Gut microbiota in neonates with congenital gastrointestinal surgical conditions: a prospective study

Background There is limited information on gut microbiota of neonates with congenital gastrointestinal surgical conditions (CGISCs) available. Methods This study compared stool microbiota and short-chain fatty acids (SCFAs) of 37 term infants with CGISCs with 36 term healthy infants (HIs). Two stool samples were collected from each infant: as soon as possible after birth (week 1) and 10–14 days of life (week 2). Results Bacterial richness and alpha diversity were comparable between CGISCs and HIs at week 1 and week 2 (all p > 0.05). Beta diversity analysis revealed that at week 1, CGISCs had similar community structures to HIs ( p = 0.415). However, by week 2, community structures of CGISCs were significantly different from HIs ( p = 0.003). At week 1, there were no significant differences in the relative abundances of genera Bifidobacterium and Bacteroides between CGISCs and HIs. At week 2, the relative abundance of Bifidobacterium was significantly lower in CGISCs (mean percentage 7.21 ± 13.49 vs. 28.96 ± 19.6; p = 0.002). Bacteroides were also less abundant in the CGISC group (mean percentage 0.12 ± 0.49 vs. 6.59 ± 8.62; p = 0.039). Relative abundance of genera Pseudomonas and Escherichia–Shigella were higher in CGISCs. At week 2, stool concentrations of all SCFAs were lower in CGISCs (all p