# Metabolomics and Microbiomics Reveal the Cultivation-Dependent Divergence in Ginsenoside Biosynthesis and Rhizosphere Ecology of Panax ginseng

## TL;DR

This study shows that growing ginseng in a natural-like environment boosts its valuable ginsenoside content and supports a healthier soil microbiome compared to greenhouse cultivation.

## Contribution

The study reveals a microbiome-mediated mechanism linking cultivation environments to ginsenoside biosynthesis in Panax ginseng.

## Key findings

- Ginseng grown in simulative habitats has higher ginsenoside Re levels than greenhouse-grown ginseng.
- Bradyrhizobium and other microbes are enriched in simulative habitats and correlate with increased ginsenoside accumulation.
- Arched greenhouse cultivation leads to a more complex microbial structure with increased negative interactions.

## Abstract

Background: Cultivation environments impose distinct abiotic and biotic stresses that act as primary drivers reshaping the metabolic profile and microbiome assembly of medicinal plants. This study investigates the impact of simulative habitat versus arched greenhouse cultivation on the synthesis of bioactive ginsenosides and the associated root microbiome structure in Panax ginseng. Methods: A combined metabolomics and microbiomics approach was applied to compare ginsenoside accumulation and rhizosphere microbial community composition under the two cultivation modes. Results: Ginseng from simulative habitat cultivation exhibited significantly higher ginsenoside content, particularly ginsenoside Re, compared to arched greenhouse cultivation, with this advantage being more pronounced in long-term cultivation. Microbiome profiling revealed that specific taxa, including Bradyrhizobium, were strongly enriched in simulative habitats and positively correlated with enhanced ginsenoside accumulation, suggesting a microbiome-mediated mechanism for metabolic plasticity. In contrast, arched greenhouse cultivation was associated with a more complex microbial structure characterized by increased negative interactions, which may compromise metabolic quality. Conclusions: These findings, utilizing multi-omics correlations, provide a theoretical basis for optimizing Panax ginseng quality through ecological cultivation strategies that leverage stress-responsive microbe–metabolite interactions.