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PubMed2025

A global survey of taxa-metabolic associations across mouse microbiome communities.

Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.

Animals↗
PubMed2026

Integrated Metabolomic and Transcriptomic Analysis Reveals Tissue-Specific Secondary Metabolic Differentiation and Indole Alkaloid Accumulation in Evodia rutaecarpa.

Evodia rutaecarpa is a valuable medicinal plant, yet its non-medicinal tissues remain largely underexplored. Here, we integrated ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics and RNA sequencing (RNA-seq) transcriptomics to systematically profile the metabolic and transcriptional landscapes of roots, stems, leaves, and flowers of Evodia rutaecarpa (Juss.) Benth. Our aim was to characterize tissue-specific metabolic differentiation and its underlying transcriptional regulatory mechanisms. Metabolomic analysis, employing principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) with robust model parameters (R2Y > 0.9, Q2 > 0.5), identified 3090 differential metabolite features (variable importance in projection, VIP > 1.0; p < 0.05) across the four tissues, which exhibited distinct tissue-specific clustering patterns. Integrated Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and weighted gene co-expression network analysis (WGCNA) revealed that roots specifically accumulated quinolone alkaloids and flavonoid glycosides, accompanied by the coordinated upregulation of genes involved in flavonoid and phenylpropanoid biosynthetic pathways. In contrast, stems, leaves, and flowers were enriched in indole alkaloids (evodiamine and rutaecarpine) and volatile oil precursors, with concurrent upregulation of genes involved in tryptophan metabolism and indole alkaloid biosynthesis (e.g., tryptophan decarboxylase, TDC; s N-methyltransferase, NMT). Notably, leaves and flowers displayed particularly high accumulation levels of these bioactive alkaloids, suggesting their potential as alternative sources for industrial and pharmaceutical applications. WGCNA further identified multiple transcription factors and structural gene modules tightly correlated with evodiamine accumulation, offering promising candidate regulators for future biosynthetic pathway engineering. Collectively, this multi-omics integration study systematically elucidates the tissue-partitioned secondary metabolism of Evodia rutaecarpa (Juss.) Benth. and provides a solid scientific foundation for full-plant resource utilization, targeted development of non-medicinal tissues, and future metabolic engineering of indole alkaloid production.

Evodia rutaecarpa↗
PubMed2025

Root growth promotion by Penicillium melinii : mechanistic insights and agricultural applications.

This study characterizes Penicillium melinii , an endophytic fungus isolated from Arabidopsis thaliana roots, as a plant growth-promoting fungus with potential use as a model to study root development and as a biostimulant for sustainable agriculture. Although endophytes are known to promote plant growth, the underlying molecular mechanisms often remain poorly understood. Here, we aimed to elucidate how P. melinii enhances root system development and to assess its applicability across different crops. Phenotypic assays were conducted in Arabidopsis, quinoa and tomato under in vitro , greenhouse and field conditions. Root architecture and biomass were quantified using image-based phenotyping. Transcriptomic and phytohormone profiling assessed plant responses, and fungal genome sequencing coupled with secretome analysis was used to identify candidate effectors and metabolic traits. P. melinii consistently promoted root growth and increased plant biomass across species and environments, both in vitro and in the greenhouse. In tomato field trials, this translated into a significant increase in yield. The fungus colonized root surfaces without vascular penetration and triggered a mild transcriptomic response: early activation of stress-response genes followed by their attenuation and sustained upregulation of auxin-related pathways. Notably, the interaction modulates the SLR-ARF-LBD pathway and the number of pre-branch sites probably through increased auxin signalling in the oscillation zone. Additional hormonal changes were limited and mainly associated with the attenuation of the plant response to microorganisms. P. melinii enhances lateral root formation through a subtle molecular and metabolic dialogue with the host plant, underscoring its relevance as a model for studying root developmental plasticity. Its strong and reproducible growth-promoting effect, demonstrated with different fungal strains and under controlled and field conditions, supports its potential as a biostimulant for sustainable crop production.

