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Inflammatory bowel disease (IBD) is associated with dysbiosis and intestinal barrier dysfunction, as indicated by epithelial hyperpermeability and high levels of mucosal-associated bacteria. Changes in gut microbiota may be correlated with IBD pathogenesis. Additionally, microbe-based treatments could mitigate clinical IBD symptoms. Plasmon-activated water (PAW) is known to have an anti-inflammatory potential. In this work, we studied the association between the anti-inflammatory ability of PAW and intestinal microbes, thereby improving IBD treatment. We examined the PAW-induced changes in the colonic immune activity and microbiota of mice by immunohistochemistry and next generation sequencing, determined whether drinking PAW can mitigate IBD induced by 2,4,6-trinitrobenzene sulfonic acid (TNBS) and dysbiosis through mice animal models. The effects of specific probiotic species on mice with TNBS-induced IBD were also investigated. Experimental results indicated that PAW could change the local inflammation in the intestinal microenvironment. Moreover, the abundance of <i>Akkermansia</i> spp. was degraded in the TNBS-treated mice but elevated in the PAW-drinking mice. Daily rectal injection of <i>Akkermansia muciniphila</i>, a potential probiotic species in <i>Akkermansia</i> spp., also improved the health of the mice. Correspondingly, both PAW consumption and increasing the intestinal abundance of <i>Akkermansia muciniphila</i> can mitigate IBD in mice. These findings indicate that increasing the abundance of <i>Akkermansia muciniphila</i> in the gut through PAW consumption or other methods may mitigate IBD in mice with clinically significant IBD.