Intestinal Microbial Ecology in Premature Infants Assessed with Non–Culture-Based Techniques

Objectives—To utilize high throughput techniques to analyze intestinal microbial ecology in premature neonates, who are highly susceptible to perturbations of the luminal environment associated with necrotizing enterocolitis (NEC) and late onset sepsis.. Study design—Using non-culture based techniques we evaluated intestinal microbiota shortly after birth and during hospitalization in 23 neonates born at 23-32 weeks gestational age. Microbiota compositions were compared in six preterm infants who developed NEC and/or signs of systemic inflammation versus matched controls using 16S rRNA pyrosequencing. Results—Microbial DNA was detected in meconium suggesting an intrauterine origin. Differences in diversity were detected in infants whose mothers intended to breast feed (p=0·03), babies born to mothers with chorioamnionitis (p=0·06) and in babies born at less than 30 weeks gestation (p=0·03). A 16S rRNA sequence analysis detected Citrobacter-like sequences only in cases with NEC (three out of four) as well as an increased frequency of Enterococcus-like sequences in cases and Klebsiella in controls (p=0·06). The overall microbiota profiles in cases with NEC were not distinguishable from that in controls. Conclusions—Microbial DNA in meconium of premature infants suggests prenatal influences. Microbial ecology alterations prior to NEC and sepsis suggest intestinal microbial origins.