Shigella flexneri is the causative agent of bacillary dysentery in humans. Shigella spp. are one of the leading causes of diarrheal morbidity and mortality, especially among children in low- and middle-income countries. The rise of antimicrobial resistance combined with the lack of an effective vaccine for Shigella heightens the importance of studies aimed at better understanding previously uncharacterized aspects of Shigella pathogenesis.

The role of the gut microbiota in the pathogenesis of Shigella flexneri remains largely unknown. To understand the impact of the gut microbiota on S. flexneri virulence, we examined the effect of interspecies interactions with Bacteroides thetaiotaomicron (Bt), a prominent member of the human gut microbiota, on S. flexneri invasion. When grown in Bt conditioned medium, S. flexneri showed reduced invasion of human epithelial cells. This decrease in invasiveness of S. flexneri resulted from a reduction in the level of S. flexneri's master virulence regulator VirF. Reduction of VirF corresponded with a decrease in expression of a secondary virulence regulator virB, as well as expression of S. flexneri virulence genes required for invasion, intracellular motility, and spread. Repression of S. flexneri virulence factors by Bt conditioned medium was not caused by either a secreted metabolite or protein, but rather, was due to the presence of Bt outer membrane vesicles (OMVs) in the conditioned medium. The addition of purified Bt OMVs to S. flexneri growth medium recapitulated the inhibitory effects of Bt conditioned medium on invasion, virulence gene expression, and virulence protein levels.Total lipids extracted from either Bt cells or Bt OMVs also recapitulated the effects of Bt condition medium on expression of the S. flexneri virulence factor IpaC, indicating that Bt OMV lipids, rather than a cargo contained in the vesicles, are the active factor responsible for the inhibition of S. flexneri virulence.