Objective To explore the community characteristics of endophyte in Sophora tonkinens and its correlation with the main active components of medicinal materials. To clarify the key functional bacteria that affect the pharmacodynamic components, and lay a foundation for the establishment of high-quality cultivation techniques of S. tonkinens based on microbial community regulation.

Method High-throughput sequencing was employed to analyze the endophytic bacterial and fungal community structures in 2-year-old (R2), 4-year-old (R4), and 6-year-old (R6) S. tonkinens. This was combined with the determination of alkaloid component content using high-performance liquid chromatography (HPLC). Spearman correlation analysis was then used to elucidate the relationships between the microbial communities and the bioactive components.

Result With the increase of planting years, the richness and diversity of endophytic bacteria increased significantly, while the diversity and richness of endophytic fungi changed little. The dominant phylum of endophytic bacteria was Proteobacteria, and the dominant phylum of fungi was Ascomycota. The dominant bacterial genera varied with years: R2 and R4 were unclassified_f__Alcaligenaceae, with relatively high abundance of 89.35% and 60.09%, respectively. R6 was Pseudomonas, and the relative abundance was 52.20%. The dominant fungal genera also changed significantly with years, the dominant genus of R2 was Minimelanolocus, the dominant genus of R4 was Codinaea, and the dominant genus of R6 was unclassified_k__Fungi. The content analysis of effective components showed that the content of matrine in R4 was 0.30 mg/g, which was significantly higher than R6 (P＜ 0.01). The content of oxymatrine was 16.26 mg/g, which was significantly higher than that of R2 and R6 (P＜ 0.001). The content of cytisine and N-methylcytisine in R6 was 0.99 mg/g and 0.052 mg/g, respectively, both significantly higher than that in R4 (P＜ 0.01). Correlation analysis showed that endophytic bacteria such as unclassified_f__Alcaligenaceae, Pseudomonas and Pantoea were significantly correlated with active ingredients (P＜ 0.05). Endophytic fungi of Dactylonectria also had a significant effect on the accumulation of active ingredients (P＜ 0.05).

Conclusion This study clarified the potential endophytic bacteria and fungi closely related to the active components of S. tonkinens, revealed the key role of specific functional bacteria in regulating the quality formation of medicinal materials, and provided a scientific basis for further analysis of the mechanism of endophytic bacteria-host interaction affecting the quality of medicinal materials and the formulation of high-quality cultivation strategies.