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Background  A foodborne pathogen,  Vibrio vulnificus , encounters normal microflora inhabiting the gut environments prior to causing fatal septicemia or gastroenteritis and should overcome the barriers derived from the gut commensals for successful infection. Its interactions with gut commensals during the infection process, however, have not yet been understood. In the present study, the effect of  V. vulnificus  on the community structures of gut microbiota in mice was examined.    Results  Analyses of microbiota in the fecal samples of mice that died due to  V. vulnificus  infection revealed the decreased abundance of bacteria belonged to Bacteroidetes, notably, the species  Bacteroides vulgatus . In vitro coculturing of the two bacterial species resulted in the decreased survival of  B. vulgatus . The antagonistic effect of  V. vulnificus  against  B. vulgatus  was found to be mediated by cyclo-Phe-Pro (cFP), one of the major compounds secreted by  V. vulnificus . cFP-treated  B. vulgatus  showed collapsed cellular morphology with an undulated cell surface, enlarged periplasmic space, and lysed membranes, suggesting the occurrence of membrane disruption. The degree of membrane disruption caused by cFP was dependent upon the cellular levels of ObgE in  B. vulgatus . Recombinant ObgE exhibited a high affinity to cFP at a 1:1 ratio. When mice were orally injected with cFP, their feces contained significantly reduced  B. vulgatus  levels, and their susceptibility to  V. vulnificus  infection was considerably increased.    Conclusions  This study demonstrates that  V. vulnificus -derived cFP modulates the abundance of the predominant species among gut commensals, which made  V. vulnificus  increase its pathogenicity in the hosts.Video abstractSupplementary Information  The online version contains supplementary material available at 10.1186/s40168-021-01095-w.

Vibrio vulnificus induces the death of a major bacterial species in the mouse gut via cyclo-Phe-Pro