Mount Sinai researchers report new method to restore microbiome of newborns delivered via C-section

Scientists from the Icahn Institute for Genomics and Multiscale Biology at the Icahn School of Medicine at Mount Sinai, collaborating with NYU Langone Medical Center and a multi-center team of researchers, demonstrated for the first time that the microbiome of newborn babies delivered via cesarean section (C-section) can be partially restored to resemble that of vaginally delivered infants. By swabbing newborns with a gauze containing vaginal fluids from their mothers, and later testing samples collected from these newborns and their mothers using state-of-the-art genomic technology and computational methods, the research team showed that C-section infants became enriched in vaginal bacteria such as Lactobacillus, which were nearly absent in untreated infants. The team published its findings today in the journal Nature Medicine.

C-section rates have increased significantly worldwide over the last few decades. More than a third of all births in the U.S. are now by C-section, well above the 10 to 15% recommended by the World Health Organization. Although often a life-saving procedure for mothers and infants, this procedure comes with undesirable side effects for the newborn, including an increased risk for immune and metabolic conditions. This risk has been attributed to the aberrant microbiome found in newborns delivered via C-section, resulting from their lack of exposure to maternal vaginal microbes. The human microbiome encompasses the trillions of bacteria harbored in the body that are essential to our well-being.

"There is a clear association between C-section and increased risk for several diseases," said senior author of the study Jose C. Clemente, PhD, Assistant Professor of Genetics and Genomics and a member of the Icahn Institute at the Icahn School of Medicine at Mount Sinai, "but to date, only a few research studies in mice have demonstrated that this is caused by difference in the microbiome early in life. Our work is the first to demonstrate in humans that we can modify the abnormal bacterial communities found in C-section babies."

The pilot study recruited seven mothers expected to deliver vaginally and 11 by scheduled C-section, out of which four agreed to have their babies swabbed upon birth. A sterile gauze was incubated in the maternal vagina during the hour previous to the C-section, and the babies were swabbed on their mouth, face, and body immediately after delivery.

Over 1,500 samples were collected at multiple time points from several body sites of the infants and their mothers during the first month of life. The research team harnessed recent advances in DNA sequencing and big data analytics to characterize, for the first time, the microbial communities found in the infants delivered vaginally and by C-section. Analysis of these results determined that C-section infants exposed to their maternal vaginal fluids had a microbiome enriched in bacteria commonly found in vaginally delivered babies, such as Lactobacillus and Bacteroides. These bacteria, nearly absent in C-section children that were not swabbed, have been linked to a proper development of the immune system, and could provide an explanation for the lowered disease risks associated with vaginal delivery.

"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", said Dr. Clemente. "Studies that target children at risk for immune disorders, such as allergies, will be required to determine how microbial restoration affects health outcomes".