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

Outer membrane vesicles (OMVs) are tractable, cell-free microbial outputs that can shape innate immune programs. Here, we compared OMVs from the probiotic Escherichia coli Nissle 1917 (EcN) and the commensal strain ECOR12 in a paired within-donor model of human monocyte-derived dendritic cells (Mo-DCs) (N = 20). In the core integrated arm, Mo-DCs were exposed to iDC control, EcN OMVs, or ECOR12 OMVs (10 µg/mL, 24 h) and profiled for maturation markers (CD14, CD83, CD209), cytokines (IL-6, TNF-α, IL-10), and a targeted miRNA panel (miR-155-5p, let-7i-3p, miR-146b-5p, miR-29a-5p). Both OMV types promoted maturation (increased CD83 and reduced CD14), but generated distinct cytokine–miRNA configurations, with ECOR12 tending toward an IL-10–high profile and EcN toward higher IL-6/TNF-α tendencies. Multivariate integration separated conditions into reproducible, strain-specific immune fingerprints, supporting the key take-home that probiotic versus commensal E. coli OMVs imprint distinguishable coordinated response states in human DCs. In an extended phenotyping arm, ECOR63 OMVs were evaluated by ELISA and flow cytometry only and were not included in miRNA profiling or integrated PCA due to unavailable matched miRNA measurements.