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Restoring microbes in infants born by cesarean section

Trillions of microbes-including bacteria, fungi, and viruses-live in and on the human body. Some of these microbes cause illnesses, but many are necessary for good health.

Babies delivered via the birth canal acquire a microbial community (microbiota) that resembles that of their mother's vagina. Babies born by cesarean section tend to acquire a microbial community that more closely resembles that of their mother's skin. The microbiota acquired by a newborn are thought to be essential for the development of a healthy immune system and metabolism.

A research team led by Dr. Maria Dominguez-Bello at NYU Langone Medical Center and Dr. Jose C. Clemente at Icahn School of Medicine in Mount Sinai, New York, set out to determine whether they could alter the microbiota of babies born by C-section by exposing them to maternal vaginal fluids at birth. The study was funded in part by NIH's National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). The findings appeared online on Feb. 1 in Nature Medicine.

Eighteen healthy mothers participated in the small pilot study. Seven delivered vaginally. Of the 11 who delivered by scheduled C-section, 4 elected to have their newborns swabbed. For the procedure, a sterile gauze pad was incubated in the mother's birth canal an hour before the C-section. The newborn was then swabbed with the gauze within the first 1-3 minutes after birth, starting with the mouth, then the face, and then the rest of the body.

All women who participated in the microbial transfer were first tested to ensure they didn't have any viral infections or sexually transmitted diseases. All mothers received standard treatment, including preventive prenatal antibiotics when necessary.

The infants and mothers were later swabbed for bacterial DNA analysis at 6 time points up to 30 days after birth. More than 1,500 samples were collected from areas that included the mouth, forehead, arm, foot, anal region of the baby, and vaginal region of the mother.

The researchers found that the microbiomes (all of the DNA, or genomes, of all of the microbes) of the C-section-delivered infants exposed to vaginal fluids resembled those of vaginally delivered infants, especially during the first week of life. Their gut, mouth, and skin bacterial communities during the first 30 days of life were enriched in vaginal bacteria. These bacteria were underrepresented in the C-section-delivered infants that weren't swabbed with vaginal fluids.

"This study has allowed us to demonstrate the feasibility of bacterial restoration in a small cohort, but we do not know yet whether this procedure alone is sufficient to restore the health benefits associated with vaginal delivery," Clemente says.

"The current study represents proof of a principle in a small cohort, and shows that our method is worthy of further development as we seek to determine the health impact of microbial differences," Dominguez-Bello says. "Larger studies that measure the effect of early microbiome restoration on health outcomes would begin to answer whether or not it averts future disease risk."

-by Carol Torgan, Ph.D.

--From the National Institute of Health

For further information on this and other health topics, visit the web site of the National Institute of Health at

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