Comparison of Gut Microbiomes Between Neonates Born by Cesarean Section and Vaginal Delivery: Prospective Observational Study

Abstract

Background: Balanced diversity and abundance of gut microbiome play important roles in human health, including neonatal health. Though not established, there is evidence that the delivery route could alter the diversity of neonatal gut microbiomes. Objective: The objective of the study was to investigate the differences in the gut microbiomes of neonates delivered via cesarean section compared to those born by vaginal delivery and to identify the predominant microbial taxa present in each group. Study Design: A prospective observational study of 281 healthy neonates born between February 2021 and April 2023 at Her Royal Highness Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Thailand, was performed. The study population was divided into two groups: 139 neonates born via vaginal delivery and 141 neonates born via cesarean section. The microbiota composition of each neonate's fecal sample was identified by using 16S ribosomal ribonucleic acid metagenomic sequencing. Results: Neonates delivered vaginally exhibited a gut microbiome with higher abundance and diversity than those delivered by cesarean delivery. Bifidobacterium was the dominant genus in both groups. Bifidobacterium breve was the dominant species and was significantly higher in cesarean-delivered neonates compared to those delivered vaginally (24.0% and 9.2%, respectively) (p < 0.001). However, the taxonomy of only 89 (64.0%) and 44 (31.43%) fecal samples could be identified from the vaginal and cesarean delivery groups, respectively. Conclusion: Route of delivery is associated with neonatal gut microbiome abundance and diversity. Neonates delivered via vaginal delivery exhibited higher diversity but lower abundance of the dominant species in the gut microbiome. Trial Registration: Thai Clinical Trials Registry identifier: TCTR20221024003.

Keywords: 16S rRNA; cesarean section; gut microbiome; neonates; vaginal delivery.

Figure 1

Flow chart of the study enrollment process.

Figure 2

Steps of the process performed.

Figure 3

Data analysis of next-generation sequencing workflow.

Figure 4

Genus of gut microbiome profiles generated by 16S rRNA full-length gene using Oxford nanopore sequencer. Eighty-nine samples of VG represented 16 bacteria genera with a percentage of relative abundance more than 0.5% and 44 samples of CS represented 10 bacteria genera with a percentage of relative abundance more than 0.5%.

Figure 5

Species of gut microbiome profiles generated by 16S rRNA full-length gene using Oxford nanopore sequencer.