Researchers from Sweden and Scotland followed gut microbiota development in 24 children up to the age of two in the Swedish provinces of Ostergotland and Smaland.
Nine were delivered through Caesarean and 15 delivered naturally, through vaginal birth.
The study used a type of molecular biology analysis, which gives a broad overview of the varieties of bacteria present in the intestines.
Children delivered by Caesarean section had a less diverse gut microbiota during their first two years of life than those born vaginally.
Thus, these children may run greater risk of developing allergies, but diabetes and irritable bowel syndrome are also more common among children born by Caesarean.
"Sometimes Caesarean sections are necessary. But it is important that both expectant mothers and doctors are aware that such a delivery may affect the child's health," said Maria Jenmalm, professor of Experimental Allergology at Linkoping University in Sweden and one of the authors of the study.
With natural birth the child is exposed to bacteria in the mother's birth canal, a good start to the formation of the child's own gut microbiota.
"It might not be so good to have six months of only breast feeding. Earlier exposure to ordinary solid food may stimulate a higher diversity of the gut microbiota," Jenmalm said.
Besides a greater diversity in their intestinal flora, children delivered vaginally in the study also had higher blood plasma levels of substances linked to Th1 cells, a kind of "chief cells" in the immune system, which can inhibit allergic immune responses.
The study was published in the journal Gut.
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