Gut Microbiome-Derived Metabolism Screen System Reveals Dehydrogenation Metabolism of Isorhynchophylline

Plant-derived natural products are commonly consumed orally and can be structurally modified by the gut microbiota, potentially altering their biological activity. However, high-throughput studies on their microbial metabolism remain limited. This study applied an <i>in vitro</i> screening system for microbiome-derived metabolism using liquid chromatography-mass spectrometry to analyze the metabolism of 200 natural products by human gut microbiota, and successfully annotated 118 natural products metabolized by gut microbiota. For the first time, metabolic reactions of isorhynchophylline and wilforgine in the intestine were documented. Notably, a substantial increase in the plasma concentration of isocorynoxeine was observed in human microbiota-colonized rats following isorhynchophylline administration compared to those without colonization, suggesting that the dehydrogenation of isorhynchophylline by gut microbiota observed in the <i>in vitro</i> screening system also occurs <i>in vivo</i>. 16S rRNA gene sequencing further revealed an increased abundance of <i>Klebsiella</i> and <i>Escherichia-Shigella</i> following isorhynchophylline administration, suggesting that these genera may influence its microbial transformation or pharmacological activity.