Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells.

Sheikh, A.; Scano, C.; Xu, J.; Ojo, T.; Conforti, J. M.; Haberman, K. L.; King, B.; Martinez, A. S.; Pujol, M.; Watkins, J.; Lotter, J.; Lin, E. L.; Zechmann, B.; Sevcik, A.; Sayes, C.; Gallagher, E. S.; Lang, S. P. L.; Mell, J.; Ehrlich, G. D.; Taube, J. H.; Greathouse, K. L.

doi:10.1101/2025.06.25.661399

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bioRxiv · 10.1101/2025.06.25.661399

Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells.

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Abstract

Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbe-derived RNAs carried by outer membrane vesicles (OMVs) to host immune responses remain unclear. This study investigated the role of OMVs and OMV-associated small RNA (sRNA) species from pathogenic and commensal Bacteroides fragilis (ETBF and NTBF respectively) in eliciting different immune responses from intestinal epithelial cells. To distinguish the differences in the sRNA profiles of the two strains and their OMVs, RNA-seq, qRT-PCR, and northern blotting were conducted to identify enrichment of discrete sRNA species in OMVs, which were also differentially expressed between the two strains. Specifically, both coding and non-coding RNAs were enriched in OMVs from NTBF and ETBF, with BF9343_RS22680 and BF9343_RS17870 being significantly enriched in ETBF OMVs compared to NTBF. To understand the effects of OMVs on pattern recognition receptors, reporter cells of Toll-like receptor (TLR) activation were treated with OMVs, demonstrating activation of TLRs 2, 3, and 7. Treatment of Caco-2 and HT29-MTX cells with OMVs demonstrated increased expression of IL-8. Surprisingly, we discovered that degradation of RNase-accessible RNAs within ETBF OMVs, but not NTBF OMVs, resulted in vesicles with enhanced capacity to stimulate IL-8 expression, indicating that these extravesicular RNAs exert an immunosuppressive effect. This suggests a dual role for OMV-associated RNAs in modulating host immune responses, with implications for both bacterial pathogenesis and therapeutic applications. Graphical Abstract

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Sheikh, A., Scano, C., Xu, J., Ojo, T., Conforti, J. M., Haberman, K. L., King, B., Martinez, A. S., Pujol, M., Watkins, J., Lotter, J., Lin, E. L., Zechmann, B., Sevcik, A., Sayes, C., Gallagher, E. S., Lang, S. P. L., Mell, J., Ehrlich, G. D., Taube, J. H., Greathouse, K. L.. 2025-06-27. Outer membrane vesicles from Bacteroides fragilis contain coding and non-coding small RNA species that modulate inflammatory signaling in intestinal epithelial cells.. https://doi.org/10.1101/2025.06.25.661399

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