INTRODUCTION. Previous research has identified delivery mode as an important factor influencing infant gut microbiome composition, with caesarean delivered infants having delays in colonisation of bacteria such as Bacteroides and Bifidobacterium. However, most women who undergo caesarean section receive intravenous prophylactic antibiotics prior to undergoing surgery, which exposes baby to antibiotics perinatally. Hence the primary aim of this pilot study was to evaluate whether delivery mode or perinatal maternal antibiotic use is more important for composition of the infant and maternal gut microbiota at 6 weeks post-partum.
METHODS. The profile of 25 mother-infant dyads (n = 9 vaginal delivery-no antibiotics (VnAB), n = 9 caesarean delivery – antibiotics (CS), n = 7 vaginal delivery – antibiotics (VAB)) gut microbiota at 6 weeks post-partum was assessed by shotgun metagenomic sequencing. Quality control was conducted in Galaxy and composition was assessed using MetaPhlAn 4.0. Analysis of results was conducted in R with packages ‘phyloseq’, ‘mixOmics’, ‘vegan’ and ‘ancombc’.
RESULTS. The maternal gut microbiome was less even in women delivered by C-section (P<0.001) and those exposed to perinatal antibiotics (P<0.05) at 6 weeks post-partum. Women delivered by C-section also had increased abundance of Prevotellaceae in their gut microbiome. For the infants, mode of delivery (P=0.007) but not perinatal antibiotics exposure changed the beta diversity but not the alpha diversity of the gut microbiome. When considering the evenness by both antibiotic and delivery mode status, VAB formed an intermediate step between VnAB and CS. Bacteria of the genus Bacteroides were significantly reduced in caesarean delivered infants and these infants also had a reduced abundance of the L-ornithine biosynthesis pathway, which could imply a reduced integrity of the gut wall. However, no differences were detected by antibiotic use status at the genus level. Caesarean delivered infants shared less species with their mothers (P<0.05) than vaginally delivered infants. However, perinatal antibiotics had no effect on shared bacteria.
CONCLUSION. In this small sample, it seems both delivery mode and maternal antibiotic use just prior to birth influence infant and maternal gut microbiomes, though delivery mode may be the stronger factor, particularly in infants. As maternal gut microbiomes also seem to be altered by delivery mode and maternal antibiotic use – this raises the question of whether this may have implications for ongoing transmission after birth. However, this was a small study and potentially influenced by batch effects, hence more research is needed in this area.