Journal Article↗
PubMedDate not supplied

Metabolic factors and the utilization of phosphorus by plants.

The overall process of entry and transport of phosphate by plants has been separated into its component parts. Rapid esterification is involved but a small proportion of the total transport may occur by a non-metabolic route. Mannose alters the metabolism of phosphate in roots of cereals and thereby reduces the transport to the shoot by as much as 99% whereas dicotyledonous species are much less sensitive. The sequestration of phosphate as mannose 6-phosphate is reversible in some species depending on the extent of its conversion into fructose 6-phosphate and it is possible that in vivo controls of this type operate in whole plants. The factors involved in the control of distribution of inorganic phosphate between cellular organelles and throughout the plant are discussed. Enzymic hydrolysis of organic forms by roots and associated microorganisms may also be important in soils where available orthophosphate is limiting. Other inorganic nutrients, particularly boron, play an important role during the transport of phosphate across membranes. Major differences have been found in the capacities of different species to transport absorbed phosphate to the shoot. Peas and field beans absorb efficiently in the early weeks of growth but the rate of transport is about one thirtieth that of oats, barley, mung bean or sunflower. The relevance of the experimental findings to the wider problem of efficiency of fertilizer use and the possible selection of genotypes with high capacities for absorption and transport are discussed.

Absorption↗
PubMed2026

A chromosome-level genome assembly of Lycoris radiata reveals the evolutionary origin of Amaryllidaceae alkaloids and elucidates the complete galanthamine biosynthetic pathway.

Amaryllidaceae alkaloids (AmAs) comprise a structurally diverse group of specialized metabolites produced almost exclusively by species of the Amaryllidoideae subfamily and are of substantial pharmacological importance. However, the limited availability of high-quality genomes from Amaryllidoideae plants has constrained systematic investigations of the genes and evolutionary processes underlying AmA biosynthesis. Here, we present a chromosome-level genome assembly of Lycoris radiata, which enabled the discovery of key downstream enzymes in the galanthamine biosynthetic pathway and uncovered reversible reactions between two critical metabolite pairs. These findings provide new mechanistic insight into pathway architecture and enable reconstruction of the galanthamine biosynthetic pathway in Yarrowia lipolytica. Comparative genomic analyses indicate that several core genes for AmA biosynthesis originated in ancestral angiosperms, whereas the complete pathway was likely assembled in the Amaryllidoideae subfamily through gene duplication and neofunctionalization. Furthermore, integrated metabolomic and transcriptomic analyses suggest that roots contribute actively to AmA metabolism in Lycoris. Together, these findings provide a genomic and biochemical framework for understanding the evolution and engineering of AmA biosynthesis.

Lycoris↗
PubMed1979

Accelerated mineralization of two organophosphate insecticides in the rhizosphere.

Numerous xenobiotic compounds, including the organophosphate insecticides O, O-diethyl-O-(2-isopropyl-6-methyl-4-pyrimidinyl) phosphorothioate (diazinon) and O, O-diethyl-O-p-nitrophenyl phosphorothioate (parathion), appear to be degraded in the soil environment by an initial cometabolic attack. Comparing the mineralization rates of radiolabeled diazinon and parathion in root-free and in rhizosphere soil, we tested our hypothesis that, because of the presence of root exudates, the rhizosphere is an especially favorable environment for such co-metabolic transformations. The insecticides were added individually at 5 mug/g to sealed flasks containing either soil permeated by the root system of a bush bean plant or identical soil without roots. Periodically, the flask atmospheres were flushed through traps and the evolved (14)CO(2) was quantitated. Bush bean plant roots without associated rhizosphere microorganisms failed to produce a significant amount of (14)CO(2). During 1 month of incubation, rhizosphere flasks mineralized 12.9 and 17.9% of the added diazinon and parathion radiocarbon, respectively, compared to 5.0 and 7.8% by the soil without roots. The mineralization of parathion but not of diazinon was stimulated in a similar manner when soil without roots was repeatedly irrigated with a root exudate produced in aseptic solution culture. Viable counts of microorganisms on soil extract agar were not significantly altered by root permeation or by root exudate treatment of the soil, leaving population selection and/or enhanced cometabolic activity as the most plausible interpretations for the observed stimulatory effects. Rhizosphere interactions may substantially shorten the predicted half-lives of some xenobiotic compounds in soil.

