Plant Metabolomics Reviews

Obesity and type 2 diabetes mellitus (T2DM) are associated with heterogeneous changes in gut microbial composition and function, while mechanistic studies support plausible links among diet, microbial metabolism, intestinal barrier function, immune signaling, and host metabolism. This narrative review integrates diet-microbiome mechanisms, dietary-assessment and multi-omics methodology, major dietary patterns, quantitative clinical intervention evidence, treatment-related microbiome modulation,...

Metabolomics has transformed plant biology by delivering high-resolution insights into the biochemical networks that govern growth, adaptation, and environmental responsiveness. The plant metabolome, encompassing both primary and specialised metabolites, acts as a dynamic interface between genotype and phenotype, capturing the interplay of intrinsic genetic regulation with extrinsic environmental cues. Significant technological progress has enabled increasingly comprehensive metabolic profiling,...

Coevolution between plants and herbivores has been proposed as a major evolutionary force that resulted in their radiation and diversification. Plants have evolved a broad array of strategies that directly or indirectly avoid, repel, deter, or kill herbivore attackers. These include (but not limited to) tolerance to damage through compensatory growth of tissue lost from herbivory, resistance via physical and chemical defenses, induced responses, and avoidance through reduced apparency or...

Plants respond to water extremes through dynamic, organelle-level reprogramming of resource allocation rather than metabolic shutdown. Recent advances suggest that drought and flooding induce coordinated metabolic reorganization between chloroplasts and mitochondria, shifting energy distribution from growth to stress acclimation via retrograde signaling pathways. These signals are integrated by the trehalose-6-phosphate (Tre6P)-sucrose non-fermenting 1-related protein kinase 1 (SnRK1)-target of...

1. Coumarins are plant-derived secondary metabolites widely present in foods, spices, and medicinal plants. Their limited intestinal absorption and extensive host metabolism allow a variable fraction to reach the colon, where gut microorganisms can transform them into metabolites with distinct physicochemical and biological properties.2. This review synthesizes current evidence on gut microbiota-mediated coumarin biotransformation, focusing on microbial taxa, metabolic reactions, structural...

INTRODUCTION: Compartment-resolved metabolite baselines for legumes grown under field conditions are notably scarce. Most root exudate data are obtained from hydroponic or pot systems using targeted assays. These methods fail to accurately represent the soil-borne and microbially derived chemical environments surrounding roots in situ. Furthermore, no such baseline has been established for soybeans grown on the calcareous Vertisols of central and western India, where phosphorus, Zn, and Fe...

Antimicrobial resistance creates an urgent need for new antibacterial strategies, and medicinal plants remain an important source of chemically diverse bioactive metabolites. This study investigated the antibacterial potential of Arctium lappa L. (greater burdock) naturalized in the United States using a genome-guided approach integrated with microbiological and mechanistic assays. Genome mining identified 35 putative biosynthetic gene clusters associated with diverse specialized metabolite...

Grafting has transformed the propagation and productivity of perennial tree crops, but genetically variable rootstocks and functional stock-scion interactions can limit the uniform expression of elite scion potential. Evidence from Hevea brasiliensis highlights the need for compatible and uniform rootstocks, self-rooted planting material, and emerging graft assisted biotechnological approaches to improve plantation uniformity and productivity. Due to high heterozygosity and difficulty in fixing...

Legumes are increasingly used as functional ingredients in plant-based foods. However, their compact endogenous structure restricts techno-functional properties. Conventional fractionation methods that isolate proteins further impair these properties and generate co-products. Solid-state fermentation (SSF), which involves growth of microorganisms on moist solid legumes for in situ enzymatic modification, is a gentle and sustainable strategy to enhance techno-functionality. However, the...

The increasing limitations of chemical pesticides such as environmental pollution, pathogen resistance, and threats to human and ecosystem health have increased the demand for sustainable, biologically based crop protection methods. Eco-smart biocontrol has emerged as a game-changing paradigm that uses beneficial microorganisms associated with plants to suppress phytopathogens, boost plant immunity, and make agroecosystems more resilient over time. Moving beyond traditional single-strain...

