Metagenomes from human infant fecal samples with and without necrotizing enterocolitis

Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. This study compares microbial communities of 10 co-hospitalized infants, five of which had a diagnosis of necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, a genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants that developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically-relevant time scales.