Metabolites

17 pages, 2378 KB

Open AccessEditor’s ChoiceArticle

Eliciting Clavulanic Acid Biosynthesis: The Impact of Bacillus velezensis FZB42 on the Metabolism of Streptoyces clavuligerus ATCC 27064

by Luisa F. Patiño, Carlos Caicedo-Montoya, Laura Pinilla-Mendoza, Jaison H. Cuartas and Rigoberto Ríos-Estepa

Metabolites 2025, 15(5), 337; https://doi.org/10.3390/metabo15050337 - 19 May 2025

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Abstract

Background/Objectives: Clavulanic acid (CA) is produced by cell suspension cultures of Streptomyces clavuligerus ATCC 27064, and is widely used as a beta-lactamase inhibitor to combat antibiotic resistance. CA titers are moderate due to bioprocess complexity, prompting ongoing efforts to overcome these limitations. Methods: [...] Read more.

Background/Objectives: Clavulanic acid (CA) is produced by cell suspension cultures of Streptomyces clavuligerus ATCC 27064, and is widely used as a beta-lactamase inhibitor to combat antibiotic resistance. CA titers are moderate due to bioprocess complexity, prompting ongoing efforts to overcome these limitations. Methods: In this study, we aimed to evaluate the effect of live and inactivated Bacillus velezensis FZB42 cells on CA production in S. clavuligerus, and to explore the transcriptional response underlying this interaction using RNA-seq technology. Results: The addition of dead and live cells of B. velezensis improved CA production by 1.4 and 2.0-fold, respectively. Furthermore, the transcriptome of S. clavuligerus, obtained with live cells of B. velezensis FZB42 at the peak of maximum CA production, revealed that 410 genes were up-regulated and 594 were down-regulated under these conditions, with a padj < 0.05. Most of the genes from the cephamycin C and CA clusters were up-regulated, which correlates well with the increase in CA production. Likewise, S. clavuligerus ATCC 27064 enhanced the expression of genes encoding enzymes that scavenge endogenous H₂O₂, as well as other genes related to oxidative stress defense. Regarding downregulated genes, we found that S. clavuligerus decreased the expression of genes involved in the biosynthesis of terpenoids, polyketides, and lantibiotics, as well as the expression of the operon involved in the synthesis of the pyrroloquinoline quinone (PQQ) cofactor. Conclusions: These findings contribute to the understanding of S. clavuligerus metabolism and pave the way for future metabolic engineering efforts aimed at obtaining CA-overproducing strains. Full article

(This article belongs to the Section Microbiology and Ecological Metabolomics)

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42 pages, 830 KB

Open AccessEditor’s ChoiceReview

Gut–Brain Inflammatory Pathways in Attention-Deficit/Hyperactivity Disorder: The Role and Therapeutic Potential of Diet

by Naomi Lewis, Jim Lagopoulos and Anthony Villani

Metabolites 2025, 15(5), 335; https://doi.org/10.3390/metabo15050335 - 19 May 2025

Cited by 2 | Viewed by 4447

Abstract

Attention-deficit/hyperactivity disorder (ADHD) is a common childhood-onset neurodevelopmental disorder that often persists into adulthood, leading to various adverse outcomes. Its underlying pathology is multifactorial, involving neurotransmitter imbalances, gut microbiota alterations, and oxidative and inflammatory dysregulation. Diet, a key environmental modifier of gut ecology, [...] Read more.

