Strain-Specific microRNA Reprogramming of Human Dendritic Cells by Probiotic and Commensal Escherichia coli Outer Membrane Vesicles

Outer membrane vesicles (OMVs) from gut Escherichia coli are emerging postbiotic candidates, yet how probiotic versus commensal strains differentially program human dendritic cells (DCs) remains poorly defined. Here we compared OMVs from probiotic E. coli Nissle 1917 (EcN) and commensal strains ECOR12 and ECOR63 in human monocyte-derived DCs, integrating cytokines and microRNAs (miRNAs). All OMVs drove DC maturation, increasing CD83 and secretion of IL-6, IL-10 and TNF-α, but with strain-specific patterns: ECOR12 preferentially increased IL-10, whereas EcN and ECOR63 induced stronger IL-6/TNF-α outputs. EcN and ECOR12 OMVs upregulated miR-155-5p and let-7i-3p, while ECOR12 selectively boosted miR-146b-5p and EcN preferentially induced miR-29a-5p, linking vesicle origin to regulatory circuits controlling TLR signalling and epithelial barrier–related pathways. Principal component analysis showed that the first two components captured 96.2% of total variance, clearly segregating strains. MANOVA confirmed a robust multivariate strain effect (Pillai = 1.99, p < 2.2×10⁻¹⁶), and univariate models showed that strain explained 78–91% of cytokine variance and 98–99% of miRNA variance (R² up to 0.993). These data support OMVs as nanoscale conveyors of strain-encoded information that imprint distinct cytokine/miRNA fingerprints on DCs and provide mechanistic biomarkers for microbiota–immune crosstalk.