bacterial  metagenome
Phellodendri amurensis cortex is a traditionally Chinese medicine used as antiphlogistic, antibacterial, and anti-inflammatory agent. The secondary metabolism of plant roots is intricately linked to the microbial communities that surround them. However, the specific microbiomes of P. amurense and its correlation with bioactive compounds remain poorly understood. Here, the metabolic profiles and microbiome of P. amurense roots, rhizosphere, and bulk soils were analyzed, revealing significant differences in the relative content of plant-specialized metabolites. The composition of the bulk and rhizosphere microbiome was found to differ significantly from that of the endosphere microbiome. Furthermore, seven bisbenzylisoquinoline alkaloids significant positive correlations with Nectriaceae and Sphingobacteriaceae. These findings provide valuable insights into the correlation between P. amurense root-associated microorganisms and bioactive compounds. This understanding opens up new possibilities for manipulating the production of bioactive compounds, thereby enhancing the industrial and medicinal value of P. amurense.