Bacteria↗
PubMed1979

GH secretion in open-angle glaucoma.

Open-angle glaucoma is frequently observed in patients with acromegaly suggesting that the somatotropic hormone might facilitate a condition of glaucoma. The open-angle glaucoma patients studied, displayed higher plasma human growth hormone (HGH) levels than control subjects 60 min (30.3 +/- 1.7 against 16.8 +/- 2.7 ng/ml; p less than 0.001) and 90 min (19.0 +/- 1.9 against 9.3 +/- 1.2 ng/ml; p less than 0.001) after intravenous administration of arginine (25 g in 30 min). The authors support the hypothesis that the increased plasma HGH level may interfere with the regulation of ocular pressure by modifying the flow of aqueous humor from the eyeball via changes in the sclero-corneal trabecular meshwork; these changes are also found in diabetic subjects. The interplay between HGH and changes of carbohydrate metabolism (frequently occurring in glaucomatous patients) may be at the root of the variations of intraocular pressure in open-angle glaucoma.

Arginine↗
PubMed2025

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth.

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Streptomyces↗
PubMed2026

Quantitative trait locus qLDC5 regulates primary root branching in an auxin-dependent manner.

L-type lateral root (LLR) density determines root system architecture, affecting nutrient acquisition in rice (Oryza sativa L.), particularly under low-phosphorus conditions. Previous studies identified genotypic differences in LLR density and a quantitative trait locus (QTL) enhancing LLR density on crown roots (qLDC5). We showed that LLR densities on crown and primary roots were closely correlated and confirmed higher LLR density on primary roots in qLDC5 donor DJ123 compared with the African variety NERICA4 using X-ray micro-computed tomography. We confirmed the qLDC5 effect in a field experiment for LLR density on primary roots. LLR densities on primary and crown roots, therefore, appear under similar genetic control. Developmental analyses revealed that DJ123 and NDJ188-a derivative line harboring qLDC5-initiate more lateral root primordia than NERICA4, with a higher proportion progressing to elongation, but that exogenous auxin application reversed this ranking. Within qLDC5, auxin biosynthesis gene OsYUCCA2 and auxin response factor OsARF15 were up-regulated in DJ123. Transcriptome analysis revealed an indirect auxin-mediated regulatory network underlying LLR variation. Differentially expressed genes in DJ123 and NDJ188 were enriched for ent-kaurene and gibberellin metabolism, including the robust induction of OsGA2ox5. These findings suggest qLDC5 increases lateral root density by coordinating gibberellin, auxin, and terpene pathways.

Oryza↗
PubMed1976

Recent advances in calcium metabolism. II. Disorders of calcium homeostasis.

Abnormalities of calcium and mineral metabolism are described in relation to the differential diagnosis, clinical characteristics, diagnostic procedures, and treatment of infants and children with hypocalcemia, hypercalcemia, rickets, chronic renal insufficiency, and other disorders of calcium metabolism. Understanding of the basic pathogenesis of each abnormality of calcium homeostasis is essential for the rational management of affected patients.

Adolescent↗
PubMed1979

Changes in metabolic activities of Fusarium oxysporum f. fabae and Rhizoctonia solani in response to Dithan A-40 fungicide.

