Experimental data related to the study analyzing the effects of extracellular vesicles (EVs) derived from probiotic and commensal E. coli strains on liver function via the gut-liver axis. The study includes results from an in vivo model of neonatal rats and from HepG2 cells. In the in vivo model, neonatal rats received daily by oral gavage EVs from the probiotic EcN and the commensal EcoR12 from day 2 to day16 of life. Plasma and liver samples were collected on days 8 and 16 for analysis. The impact of the interventions on intestinal permeability was assessd by measuring plasma zonulin levels. The presence of EVs in the liver was confirmed by immunoblot detection of lipopolysaccharide (LPS) and outer membrane protein A (OmpA). The effects of adminstered EVs on liver function were evaluated by analyzing the expression of genes related to inflammation, oxidative stress, and lipid metabolism using RT-qPCR analysis . The modulatory effects observed in vivo were further validated in vitro by direct stimulation of HepG2 cells with EVs.