As soon as babies are born, microorganisms start to colonize their bodies, building up their gut microbiomes. But how those babies enter the world can influence the makeup of their gut collections. Now a study of 596 babies’ gut microbiomes—the largest study of its kind to date—suggests that not only do babies born by cesarean section have different gut microbiomes from babies born vaginally, but their guts contain more microbes from the surrounding hospital environment, including bacteria with antimicrobial-resistance genes (Nature 2019, DOI: 10.1038/s41586-019-1560-1).
The results are the first set of findings from the Baby Biome Study, which researchers hope will help explain how clinical decisions affect the microbiome. Researchers collected feces samples from mothers and healthy babies at three hospitals in the UK. Some moms also sent the scientists follow up samples from their babies. It seems that baby poop is pretty stable in the mail.
Trevor Lawley’s team at the Wellcome Sanger Institute performed whole-genome sequencing of over 800 bacterial strains found in the samples and determined that babies born vaginally had gut microbiomes with similar compositions as those of their moms, with Bifidobacterium, Escherichia, Bacteroides, and Parabacteroides species in the majority. Babies born by C-section had fewer of those bacteria and instead had more species commonly found in hospitals.
Last year, Paul Wilmes at the Luxembourg Center for Systems Biomedicine and coworkers published results that suggested that cesarean delivery disrupts the transfer of gut microbes from mother to baby (Nat. Commun. 2018, DOI: 10.1038/s41467-018-07631-x). Lawley thinks this disrupted transfer partially explains his team’s results, but he also points out that moms who deliver by C-section take antibiotics before the operation. He says it’s probably the combination that leaves babies open to colonization by outside bacteria.
Wilmes says it’s concerning that babies delivered by C-section acquire microbes found in hospitals, including those with antimicrobial resistance genes, because the microbiomes we get at birth sometimes get locked in and remain with us as we grow up.
What that means for long-term health is unclear, says pediatrician Carine de Beaufort at the Luxembourg Hospital Center, who works with Wilmes. She points out that people born via C-section have higher rates of some conditions like autoimmune diseases. But, she says, scientists don’t currently understand why those rates are higher.
The UK team, Wilmes, and de Beaufort all plan to follow how baby gut microbiomes and health change over time.