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Gut microbiota have important implications for health by affecting the metabolism of diet and drugs. However, the specific microbial mediators and their mechanisms in modulating specific key intermediate metabolites from fungal origins still remain largely unclear. Toluquinol, as a key versatile precursor metabolite, is commonly distributed in many fungi, including <i>Penicillium</i> species and their strains for food production. The common 17 gut microbes were cultivated and fed with and without toluquinol. Metabolic analysis revealed that four strains, including the predominant <i>Enterococcus</i> species, could metabolize toluquinol and produce different metabolites. Chemical investigation on large-scale cultures led to isolation of four targeted metabolites and their structures were characterized with NMR, MS, and X-ray diffraction analysis, as four toluquinol derivatives (<b>1</b>–<b>4</b>) through O1/O4-acetyl and C5/C6-methylsulfonyl substitutions, respectively. The four metabolites were first synthesized in living organisms. Further experiments suggested that the rare methylsulfonyl groups in <b>3</b>–<b>4</b> were donated from solvent DMSO through Fenton’s reaction. Metabolite <b>1</b> displayed the strongest inhibitory effect on cancer cells A549, A2780, and G401 with IC₅₀ values at 0.224, 0.204, and 0.597 μM, respectively, while metabolite <b>3</b> displayed no effect. Our results suggest that the dominant <i>Enterococcus</i> species could modulate potential precursors of fungal origin and change their biological activity.