Multi-Omics Insights into Stress-Induced Metabolism of Bioactive Plant Compounds

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Plant Metabolism".

Deadline for manuscript submissions: 15 July 2026 | Viewed by 995

Special Issue Editors

China Academy of Chinese Medical Sciences, Beijing, China
Interests: Fritillaria cirrhosa; bioactive compounds; transcriptomic and metabolomic approaches; molecular plant breeding; fruit extracts

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Guest Editor
Center for Molecular Metabolism, Nanjing University of Science & Technology, Nanjing, China
Interests: functional metabolomics; natural products chemistry; traditional Chinese medicines; bioinformatics
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Special Issue Information

Dear Colleagues,

Plants are continuously challenged by a wide range of biotic and abiotic stresses, including temperature extremes, ultraviolet radiation, drought, salinity, heavy metal exposure, and pathogen attack. These environmental pressures profoundly reshape plant metabolic processes, often triggering the reprogramming of specialized metabolism and the accumulation of bioactive compounds. Such stress-induced metabolic responses not only contribute to plant survival and adaptation but also critically influence the chemical composition, bioactivity, and therapeutic potential of medicinal and functional plants.

With the rapid advancement of high-throughput sequencing and analytical technologies, multi-omics approaches have become indispensable tools for elucidating the complex regulatory mechanisms underlying plant metabolic plasticity. Integrative analyses combining genomics, transcriptomics, proteomics, metabolomics, and epigenomics now enable systems-level dissection of metabolic pathways, gene–metabolite associations, and regulatory networks that govern stress-responsive metabolism.

This Special Issue aims to provide a comprehensive forum for cutting-edge research on stress-induced metabolism of bioactive plant compounds, with particular emphasis on comparative metabolomics, multi-omics integration, and network-based analyses. Contributions focusing on medicinal plants and functional crops are especially encouraged, including studies that link stress-driven metabolic changes with biological activities and therapeutic relevance through network pharmacology and systems biology approaches.

Climate change and environmental degradation are intensifying stress conditions for plants worldwide, posing serious threats to crop productivity and medicinal plant quality. Understanding how stress reshapes plant metabolism and bioactivity is therefore essential for the sustainable utilization of plant resources, quality control of herbal medicines, and the development of stress-resilient plant materials.

Topics of interest include, but are not limited to, the following:

  • Stress-induced reprogramming of plant primary and secondary metabolism;
  • Comparative metabolomics across species, genotypes, or environmental gradients;
  • Multi-omics integration in plant stress biology;
  • Regulation of bioactive phytochemicals under biotic and abiotic stresses;
  • Gene–metabolite and metabolic regulatory network analysis;
  • Network pharmacology linking plant metabolites to biological and therapeutic activities;
  • Medicinal plant metabolism and quality formation under environmental stress;
  • Systems biology approaches to plant adaptation and resilience;
  • Discovery of stress-responsive metabolites with pharmacological potential.

Dr. Dan Gao
Prof. Dr. Junsong Wang
Guest Editors

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Keywords

  • stress-induced metabolism
  • plant secondary metabolites
  • bioactive phytochemicals
  • medicinal plant compounds
  • multi-omics integration
  • comparative metabolomics
  • plant stress biology
  • metabolic and regulatory networks
  • network pharmacology

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Published Papers (1 paper)

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Research

18 pages, 4423 KB  
Article
Metabolomics and Microbiomics Reveal the Cultivation-Dependent Divergence in Ginsenoside Biosynthesis and Rhizosphere Ecology of Panax ginseng
by Siqi Liu, Dehua Wu, Wenqi Ma, Tielin Wang, Binbin Yan, Yang Ge, Feng Xiong, Hongyang Wang and Chuanzhi Kang
Metabolites 2026, 16(2), 138; https://doi.org/10.3390/metabo16020138 - 18 Feb 2026
Viewed by 666
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 [...] Read more.
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. Full article
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