The genus Panax contains traditional herbs that have been widely used in traditional medicine. The active constituents, collectively known as ginsenosides, are well characterized in the most representative species, P. notoginseng. However, the major bioactive chemical constituents of P. stipuleanatus together with P. vietnamensis are relatively less studied. In this study, an untargeted metabolomic analysis was performed in P. notoginseng, P. stipuleanatus, and P. vietnamensis using root and leaf organs. Further metabolomic differences in P. stipuleanatus were compared with those of the two most prevalent species. The analysis results revealed tissue-specific qualitative and quantitative metabolic differences in each species. Several differentially accumulated metabolites were enriched in the biosynthesis of secondary metabolites, including the biosynthesis of ginsenosides I. The ginsenosides Rb1, Rf, Rg1, Rh1, Rh8, and notoginsenosides E, M, and N had a higher abundance level in the roots of both P. notoginseng and P. vietnamensis. In P. stipuleanatus, the accumulation of potentially important ginsenosides is mainly found in the leaf. In particular, the dammarane-type ginsenosides Rb3, Rb1, Mx, and F2 as well as the notoginsenosides A, Fe, Fa, Fd, L, and N were identified to have a higher accumulation in the leaf. The strong positive correlation network of different ginsenosides probably enhanced secondary metabolism in each species. The comparative analysis revealed a significant differential accumulation of metabolites in the leaves of both species. The various compounds of dammarane-type ginsenoside, such as Rb1, Rg1, Rg6, Rh8, Rh10, Rh14, and majoroside F2, had a significantly higher concentration level in the leaves of P. stipuleanatus. In addition, several notoginsenoside compounds such as A, R1, Fe, Fd, and Ft1 showed a higher abundance in the leaf. These results show that the abundance level of major ginsenosides is significant in P. stipuleanatus and provides an important platform to improve the ginsenoside quality of Panax species.

Polygonatum kingianum Coll. (PKC) is a valuable medicinal herb native to Yunnan, China, but its yield and quality are severely threatened by root rot. To elucidate the rhizosphere microbial dynamics associated with this disease and to identify location-transcending patterns, we collected rhizosphere soils from healthy and diseased PKC plants at three planting bases in Lincang, Qujing, and Kunming. Soil properties were measured, and bacterial (16S rRNA) and fungal (ITS) communities were characterized by amplicon sequencing. Geographic origin emerged as the dominant factor associated with microbial community structure, with soil moisture, organic matter, and nutrients all showing significant associations. The effect of disease on microbial diversity was site-specific. Nevertheless, LEfSe analysis identified cross-location-consistent indicator genera: Acidiferrimicrobium and HSB_OF53_F07 were enriched in healthy soils, while Burkholderia-Caballeronia-Paraburkholderia and Rhodanobacter were enriched in diseased samples. At the trophic mode level, a consistent pattern was observed: diseased rhizosphere soils had higher relative abundance of pathotrophic fungi and lower abundance of symbiotrophic fungi compared to healthy soils. However, at the finer guild level, no individual guild showed statistically significant differences after FDR correction. Co-occurrence network analysis revealed a striking structural reorganization: healthy plants harbored a fungus-dominated network (57.04% fungi), whereas diseased plants shifted to a bacterium-dominated network (55.71% bacteria), accompanied by an increased proportion of negative correlations. Redundancy analysis (RDA) and Mantel tests further confirmed that soil physicochemical properties, rather than health status, were the primary factors associated with microbial community variation (Mantel’s r = 0.725 for bacteria, 0.768 for fungi). Collectively, this study provides the first systematic evidence of cross-location common microbial shifts and network reorganization associated with PKC root rot. These findings offer a microecological basis for developing green prevention and control strategies against this devastating disease.