Drought-mediated declines in grain nutritional quality and cereal yield put global food security at risk, yet the rhizosphere microbiome provides an alternative solution for improving crop tolerance. Our review synthesised existing knowledge on how soil microbiomes, particularly arbuscular mycorrhizal fungi (AMF) and plant-growth-promoting rhizobacteria (PGPR), simultaneously regulate three interlinked pillars of crop performance (stress tolerance, grain nutrient uptake, and yield) under...

Medicinal-plant immunity and specialized metabolism are mechanistically linked, but rigorous receptor validation, causal multi-omics, and field trials are needed for reliable translational applications. Medicinal plants combine classical immune signaling with lineage-specific specialized metabolism. This review focuses on the immune systems of medicinal plants and on how pathogen perception reshapes the biosynthesis of pharmacologically valuable secondary metabolites. We synthesize evidence for...

Recent advances in single-cell and spatial multi-omics have enabled high-resolution profiling of plant cellular heterogeneity and tissue organization. Single-cell RNA sequencing (scRNA-seq) captures transcriptional variation across cell types and states, while single-nucleus ATAC sequencing (snATAC-seq) provides information on chromatin accessibility and regulatory elements. Spatial transcriptomics (ST) and spatial metabolomics preserve spatial context, enabling in situ mapping of molecular and...

Mulberry leaf is a promising sustainable plant-based feed resource; however, high dietary inclusion of raw mulberry leaf impairs growth in carnivorous fish. Fermentation degrades anti-nutritional components and enhances nutrient availability, yet the dose-dependent effects and underlying mechanisms of fermented mulberry leaf (FML) in Acipenser schrenckii remain unclear. This study assessed graded dietary FML inclusion (0%, 2%, 4%, and 6%) as a partial replacement for fishmeal in Amur sturgeon,...

Mulberry leaf is a promising plant feed resource for aquaculture, yet high inclusion limits its application due to anti-nutritional factors. Exogenous enzyme supplementation can improve the utilization efficiency of bioactive compounds in mulberry leaf-containing diets. This study aimed to evaluate the dose-dependent effects of mulberry leaf powder supplemented with a multi-enzyme premix (MLE) on growth, intestinal health, antioxidant and immune responses, as well as intestinal microbiota and...

Genome-wide association studies (GWASs) have become a central tool in plant genomics, providing high-resolution access to the genetic architecture of complex traits in cereal crops. This review observes the application of GWASs to biotic and abiotic stress responses and nutritional quality in rice (Oryza sativa), wheat (Triticum aestivum), maize (Zea mays), and barley (Hordeum vulgare). However, conventional SNP-based GWASs may overlook structural and presence-absence variation, and significant...

Drought stress is a major constraint on global forestry productivity and poses a significant threat to economically important tree species such as Populus. Abscisic acid (ABA) signaling plays a central role in drought tolerance by regulating molecular, physiological, and biochemical processes. This review summarizes current knowledge of ABA signaling pathways and their roles in drought resilience in Populus. It covers physiological responses, molecular regulatory networks, hormonal crosstalk,...

The intensification of Cannabis sativa cultivation has increased the need for effective and sustainable plant-health strategies. Pathogen control is particularly challenging because pesticide residues may compromise product safety and quality, while repeated chemical treatments can favour the emergence of fungicide-resistant populations. Microbial biological control agents (BCAs) represent a promising component of integrated disease management, although their discovery and validation remain...

Green chemistry provides a conceptual and technological framework for redesigning agricultural inputs and analytical workflows toward safer, more efficient, and more sustainable crop production. In this review, molecular crop quality is proposed as a chemical and metabolomic endpoint of green chemistry in sustainable agriculture. Rather than evaluating agricultural interventions proposed as compatible with green chemistry only through yield, input reduction, or environmental performance, this...

Plant specialized metabolism changes throughout development, but developmental context remains inconsistently incorporated into phytochemical interpretation. This integrative narrative review synthesizes evidence on chemical ontogeny in plants, defined here as the qualitative and quantitative reorganization of specialized metabolism along plant and organ development. We distinguish ontogenetic variation from phenology, seasonality, organ maturation, developmental plasticity, and environmentally...