Shigella infections remain a major public health issue in developing countries. One model of Shigella pathogenesis suggests that the microfold epithelial cells in the small intestine are the preferred initial site of infection. However, a growing body of evidence supports an alternative model whereby Shigella primarily infects a much wider range of epithelial cells that reside primarily within the colon. Here, we investigated whether the luminal pH difference between the small intestine and colon could provide evidence in support of either model of Shigella flexneri pathogenesis. As virulence factors leading to cellular invasion are linked to biofilms in S. flexneri, we examined the effect of pH on S. flexneri's ability to form and maintain adherent biofilms when induced by deoxycholate. We showed that a basic pH inhibited formation and dispersed pre-assembled mature biofilms while an acidic pH (similar to the colonic environment) did not have either of these effects. To further elucidate this phenomenon at the molecular level, we probed the transcriptomes of biofilms and S. flexneri grown in different pH conditions. We identified specific amino acid metabolic pathways (cysteine and arginine) that were enriched in the bacteria that formed the biofilms, but decreased upon pH increase. We then utilized a type III secretion system reporter strain to show that increasing pH reduced deoxycholate-induced virulence of S. flexneri in a dose dependent manner. Taken together, these experiments support a model whereby Shigella infection is favored in the colon because of the local pH differences in these organs. ### Competing Interest Statement The authors have declared no competing interest.
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