Development of the preterm infant gut and gastric residuals microbiome

Prematurity, defined as birth before 37 completed weeks of gestation, is the leading cause of mortality in children under five and affects approximately 11% of live births globally--around 15 million infants each year. Despite advances in neonatal care, preterm infants remain at an increased risk for a range of complications. One widely used clinical practice in neonatal intensive care units (NICUs) is the monitoring of gastric residuals (GRs) to assess feeding tolerance and guide enteral nutrition. While the clinical significance of GRs is debated, their microbial composition has not been extensively studied. In this study, we performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize their gut and stomach microbiomes. To our knowledge, this is the first study to describe the microbial landscape of GR in preterm infants. We identified 11 distinct GR clusters, often dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with GR aspiration frequency. Longitudinal analysis revealed temporal colonization patterns, with early dominance of Staphylococcus epidermidis and Bradyrhizobium, and later emergence of Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. In stool samples, 8 microbial clusters were found, frequently enriched with Enterobacteriaceae. Early samples rich in S. epidermidis were associated with higher gestational age and lower microbial richness, while Bifidobacterium breve, a beneficial gut commensal, appeared later in hospitalization. Comparative analysis showed overlap between gut and gastric microbiota, though stomach samples were more dynamic and exhibited less intra-subject similarity. Strain-level resolution revealed both subject-specific (e.g., E. coli, K. pneumoniae) and widely shared (e.g., S. epidermidis) taxa. We also identified a pathogenic Klebsiella aerogenes strain associated with bacteremia with distinct genomic features a week ahead of its first clinical isolation. These findings provide novel insights into the dynamic and niche-specific microbial colonization of preterm infants.