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Metabolites
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Metabolomics in Plant Natural Products Research, 2nd Edition
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Metabolomics in Plant Natural Products Research, 2nd Edition

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

Deadline for manuscript submissions: 30 December 2025 | Viewed by 1903

Special Issue Editor

Prof. Dr. Junsong Wang

E-Mail Website
Guest Editor
Center for Molecular Metabolism, School of Environmental & Biological Engineering, Nanjing University of Science & Technology, Nanjing 210094, China
Interests: functional metabolomics; natural products chemistry; traditional Chinese medicines; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to announce the launch of a new Special Issue, “Metabolomics in Plant Natural Products Research, 2nd Edition”, a continuation of a previous successful Special Issue.

This Special Issue on plant natural product research and metabolomics aims to bring together works that advance our understanding of plant–environment interactions, the determination of chemical markers, and the prioritization and targeted isolation of active principles from medicinal plants. The natural products of plants have been a reliable source of potential drug-active components, and the bioactivity of natural extracts can be characterized by the synergism between different metabolites. Metabolomic approaches, such as LC/MS, GC/MS, and NMR, are appropriate means by which to assess complex interactions and identify various factors that may affect the production and accumulation of specialized metabolites in different species

Prof. Dr. Junsong Wang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • natural products
  • metabolomics
  • plant–environment interactions
  • chemical markers
  • active principles
  • LC/MS
  • GC/MS
  • NMR

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Published Papers (3 papers)

