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Background  Studies of microbiota composition of infants with small intestinal ostomy due to various etiologies are limited. Here, we characterized the intestinal microbiota of neonates with ileostomy resulting from distinct primary diseases.    Methods  Fifteen patients with necrotizing enterocolitis, eight patients with meconium peritonitis, and seven patients with Hirschsprung’s disease were included in the study. The small intestinal microbiota composition in infants with ileostomy caused by these diseases was studied.    Results  Microbial diversity in neonatal ileostomy fluid was generally low, and was dominated by members of the Proteobacteria and Firmicutes phyla. At the genus level, the most abundant were  Klebsiella ,  Escherichia-Shigella ,  Streptococcus ,  Clostridium  sensu stricto 1,  Enterococcus , and  Lactobacillus .  Streptococcus  and  Veillonella  are related to carbohydrate metabolism and immunity, and breastfeeding can increase the proportion of these potentially beneficial bacteria. The proportion of  Bifidobacterium  in the breastfeeding group was higher than that in the non-breastfeeding group, and incidence of colitis and sepsis was reduced in the breastfeeding group. The proportion of  Bifidobacterium  increased and incidence of colitis and sepsis decreased in the breastfeeding group compared with the non- breastfeeding group, but there was no significant difference. The increase in body weight in the breastfeeding group was observed to be higher than in the non-breastfeeding group.    Conclusions  Excessive  Klebsiella  and  Escherichia-Shigella  and low abundance of  Streptococcus ,  Veillonella  and  Faecalibacterium  suggests that the small intestinal microbiota is in an unhealthy state after ileostomy. However,  Streptococcus ,  Faecalibacterium , and  Veillonella  species were frequently present, suggesting that expansion of these bacteria might assist the development of the immune system after surgery.

Small intestinal microbiota composition and the prognosis of infants with ileostomy resulting from distinct primary diseases