The effect of different concentrations of Dithan A-40 fungicide on the metabolic activities of the wilt fungus Fusarium oxysporum f. fabae and the root rot agent Rhizoctonia solani was studied. All toxicant concentrations reduced energy generation, total phosphorus and nitrogen content of both fungi. In addition, the toxicant caused a shift in free amino acids pool. As a result of these changes, the mycelium dry weight of both fungi was greatly reduced. R. solani was more sensitive to the toxic effect of Dithan A-40 than F. oxysporum.

Amino Acids↗
PubMed1979

[Recessive microencephaly linked to the X chromosome].

A family with X-linked recessive microcephaly is reported. As patients there were found 8 men or boys respectively out of 3 generations, all of them being related by their mentally healthy mothers. Besides microcephaly the patients showed growth retardation and obesity. Some of them, in addition, had various anomalies as inguinal or umbilical hernias, cryptorchism, tapering fingers, contractures, deeply rooted thumbs and club-feet. There were no hints for a metabolic defect or a chromosomal aberration. The dermatoglyphics could be investigated in 5 patients and showed in all of them a shifting of the axial triradius into the distal position t'. Comparing the own findings with case reports on X-linked microcephalies, the above mentioned family was found not to correspond to any of these observations. It is assumed that in this family, a new disease has occurred which until now has not yet been described, so that the X-linked microcephalies seem to be a heterogenous group of disease from the genetic point of view.

Adult↗
PubMed1977

Pharmacokinetics of vindesine and vincristine in humans.

Vindesine, a new Phase 1 Vinca alkaloid congener, exhibited serum pharmacokinetic behavior in humans compatible with a three-compartment, open mammilary model. The kinetic parameters included: t1/2 alpha=3.24+/-1.14 min, t1/2beta=99.0+/-44.5 min, t1/2gamma=1213+/-493 min, Vc (Valpha)=4.81+/-2.12 liters, Vbeta=58.2+/-50.5 liters, Vgamma=598+/-294 liters. Vincristine, studied only for the first 4 hr, behaved like a two-compartment system, with values of t1/2 alpha=3.37+/-0.72 min, t1/2beta=155+/-18 min, Valpha=4.53+/-0.49 liters, and Vbeta=57.3+/-21.1 liters. Urine excretion data demonstrated that most drug elimination occurred within the first 24 hr and amounted to 13.2+/-5.9% for vindesine and 9.5+/-5.1% for vincristine.

Humans↗
PubMed2024

Genetic modification of the shikimate pathway to reduce lignin content in switchgrass (Panicum virgatum L.) significantly impacts plant microbiomes.

UNLABELLED: Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-impact growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remain unclear. To address this, wild-type and QsuB-engineered switchgrass were grown in switchgrass field soils, and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiSeq amplicon sequencing of ITS and 16S rDNA. Compared to wild-type, QsuB-engineered switchgrass hosted different microbial communities in roots, rhizosphere, and leaves. Specifically, QsuB-engineered plants had a lower relative abundance of arbuscular mycorrhizal fungi (AMF). Additionally, QsuB-engineered plants had fewer Actinobacteriota in root and rhizosphere samples. These findings may indicate that changes in the plant metabolism impact both AMF and Actinobacteriota similarly or potential interactions between AMF and the bacterial community. This study enhances understanding of plant-microbiome interactions by providing baseline microbial data for developing beneficial bioengineering strategies and by assessing nontarget impacts of engineered plant traits on the plant microbiome. IMPORTANCE: Bioenergy crops provide an important strategy for mitigating climate change. Reducing the lignin in bioenergy crops could improve fermentable sugar yields for more efficient conversion into bioenergy and bioproducts. In this study, we assessed how switchgrass engineered for low lignin impacted aboveground and belowground switchgrass microbiome. Our results show unexpected reductions in mycorrhizas and actinobacteria in belowground tissues, raising questions on the resilience and function of genetically engineered plants in agricultural systems.

Panicum↗
PubMed1979

[Effect of drugs used for the prevention of urinary calculi recurrence on the growth and metabolism of young experimental animals].

