Newborn babies require healthy and beneficial microbes in their gut. Normal or vaginal birth provides them with these useful microorganisms, but cesarean delivery interrupts the transfer of microbes. The infant can become more susceptible to disease-causing pathogens. This study assesses the impact of a C-section on the baby’s gut health beyond the neonatal period.

Pregnant women in North Carolina were enrolled for a longitudinal study in 2013-15. Their offspring got examined for 12 months. The study examined the delivery modes of vaginal and C-section. A subset of participants was enrolled over three months for sample collection. They provided gut microbiota and fecal short-chain fatty acids(SCFA) between 3 and 12 months after birth. Gas chromatography quantified the SCFA concentrations, while Illumina MiSeq was used to sequence the 16S rRNA V4 region. Beta-binomial and linear regression were used for microbiota amplicon sequence variants(ASVs) and fecal SCFA.

The analytical sample of 70 infants had 25 or 36% C-section births. The cesarean deliveries had a differential abundance of 14 ASV and 13 ASV at 3 and 12 months. These infants had more pathobionts like C. neonatale and C.perfringens with P of 0.04. Their beneficial Bacteroides spp. and Bifidobacterium were in lower abundance.

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Cesarean infants had less beneficial microbes and were at risk of pathobiont colonization. Their fecal butyrate excretion was also higher at three months with P less than 0.005.