A major focus of gut microbiome research in early life is how delivery mode affects the newborn gut microbiota and its impact on the health of the growing child. Although previous studies revealed that infants born by Caesarean section (C-section) develop a gut microbiota composition that more closely resembles adult skin and the hospital environment, and which may predispose newborns to opportunistic pathogens, such observations may have been confounded by maternal antibiotics during labor.

Researchers from the Wilhelmina Children’s Hospital (Netherlands), Spaarne Gasthuis Academy Hoofddorp and Haarlem (Netherlands), the National Institute for Public Health and the Environment (Netherlands) and the University of Edinburgh (United Kingdom) have shown that C-section-associated gut microbiota at one week of life may predispose infants to respiratory infections in the first year, regardless of intrapartum antibiotics.

In order to rule out the impact of maternal antibiotics administered during labor on the early-life gut microbiota, the researchers postponed routine antibiotic administration to mothers until after cord clamping in 74 vaginally delivered and 46 C-section born infants.

They noted that fecal microbiota composition differed between C-section born and vaginally delivered infants during the first year of life. Vaginally delivered infants had a gut microbiota composition profile that remained quite stable over the first year of life, with an enrichment of Bifidobacterium species and a depletion of potentially pathogenic Enterococcus and Klebsiella species.

A parallel subset of infants exclusively fed with formula confirmed that the above findings were not due to infants’ indirect exposure to antibiotics via breast milk.

Beyond mode of delivery, other factors that affected fecal microbiota composition during the study period included age, breastfeeding, daycare attendance, siblings, pacifier use, and antibiotic use prior to sampling.

The authors also provided evidence of direct maternal fecal microbiota seeding during birth in vaginally delivered children. The vaginally delivered infants’ fecal microbiota composition was more similar to that of their own mothers than to that of other mothers over time, whereas C-section children’s were not.

The authors went a step further and also explored how changes in the microbiota related to the mode of delivery may affect health outcomes in children.

Although the impact of delivery mode on the overall microbial community’s composition persisted until the age of 2 months and afterwards decreased gradually, the most pronounced difference in fecal microbiota composition between vaginally delivered infants and those born by C-section was reported at 1 week of age.

Even more interesting is the fact that gut microbiota composition at one week of life was associated with the number of respiratory infection events during the first year of life. It is also worth noting that the taxa that appeared to drive this prediction—Enterococcus, Bifidobacterium, and Klebsiella—were more abundant in infants born via C-section.

Moreover, vaginally delivered children tended to be prescribed fewer courses of antibiotics in the first year of life.

This study shows that changes in gut microbiota composition driven by delivery mode may persist during the first year of life. The observation that bacterial taxa associated with respiratory infections in the first year of life were more abundant in C-section children suggests a link between mode of delivery and the growing child’s health outcomes.



Reyman M, van Houten MA, van Baarle D, et al. Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life. Nat Commun. 2019; 10(1):4997. doi: 10.1038/s41467-019-13014-7.