrate antimicrobial resistance. The findings could explain the higher prevalence of asthma, allergies and other immune conditions in babies born by caesarean.

“How your immune system functions through your life might be influenced by its first interactions with bacteria,” said Nigel Field, a senior author on the paper from University College London. “If there are differences in longer-term health outcomes by different patterns of [bacteria], that tells us something quite important about health.”

Previously it was thought that babies’ microbiomes might be shaped by bacteria that they swallow while in the birth canal. But the latest findings revealed that the microbiome of vaginally delivered newborns did not come from vaginal bacteria but from the mother’s gut – presumably picked up at the moment of birth.

This calls into question the practice of swabbing babies born by C-section with vaginal bacteria straight after birth.

“The practice of vaginal seeding is quite controversial,” said Peter Brocklehurst, a professor of women’s health at the University of Birmingham and a co-author. “Here we find no biological evidence that it would be effective anyway.”

Babies are sterile when they are in the womb, but as soon as they are exposed to the outside world they begin taking in bacteria, which rapidly colonises the gut. By six to nine months, the differences between the two groups had levelled out.

But scientists think that the initial exposure to bacteria at the moment of birth could be a “thermostat” moment for the immune system, defining its sensitivity and which strains of bacteria trigger a response.

Scientists are yet to uncover the exact mechanisms by which early exposure influences immune activity, and this needs to be worked out before the findings have any real implications for clinical practice.

Brocklehurst said it would not be advisable for parents try to give caesarean-born babies a dose of maternal gut bacteria, for instance, which could be dangerous.

“I’d be very anxious about deliberately introducing those artificially,” he said.

However, in the future it may become routine to administer a dose of bacteria to babies born through caesarean.

Experts also said the findings should not alarm women who were planning to have, or had had, a caesarean. “In many cases, a caesarean is a life-saving procedure and can be the right choice for a woman and her baby,” said Alison Wright, a consultant obstetrician and vice-president of the Royal College of Obstetricians and Gynaecologists.

“The exact role of the microbiome in the newborn and what factors can change it are still uncertain, so we don’t think this study should deter women from having a caesarean.”

The study also suggested that antibiotics, which are normally given before a caesarean, play a role in shaping the baby microbiome. Breastfeeding also had an impact on gut bacteria, the study found, but played a more minor role.

The study, published in Nature, took seven years and involved taking 1,679 faecal samples from nearly 600 babies and 175 mothers. These were posted to the Sanger Institute in Cambridgeshire and entered into a frozen archive.

The team wants to expand the study to include larger numbers of babies, including those born at home. They also want to look in more detail at how long hospital bugs with antimicrobial resistance persist, and whether this poses any risk to babies born through caesarean.

Andrew Shennan, professor of obstetrics at King’s College London, said: “This important study confirms that the way we give birth will alter our microbiome in the first year of life. Caesarean delivery results in fewer bacteria in the baby’s gut being like its mother’s.

“This is not known to be harmful and mothers who need a caesarean should not be alarmed. The further effects of this in long term health need to be evaluated.”