Using a modified fecal fermentation system, silymarin was fermented in 96-well deep well plates inoculated with feces from 20 human healthy donors. Samples of the fermentation liquid were collected at five time points (0, 2, 4, 8 and 24 h) for metabolite profiling by LC-MS and 1 H-NMR and assessment of microbial composition at 0 and 24 h by 16S rRNA sequencing.