Microbial colonization is thought to play an important role in risk of NEC. Breast feeding is one of many factors that influence the composition of the intestinal microbiota in term infants; limited studies suggest that diet may have less of an effect on the composition of the intestinal microbiota in the premature infant than other factors (such as antibiotic administration). New bioinformatic tools to correlate the extensive array of fecal metabolites and the fecal microbiota offer great promise in understanding the factors that influence the microbiota of the premature infant. Studies to date suggest that the metabolites differing between human milk-fed and formula-fed infants that are most closely associated with shaping the microbiota include sugars and fatty acids. Whether and how these metabolites differ functionally in the extremely premature infant is unknown.