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Babies Born by C-Section More Likely to Carry Opportunistic Pathogens in Gut Microbiome

NEW YORK – Infants born by caesarian section have gut microbiomes that differ from those of infants born vaginally, carrying more hospital-associated opportunistic pathogens, a new analysis from the Baby Biome Study has found.

Bacteria quickly colonize newborns after birth. The gut microbiome in particular is thought to contribute to immune system development, and perturbations to it have been associated with the later development of allergies, asthma, and diabetes. Some scientists have suggested that infants' mode of delivery might contribute to differences in the makeup of their gut microbiomes.

For their study, researchers led by the Wellcome Sanger Institute's Trevor Lawley examined more than 1,600 gut microbiome samples taken from nearly 600 healthy babies born in UK hospitals. As they reported in Nature today, the researchers found that babies born vaginally had gut microbiomes that resembled those from their mothers, while babies born by C-section had gut microbiomes marked by bacteria from the hospital environment.

"This is the largest genomic investigation of newborn babies' microbiomes to date," Lawley, the senior author of the paper, said in a statement. "We discovered that the mode of delivery had a great impact on the gut bacteria of newborn babies, with transmission of bacteria from mother to baby occurring during vaginal birth."

The researchers noted, though, that by their first birthdays, most of the differences in the infants' gut microbiomes were gone.

For their analysis, the researchers collected fecal samples from 596 healthy babies through the Baby Biome Study. All infants were sampled at least once during their first month of life and 302 were sampled again when they were a few months old. Of these babies, 314 were born vaginally and 282 by C-section.

Through their analysis, the researchers found instability in the gut microbiome during the first few weeks of life, suggesting that it is dynamic and personalized during infancy.

Still, when they stratified their cohort based on clinical covariates such as delivery mode, maternal age, or breastfeeding, the researchers found that mode of delivery had the greatest effect on gut microbiota variation during infancy. Breastfeeding and covariates associated with hospital stays, like postnatal antibiotic use, also had an effect, though a smaller one.

In particular, they found that babies born vaginally had gut microbiomes enriched with commensal bacteria like Bifidobacterium, Escherichia, Bacteroides, and Parabacteroides. Babies born by caesarian section had gut microbiomes that were depleted of those commensal bacteria, but instead harbored hospital-associated bacteria like Enterococcus faecalis, Staphylococcus epidermis, Klebsiella pneumoniae, and Clostridium perfringens.

The C-section-delivered babies also had higher percentages of opportunistic pathogens in their gut microbiomes — ones associated with hospitals — than their vaginally born counterparts. This suggested to the researchers that exposure to the hospital environment particularly affected the C-section-born infants and could predispose them to opportunistic infections.

The researchers also profiled the gut microbiomes of 178 mother-baby pairs to find that Bacteroides, Parabacteroides, Bifidobacterium, and E. coli were most frequently transmitted from mother to baby during vaginal birth. They also noted that these bacteria didn't originate from the mother's vaginal microbiome but from her gut microbiome.

Because of that, the researchers said in a statement, these findings don't provide evidence to support the practice of vaginal swabbing, in which infants born by C-section are swabbed with bacteria from the mother's vagina.

Over time, the microbiomes of both groups of infants became more similar, study author Nigel Field from University College London said in a statement. "After they have been weaned, the microbiome differences between babies born via caesarean and delivered vaginally have mainly evened out," he added. "We don't yet know whether the initial differences we found will have any health implications."