Alternative nutritional and clinical care practices for NEC prevention drive distinct profiles and functional responses in the preterm gut microbiome

Preterm infants with very low birthweight are at serious risk for necrotizing enterocolitis. To functionally analyse the principles of three successful preventive NEC regimens, we characterized faecal samples of 54 infants (< 1,500 g, n = 383) longitudinally (two weeks) with respect to gut microbiome profiles (bacteria, archaea, fungi, viruses), microbial function, virulence factors, antibiotic resistances and metabolic profiles, including human milk oligosaccharides (HMOs) and short-chain fatty acids. Probiotic Bifidobacterium longum ssp. infantis supplementation affected microbiome development globally, pointing toward the genomic potential to convert HMOs. Engraftment of Bifidobacterium substantially reduced microbiome-associated antibiotic resistance as compared to regimens using probiotic Lactobacillus rhamnosus or no supplementation. Crucially, the beneficial effects of Bifidobacterium supplementation depended on simultaneous feeding with HMOs. We demonstrate that preventive regimens have the highest impact on early maturation of the gastrointestinal microbiome, enabling the establishment of a resilient microbial ecosystem that reduces pathogenic threats in at-risk preterm infants.