Abstract:[Objective] Ginkgo biloba extract plays an important role in the prevention and treatment of cardiovascular and nervous system diseases. In consideration of the fact that gut microbiota has been identified as a new drug target, it is of great significance to study the interactions between ginkgetin and ginkgolide B with human gut microbiota, which will lay a foundation for further understanding the function and mechanism of Ginkgo biloba extract. [Methods] In this study, batch fermentation, bacterial amount detection, 16S rDNA high-throughput sequencing, GC and HPLC measurement were used to study the interactions between ginkgetin and/or ginkgolide B with human gut microbiota in vitro. [Results] Neither ginkgetin nor ginkgolide B alone had a significant effect on the total amount of gut microbiota, the composition of intestinal flora and the production of short chain fatty acids by the gut microbiota. However, when ginkgetin and ginkgolide B were added in combination, the proportion of bacterial represented by the family Coriobacteriaeae and genus Cupriavidus increased significantly, while the proportion represented by the genus Gemella decreased significantly. Functional gene prediction analysis found that genes encoding K00076, K12143, K07716, and K00220 significantly enriched in the presence of ginkgetin and ginkgolide B. Moreover, K00076 and K00220 are oxidoreductases that catalyze the transfer of electrons from the CH-OH donor group and may be involved in the metabolism and modification of ginkgetin and ginkgolide B. The degradation and modification rates of ginkgetin and ginkgolide B by human gut microbiota in vitro were ~70% and ~35%, respectively. [Conclusion] The relative percentage of some intestinal bacteria was significantly changed by the combined addition of ginkgetin and ginkgolide B in vitro. Meanwhile, human gut microbiota has the function on metabolism or modifying ginkgetin and ginkgolide B.