Intestinal microbial ecology in premature infants assessed with non-culture-based techniques

J Pediatr. 2010 Jan;156(1):20-5. doi: 10.1016/j.jpeds.2009.06.063.


Objectives: To use 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: With non-culture-based techniques, we evaluated intestinal microbiota shortly after birth and during hospitalization in 23 neonates born at 23 to 32 weeks gestational age. Microbiota compositions were compared in 6 preterm infants in whom NEC, signs of systemic inflammation, or both developed with matched control subjects by using 16S ribosomal RNA 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 = .03), babies born to mothers with chorioamnionitis (P = .06), and in babies born at <30 weeks gestation (P = .03). A 16S ribosomal RNA sequence analysis detected Citrobacter-like sequences only in cases with NEC (3 of 4) and an increased frequency of Enterococcus-like sequences in cases and Klebsiella in control subjects (P = .06). The overall microbiota profiles in cases with NEC were not distinguishable from that in control subjects.

Conclusions: Microbial DNA in meconium of premature infants suggests prenatal influences.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Bacterial / analysis*
  • Enterocolitis, Necrotizing / microbiology*
  • Feces / microbiology*
  • Female
  • Humans
  • Infant, Newborn
  • Infant, Premature
  • Infant, Premature, Diseases / microbiology*
  • Male
  • Meconium / microbiology*
  • Polymerase Chain Reaction / methods
  • RNA, Ribosomal, 16S


  • DNA, Bacterial
  • RNA, Ribosomal, 16S