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Research

16 pages, 3806 KB  
Article
Isolation and Characterization of Two Monoterpene Synthases and a Sesquiterpene Synthase from Asarum heterotropoides
by Jiayi Li, Qianhua Shen, Yongze Zhang, Hanshu Tao, Bingyi Xu, Xiaoyan Min, Haiyang Liu, Na Han and Xin Fang
Metabolites 2025, 15(11), 753; https://doi.org/10.3390/metabo15110753 - 20 Nov 2025
Viewed by 348
Abstract
Background: Asarum heterotropoides, a prominent medicinal plant in China, is well known for producing an abundance of monoterpenes and sesquiterpenes, which constitute the primary components of its essential oil and serve as the principal active compounds of the species. However, the [...] Read more.
Background: Asarum heterotropoides, a prominent medicinal plant in China, is well known for producing an abundance of monoterpenes and sesquiterpenes, which constitute the primary components of its essential oil and serve as the principal active compounds of the species. However, the biosynthetic pathways for these terpenoids remain largely unelucidated. Methods: Gas chromatography–mass spectrometry analysis, in vitro enzyme assay, subcellular localization experiment and molecular docking were used to characterize the function of terpene synthase from A. heterotropoides. Results: In this study, we isolated and characterized two monoterpene synthases and one sesquiterpene synthase from A. heterotropoides. These enzymes exhibit promiscuous activities, accepting geranyl pyrophosphate and farnesyl pyrophosphate as substrates to yield a variety of monoterpene and sesquiterpene products in in vitro enzymatic assays. All three enzymes possess a conserved RRx8W motif, a hallmark typically associated with TPS-b and TPS-d monoterpene synthases involved in cyclic monoterpene formation. However, these two monoterpene synthases yield linear instead of cyclic products. The sesquiterpene synthase (AhTPS3) is a second example of TPS-a terpene synthase harboring such motif. Conclusions: Our findings significantly expand our understanding of terpene biosynthesis, especially the role of RRx8W motif. Full article
(This article belongs to the Special Issue Metabolomics in Plant Natural Products Research, 2nd Edition)
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16 pages, 3918 KB  
Article
Multi-Omics Decoding of Potential Microbial–Genetic Synergy Underlying Polysaccharide and Glycosidic Polymer Biosynthesis in Two Cultivars of Lilium brownii var. viridulum Baker
by Tao Chang, Yajie Xue, Fan Liu, Ran Zheng, Zaiqi Zhang, Qinfang Zheng and Putao Wang
Metabolites 2025, 15(11), 712; https://doi.org/10.3390/metabo15110712 - 30 Oct 2025
Viewed by 348
Abstract
Background: The accumulation of glycosidic polymers in Lilium brownii var. viridulum Baker (Lv) bulbs fundamentally governs the nutritional and medicinal properties. Methods: In this study, metabolomic, transcriptomic, and microbiome analyses were integrated to elucidate the differential mechanisms of glycoside accumulation between [...] Read more.
Background: The accumulation of glycosidic polymers in Lilium brownii var. viridulum Baker (Lv) bulbs fundamentally governs the nutritional and medicinal properties. Methods: In this study, metabolomic, transcriptomic, and microbiome analyses were integrated to elucidate the differential mechanisms of glycoside accumulation between the elite ‘Xuefeng’ (Lv, X) and ‘Longya’ (Lv, L), each comprising three biological replicates. Results: The results demonstrate significantly elevated diversity and abundance of glycosides in X bulbs, with glucose derivatives constituting the predominant fraction. Differential expression genes (DEGs) associated with carbohydrate metabolism were primarily enriched in starch/sucrose metabolism and amino sugar metabolic pathways. Planctomycetes in rhizospheric soil, combined with Acidobacteriia and Rhodanobacteraceae in non-rhizospheric soil, were identified as key microbial taxa associated with glycoside accumulation. Variation partitioning analysis (VPA) revealed that synergistic genetic microbiota–host interactions collectively accounted for 86.8% of the metabolic variance. Conclusions: Consequently, X exhibits superior potential as a medicinal/edible cultivar and as a breeding material due to its enhanced biosynthesis of glycosidic polymers. This work, for the first time, systematically deciphers the regulatory framework of glycoside accumulation in Lv bulbs, highlighting microbiota–host synergy, and provides critical insights for the refining of biosynthetic pathways and targeted crop enhancement. Full article
(This article belongs to the Special Issue Metabolomics in Plant Natural Products Research, 2nd Edition)
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19 pages, 4128 KB  
Article
Integrating Metabolomics and Machine Learning to Analyze Chemical Markers and Ecological Regulatory Mechanisms of Geographical Differentiation in Thesium chinense Turcz
by Cong Wang, Ke Che, Guanglei Zhang, Hao Yu and Junsong Wang
Metabolites 2025, 15(7), 423; https://doi.org/10.3390/metabo15070423 - 20 Jun 2025
Cited by 1 | Viewed by 879
Abstract
Background: The relationship between medicinal efficacy and the geographical environment in Thesium chinense Turcz. (T. chinense Turcz.), a traditional Chinese herb, remains systematically unexplored. This study integrates metabolomics, machine learning, and ecological factor analysis to elucidate the geographical variation patterns and regulatory [...] Read more.
Background: The relationship between medicinal efficacy and the geographical environment in Thesium chinense Turcz. (T. chinense Turcz.), a traditional Chinese herb, remains systematically unexplored. This study integrates metabolomics, machine learning, and ecological factor analysis to elucidate the geographical variation patterns and regulatory mechanisms of secondary metabolites in T. chinense Turcz. from Anhui, Henan, and Shanxi Provinces. Methods: Metabolomic profiling was conducted on T. chinense Turcz. samples collected from three geographical origins across Anhui, Henan, and Shanxi Provinces. Machine learning algorithms (Random Forest, LASSO regression) identified region-specific biomarkers through intersection analysis. Metabolic pathway enrichment employed MetaboAnalyst 5.0 with target prediction. Antioxidant activity (DPPH/hydroxyl radical scavenging) was quantified spectrophotometrically. Environmental correlation analysis incorporated 19 WorldClim variables using redundancy analysis, Mantel tests, and Pearson correlations. Results: We identified 43 geographical marker compounds (primarily flavonoids and alkaloids). Random forest and LASSO regression algorithms determined core markers for each production area: Anhui (4 markers), Henan (6 markers), and Shanxi (3 markers). Metabolic pathway enrichment analysis revealed these markers exert pharmacological effects through neuroactive ligand–receptor interaction and PI3K-Akt signaling pathways. Redundancy analysis demonstrated Anhui samples exhibited significantly higher antioxidant activity (DPPH and hydroxyl radical scavenging rates) than other regions, strongly correlating with stable low-temperature environments (annual mean temperature) and precipitation patterns. Conclusions: This study established the first geo-specific molecular marker system for T. chinense Turcz., demonstrating that the geographical environment critically influences metabolic profiles and bioactivity. Findings provide a scientific basis for quality control standards of geo-authentic herbs and offer insights into plant–environment interactions for sustainable cultivation practices. Full article
(This article belongs to the Special Issue Metabolomics in Plant Natural Products Research, 2nd Edition)
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