Objective To identify key bacterial taxa associated with saikosaponins content. Methods Rhizosphere soil, root surface soil, and root samples of Bupleurum chinense, B. falcatum, and B. scorzonerifolium were collected. Total DNA was extracted for metagenomic analysis, and UPLC-MS was used to determine the contents of saikosaponin A (SSA), saikosaponin B₂(SSB₂), saikosaponin B₄ (SSB₄), saikosaponin C (SSC), saikosaponin D (SSD), saikosaponin E (SSE), and saikosaponin F (SSF) in the roots. Pearson correlation analysis was then employed to identify significant relationships between these medicinal components and the dominant bacterial species. Results SSD exhibited the highest content among the seven saikosaponins analyzed, with average concentrations of 217.5 μg/g in B. chinense, 116.75 μg/g in B. falcatum, and 139.7 μg/g in B. scorzonerifolium. B. falcatum had the lowest content of SSE and SSF. Metagenomic sequencing identified a total of 5 440 bacterial OTUs. The numbers of unique OTUs in the root surface, rhizosphere, and endophytic compartments were 127, 126, and 110 for B. chinense; 91, 74, and 69 for B. falcatum; and 43, 137, and 126 for B. scorzonerifolium, respectively. Azotobacter chroococcum was dominant in the rhizosphere of B. chinense and B. scorzonerifolium, whereas Streptomyces was the core taxon in the rhizosphere of B. falcatum. Klebsiella sp. and Pseudomonas were significantly enriched in the root surface and endophytic niches of B. chinense and B. falcatum, respectively. The Klebsiella sp., Cellulomonas sp., and Azotobacter chroococcum were also a highly significant positive correlated with the contents of SSA, SSB₂, SSB₄, and SSD, among the correlation network analysis. Conclusion This study revealed that Bupleurum genotype might drive saikosaponins accumulation by niche construction of specific microbial communities.

Bupleuri genus  /  saikosaponins  /  root bacterial community  /  metagenomic sequencing  /  plant-microbe interaction  /  saikosaponin A  /  saikosaponin B₂  /  saikosaponin B₄  /  saikosaponin C  /  saikosaponin D  /  saikosaponin E  /  saikosaponin F