Babies born vaginally primarily acquire the microbes that inhabit their mother’s vagina and bowel. However, those delivered surgically before membranes rupture and labor begins acquire microbes mainly from the mother’s skin and the personnel and environment in the newborn nursery.

When an emergency cesarean is performed after membranes rupture and labor has begun, the baby acquires fewer of the mother’s microbes than it would during a vaginal birth but many more than from a scheduled cesarean.

These differences in the gut microbiota were found to persist in children until at least 7 years of age, according to a study in Finland published in 2004.

Currently, about one baby in three in the United States is delivered by cesarean section, up from about one in five in the 1990s. Certainly, a surgical delivery can be lifesaving when, for example, the fetus or the mother is at risk of a serious or fatal complication from a vaginal delivery.

But other reasons for the rise in cesarean deliveries, including the readings from a fetal monitor, are less clear-cut. Even though many babies with borderline readings would be likely to be fine with a vaginal birth, women and their doctors are usually unwilling to take a chance when the monitor suggests that the fetus may be in trouble. And women who have one cesarean, which weakens the uterine wall, are more likely to have a second or third rather than risk a uterine rupture during subsequent labor and delivery.

To counter the effects of a surgical birth on the infant’s microbiome, a growing number of women whose babies are delivered by cesarean are requesting that medical staff transfer microbes from the mother’s vagina to their infants soon after birth. Some are administering the microbe exchanges themselves. However, an expert committee of the American College of Obstetricians and Gynecologists recently warned that the practice, known as vaginal seeding, was premature and possibly hazardous.

“At this time, vaginal seeding should not be performed outside the context of an institutional review board-approved research protocol until adequate data regarding the safety and benefit of the process become available,” the committee concluded. The committee cited a potential risk of transferring pathogenic organisms from the woman to the neonate.