The study, published in the journal JAMA Pediatrics, found that when an overweight woman delivered vaginally, the risk of her child being overweight was three times higher than normal.
However, the risk was five times higher than normal when the woman delivered via cesarean-section (C-section), researchers said.
"We know that maternal overweight is linked to overweight in children," said Anita Kozyrskyj, investigator at the University of Alberta in Canada.
"What our study showed is that both the type of infant delivery - vaginal birth versus cesarean section birth - and changes in gut bacteria are also involved," said Kozyrskyj, who led the study.
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Gut microbiome is the community of bacteria that live in the digestive tracts of humans.
"We have shown in our previous research that an infant's gut microbiome is influenced by the type of delivery, so we wondered if this effect could be associated with obesity risk in early childhood," Kozyrskyj said.
The research team studied over 930 mothers and their infants.
An older analysis method not used in microbiome analyses - sequential mediation - was employed.
The children's weights were assessed at one and three years of age.
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