Longitudinal 16rDNA-targeted analysis of the gut microbiome in preterm infants affected from necrotising enterocolitis and matched controls

Necrotizing enterocolitis (NEC) is the most common life-threatening gastrointestinal emergency experienced by premature infants in the New-born Intensive Care Unit. NEC has been shown to be associated with altered gut microbiota characterized by delayed bacterial colonization which may be related to the prolonged presence of facultative anaerobes rather than strict anaerobes. Several studies reported certain genera such as Lactobacillus and Bifidobacteria to be protective against NEC, while other genera such Klebsiella, Escherichia and Enterobacter, Clostridia, and Staphylococcus could be implicated in the pathogenesis of the disease. Most of studies focused on 16S rDNA metabarcoding limiting bacterial species identification. In this study, we applied 16S rRNA gene capture coupled to sequencing to identify in depth stool bacterial species. We analysed longitudinally stool samples collected one week before NEC onset, from 9 infants affected from NEC and 10 matched controls.