Impact of C-Section, Antibiotics Exposure on Infant Microbial Colonization

Baby being born or baby minutes after the birth.
Investigators assessed the impact of maternal antibiotic administration timing on infant gut colonization in babies delivered via cesarean section.

Study data published in Gut confirm that infant microbiome colonization is significantly affected by cesarean section (CS) delivery. However, the timing of maternal antibiotics administration during delivery did not appear to further affect initial microbiome acquisition.

Current CS guidelines recommend maternal antibiotic administration prior to skin incision rather than after umbilical cord clamping. However, the former procedure antenatally exposes infants to antibiotics. To assess the impact of antibiotic administration timing on infant gut colonization, investigators conducted a randomized controlled trial of women delivering via CS at an obstetrics department in Amsterdam between 2015 and 2017.

Patients were randomly assigned to receive antibiotics either prior to skin incision (n=20) or after umbilical cord clamping (n=20). A control group of women giving birth vaginally was also included (n=23). Infant fecal microbiota were characterized via 16S ribosomal RNA gene sequencing and whole-metagenome shotgun sequencing at 1, 7, and 28 days after birth and at 3 years of age.

Demographic and clinical variables were comparable between mothers in the CS groups and vaginal delivery group. CS delivery had a profound impact on the diversity and abundance of multiple phyla, genera, and species in the infant microbiome. Compared with vaginally born infants, babies delivered via CS had substantially reduced Shannon diversity in the month following birth (P <.001).

Further, infants born by CS had decreased abundance of species belonging to the Bacteroides and Bifidobacterium genera at 7 and 28 days post-delivery. Concurrent increases in the abundance of genus enterococci and phylum Proteobacteria were observed during the same time period. By 3 years of age, however, microbial differences were no longer observed at the phylum or genus level.

Diversity and abundance were not significantly different between the CS groups at any time point, suggesting that route and timing of antibiotics administration does not affect infant microbial colonization.

Results from this study confirm prior findings that CS delivery substantially affects the initial colonization of the gut. The timing of maternal antibiotic administration did not appear to change this effect. In terms of study limitations, investigators cited the small study cohort and the relatively short follow-up period, which prevented formation of conclusions about long-term gut health following CS delivery.

“Our findings suggest that maternal antibiotic administration prior to CS does not result in a second hit on the compromised microbiome,” investigators wrote. “Future studies are needed to confirm that beneficial effects for the mother by the revised guidelines do not impact long-term health of the infants.”

Disclosure: Several study authors declared affiliations with biotech, pharmaceutical, and/or device companies. Please see the original reference for a full list of authors’ disclosures. 


Dierikx T, Berkhout D, Eck A, et al. Influence of timing of maternal antibiotic administration during caesarean section on infant microbial colonisation: a randomised controlled trial. Gut. Published online November 21, 2021. doi: 10.1136/gutjnl-2021-324767