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

Alterations to the community structure and function of the microbiome are associated with changes to host physiology, including immune responses. However, the contribution of microbial-derived RNAs carried by outer membrane vesicles (OMVs) to host immune responses remain unclear. This paper investigates 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 in intestinal epithelial cells. To distinguish the differences in the sRNA profiles of both strains and their OMVs, RNA-seq, qRT-PCR, and northern blotting was conducted to identify enrichment of discrete sRNA species in OMVs that were also differentially expressed between the two strains. To understand the effects of OMVs on pattern recognition receptors, Toll-like receptor (TLR) reporter cells were treated with OMVs and activation of TLRs 2, 3, and 7 was observed. Treatment of Caco-2 and HT29-MTX cells with OMVs demonstrated increased expression of IL-8; additionally, RNase treatment of vesicles showed decreased capacity to promote IL-8 expression and increased TLR stimulation in the cell lines, highlighting a potential immunosuppressive role of unprotected RNAs. These findings suggest a key function of OMV-loaded small RNAs in modulating host immune responses.