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Open Access Highly Accessed Research

Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants

Erika C Claud12*, Kevin P Keegan3, Jennifer M Brulc3, Lei Lu1, Daniela Bartels4, Elizabeth Glass4, Eugene B Chang2, Folker Meyer34 and Dionysios A Antonopoulos23

Author Affiliations

1 Section of Neonatology, Department of Pediatrics, The University of Chicago, Chicago, IL, USA

2 Section of Gastroenterology, Department of Medicine, The University of Chicago, Chicago, IL, USA

3 Institute for Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA

4 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA

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Microbiome 2013, 1:20  doi:10.1186/2049-2618-1-20

Published: 10 July 2013

Abstract

Background

Preterm infants represent a unique patient population that is born functionally immature and must accomplish development under the influence of a hospital environment. Neonatal necrotizing enterocolitis (NEC) is an inflammatory intestinal disorder affecting preterm infants. The purpose of this study was to evaluate the progression of intestinal microbiota community development between preterm infants who remained healthy compared to preterm infants who developed NEC.

Results

Weekly fecal samples from ten preterm infants, five with NEC and five matched healthy controls were obtained. Bacterial DNA from individual fecal samples was subjected to sequencing of 16S rRNA-based inventories using the 454 GS-FLX platform. Fecal samples from control infants demonstrated a temporal pattern in their microbiota, which converged toward that of a healthy full term breast-fed infant. Microbiota development in NEC patients diverged from controls beginning three weeks prior to diagnosis. Shotgun metagenomic sequencing was performed to identify functional differences in the respective microbiota of fecal samples from a set of twins in which one twin developed NEC and one did not. The majority of the differentially abundant genes in the NEC patient were associated with carbohydrate metabolism and mapped to members of the family Enterobacteriaceae. This may indicate an adaptation of the community to an altered profile of substrate availability for specific members as a first step towards the development of NEC. We propose that the microbial communities as a whole may metabolize milk differently, resulting in differential substrate availability for specific microbial groups. Additional differentially represented gene sets of interest were related to antibiotic resistance and vitamin biosynthesis.

Conclusions

Our results suggest that there is a temporal component to microbiome development in healthy preterm infants. Thus, bacteriotherapy for the treatment or prevention of NEC must consider this temporal component of the microbial community in addition to its taxonomic composition and functional content.

Keywords:
Necrotizing enterocolitis; Preterm infant microbiome; Metagenomics; Carbohydrate metabolism