In the animal experiment should be made clear whether several medicaments which stood the test in the prevention of relapses of urinary calculi may be used without any danger also in the infantile carrier of concrements. For this purpose young rabbits high doses of diuretics, kation exchangers, aluminium oxide, extracts of the root of rubia tinctorum, succinimide and diphosphonate were given. Growth and development of the animals were negatively influenced by the medicaments, with the exception of the kation exchanger and the extracts of the root of rubia tinctorum. Numerous animals died under the administration of duiretics. The results of the examinations of metabolism only partly allow general conclusions. The medicamentous long-term metaphylaxis of the urolithiasis in childhood is also to be used like dietetic restrictions under strong indication and permanent control.

Aluminum Oxide↗
PubMed2026

Chemometric insights into Lactiplantibacillus plantarum effects on onion (Allium cepa L.) metabolism and antidiabetic activity under cadmium stress.

Cadmium (Cd) is a toxic heavy metal that causes severe physiological damage in plants, inhibiting growth and ultimately reducing crop yield. Lactic acid bacteria regulate Cd availability through bioaccumulation and biosorption. This study evaluated the Cd tolerance of Lactiplantibacillus plantarum 10CH by determining its survival capacity under Cd stress and its potential to mitigate Cd-induced stress in onion (Allium cepa L.). The bacterial strain tolerated Cd concentrations up to 100 &#xb5;M, and whole-genome sequencing identified genes involved in Cd biosorption, accumulation, and efflux. Exposure of onion to increasing CdCl2 concentrations significantly reduced root and shoot biomass. Inoculation with Lb. plantarum 10CH alleviated Cd stress at 100 &#xb5;M, enhancing root and shoot biomass, reducing Cd accumulation, lowering oxidative damage markers, and stimulating antioxidant enzyme activities. Metabolic profiling revealed that Cd stress significantly reduced primary metabolites and amino acids, particularly at 100 &#xb5;M, while bacterial inoculation restored key amino acids and peptides, including arginine, tyrosine, and glutamic acid. Chemometric analysis using unsupervised (PCA) and supervised (OPLS-DA) models revealed clear metabolite variation among untreated, Cd-stressed, and bacterial inoculated Cd-stressed onion leaves. Furthermore, leaf extracts exhibited &#x3b1;-glucosidase inhibitory activity, with the highest activity in control plants (IC50&#x2009;=&#x2009;425.2&#x2009;&#xb1;&#x2009;0.5&#xa0;&#xb5;g/mL). Cd-stressed plants showed moderate antidiabetic activity, which was significantly reduced by bacterial inoculation. Overall, these findings demonstrate that Lb. plantarum 10CH can survive under Cd stress and alleviates Cd-induced stress in onion, highlighting its potential as a bioinoculant to mitigate heavy metal stress.

Onions↗
PubMed1976

Regulation of nitrogen fixation by Rhizobia. Export of fixed N2 as NH+4.

The metabolic fate of gaseous nitrogen (15N2) fixed by free-living cultures of Rhizobia (root nodule bacteria) induced for their N2-fixation system was followed. A majority of the fixed 15N2 was found to be exported into the cell supernatant. For example, as much as 94% of the 15N2 fixed by Rhizobium japonicum (soybean symbiont) was recovered as 15NH+4 from the cell supernatant following alkaline diffusion. Several species of root nodule bacteria also exported large quantities of NH+4 from L-histidine. Evidence is presented that overproduction and export of NH+4 by free-living Rhizobia may be closely linked to the control of several key enzymes of NH+4 assimilation. For instance, NH+4 was found to repress glutamine synthetase whereas L-glutamate repressed glutamate synthase. Assimilation of NH+4 as nitrogen source for growth of Rhizobia was inhibited by glutamate. The mechanism of regulation of NH+4 production by root nodule bacteria is discussed.

Ammonia↗