Integration of Macrogenomics and Metabolomics: Comprehensive Insights into the Effects of In Vitro Fermentation with Human Milk Exosomes on Infant Gut Microbiota

The role of human milk exosomes (HMEs) in maintaining infant intestinal health has attracted considerable attention, yet the mechanisms by which they regulate the infant gut microbiota remain to be elucidated. In this study, we constructed an in vitro fermentation model, combined with macrogenomics and nontargeted metabolomics technologies, to deeply analyze the effects of HMEs on the composition of intestinal microorganisms, the expression of functional genes, and the production of metabolites. It showed that HMEs significantly reduced the potential pathogenic bacteria like Escherichia coli, Klebsiella pneumoniae, Dysgonomonas capnocytophagoides, and Shigella flexneri, but increased Bacteroides fragilis and Bifidobacterium pseudocatenulatum. Moreover, HMEs promote key metabolic pathways including propionate and butyrate metabolism, glycolysis/glycogenesis, and amino acid metabolism. Consequently, beneficial intestinal metabolites such as short-chain fatty acids (SCFAs), amino acids, indoles, and secondary bile acids were elevated. It is speculated that HMEs may act as key signaling molecules or regulators to improve infant gut microecology.