Giving birth by Caesarean section may leave a baby vulnerable to disease and allergy by upsetting its natural balance of bacteria, scientists believe.

A study found that delivery method has a major impact on the kinds of bugs carried by newborn infants. While babies born naturally appeared to acquire bacteria from their mother's vagina, those born by Caesarean section harboured microbes typically found on the skin.

The latter were dominated by strains associated with food poisoning, diphtheria and acne. Allowing the bugs in at the time of birth could affect the health of babies as they grow, say researchers. Previous studies suggest that babies born by Caesarean section may be more susceptible to certain infections and allergies than naturally delivered babies.

The transmission of a mother's vaginal bugs to her infant could offer protection against colonisation by more harmful invaders, it is claimed. More than 20 per cent of babies born in the UK today are delivered by Caesarean section, compared with only 9 per cent in 1980.

The procedure is usually carried out for safety reasons, to prevent complications that might harm either mother or baby. Two thirds of Caesarean sections are performed as a result of unexpected emergencies and a third are planned.

Dr Noah Fierer, one of the study leaders from the University of Colorado in the US, said: "In a sense the skin of newborn infants is like freshly tilled soil that is awaiting seeds for planting – in this case, bacterial communities. The microbial communities that cluster on new-borns essentially act as their first inoculation."

The findings, published in Proceedings of the National Academy of Sciences, may explain the high rate of infection by MRSA – the hospital "superbug" – in babies born by Caesarean section. One 2004 study in the US found that Caesarean-section infants accounted for between 64 per cent and 82 per cent of reported cases of skin infections by MRSA in new-borns. Other research has suggested that Caesarean-delivered babies may be more prone to asthma than infants delivered naturally.

The study was carried out in Venezuela where researchers tested nine women aged 21 to 33 and 10 newborn babies.