The gut bacteria of newborns differ between babies delivered by vaginal birth vs those delivered by cesarean birth, according to study results published in Nature. The researchers discovered that while babies delivered vaginally received most of their gut bacteria from their mothers, babies delivered by cesarean birth did not. In addition, babies delivered by cesarean harbored more bacteria commonly associated with hospital environments.

Although microbiome imbalances have been implicated in diseases, including diabetes, asthma, and allergies, the exact role of a newborn’s microbiome, how it develops, and the effects of differences in the microbiome due to different delivery methods has not been fully understood.

In this largest genomic investigation of neonatal microbiomes, researchers applied longitudinal sampling and whole genome shotgun metagenomic analysis to 1679 samples of gut microbiota (taken at several time points during the neonatal period and in infancy) from 596 full-term babies (39.5±1.37 weeks of gestation; 314 vaginal births) born in the United Kingdom. In addition, in a subset of these babies, the researchers collected matched samples from mothers (175 mothers paired with 178 babies). Using DNA sequencing and genomics analysis, the researchers identified the type of bacteria present and found a significant difference between the 2 delivery methods. Some babies in the study were also followed up until 1 year of age.

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Researchers indicated that compared with babies of cesarean birth, those of vaginal birth had many more health-associated commensal bacteria from their mothers. In the 314 babies born vaginally, gut microbes, including Bifidobacterium, Bacteroides, and Parabacteriodes, made up 68.3% (95% CI, 65.7%-71.0%) of the neonatal gut microbiota. These bacteria were scarcer in the guts of babies born by cesarean delivery. Instead, species commonly associated with the hospital environment and more likely to have antimicrobial resistance, including Enterococcus and Clostridium, accounted for 83.7% of the total microbiota composition during the neonatal period. Researchers isolated, grew, and sequenced the genomes of more than 800 of these potentially pathogenic bacteria, confirming virulence factors and clinically relevant antimicrobial resistance in opportunistic pathogens that may predispose individuals to opportunistic infections.

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The study also suggested that, along with the birth method, antibiotics delivered during birth may also determine infant gut microbiota. The study revealed that babies whose mothers took antibiotics had fewer Bacteroides, suggesting that some of the bacterial differences were related to maternal antibiotic exposure and not a lack of exposure to vaginal bacteria at birth.

Study limitations included the insufficient evidence from metagenomics and the whole-genome sequencing of cultured isolates to rule out maternal origin of the opportunistic pathogens and the lack of retrospective sampling of hospital environmental sources.

“This highlights the need for large scale, long-term cohort studies that also sample home births to better understand the consequence of the perinatal factors in hospital birth and establish whether perturbation of the neonatal microbiota negatively affects health outcomes in childhood and later life,” the researchers concluded.


Shao Y, Forster SC, Tsaliki E, et al. Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth [published online September 18, 2019]. Nature. doi:10.1038/s41586-019-1560-1

This article originally appeared on Gastroenterology Advisor