Attention-deficit/hyperactivity disorder (ADHD) is a common childhood-onset neurodevelopmental disorder that often persists into adulthood, leading to various adverse outcomes. Its underlying pathology is multifactorial, involving neurotransmitter imbalances, gut microbiota alterations, and oxidative and inflammatory dysregulation. Diet, a key environmental modifier of gut ecology, is consistently poorer in individuals with ADHD, with multiple nutrients implicated in its pathophysiology. This review examines the role of specific nutrients such as omega-3 fatty acids, key micronutrients, and potentially harmful dietary components, as well as broader dietary patterns, particularly the Western diet and Mediterranean diet (MedDiet), in relation to ADHD symptoms. It also evaluates both whole-diet and supplement-based clinical interventions, supporting the growing recognition of nutrition as a safe and relatively affordable modifiable factor in ADHD management. Additionally, the biological mechanisms linking diet to ADHD are reviewed, highlighting strong evidence for the involvement of gut dysbiosis and inflammatory processes. Despite the well-documented antioxidant, anti-inflammatory, and microbiome benefits of the MedDiet, direct research investigating its role in ADHD remains limited. Most whole-diet approaches to date have focused on elimination diets, leaving a significant gap in understanding the potential role of the MedDiet in ADHD management. Therefore, this review outlines preliminary evidence supporting the MedDiet and its key components as modulators of ADHD-related biological pathways, indicating its potential as a therapeutic approach. However, further research is required to rigorously evaluate its clinical efficacy. Finally, the limitations of observational and interventional nutritional research in ADHD are discussed, along with recommendations for future research directions. Full article

(This article belongs to the Special Issue The Roles of Diet, Gut Microbiome and Microbial Metabolome in Precision Nutrition)

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23 pages, 3896 KB

Open AccessEditor’s ChoiceArticle

Storage Profiling: Evaluating the Effect of Modified Atmosphere Packaging on Metabolomic Changes of Strawberries (Fragaria × ananassa)

by Johannes Brockelt, Robin Dammann, Jennifer Griese, Agnes Weiss, Markus Fischer and Marina Creydt

Metabolites 2025, 15(5), 330; https://doi.org/10.3390/metabo15050330 - 15 May 2025

Viewed by 1002

Abstract

Background/Objectives: Strawberries (Fragaria × ananassa) are among the most commonly consumed fruits due to their taste and nutritional benefits. However, their high rate of spoilage poses a major problem during the period from harvest and transport to further processing or marketing. [...] Read more.

Background/Objectives: Strawberries (Fragaria × ananassa) are among the most commonly consumed fruits due to their taste and nutritional benefits. However, their high rate of spoilage poses a major problem during the period from harvest and transport to further processing or marketing. The aim of this study was, therefore, to investigate the effects of passive modified atmosphere packaging on the metabolome and shelf life of strawberries as a more sustainable alternative compared to standard market storage conditions. Methods: A total of 99 strawberry samples were analyzed for microbial viable counts, water content, and metabolomic changes using non-targeted low-resolution near-infrared spectroscopy, high-resolution mass spectrometry, and microbial culture-based methods. Results: Using near-infrared spectroscopy as a rapid screening method, the linear regression model indicated that strawberries stored under modified atmosphere packaging conditions had a longer shelf life. Furthermore, lipidomic analysis using mass spectrometry showed that the levels of spoilage biomarkers, such as oxidized phosphatidylcholines and lysophosphatidylcholines, were increased under common market storage conditions without a controlled atmosphere. In contrast, the levels of these metabolites were reduced when strawberries were stored in modified atmosphere packaging. Moreover, the strawberries stored under modified atmosphere packaging had a lower number of bacteria, yeasts, and molds as well as a lower water loss throughout the entire storage period. Conclusions: Overall, the study highlights the potential of passive modified atmosphere packaging films to extend the shelf life and thus maintain the edibility of strawberries over a longer period. Full article

(This article belongs to the Special Issue Metabolomic Technology in Quality and Safety of Agricultural Products and Foods)

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27 pages, 2350 KB

Open AccessEditor’s ChoiceArticle

Exploring Postharvest Metabolic Shifts and NOX2 Inhibitory Potential in Strawberry Fruits and Leaves via Untargeted LC-MS/MS and Chemometric Analysis

by Georgia Ladika, Paris Christodoulou, Eftichia Kritsi, Thalia Tsiaka, Georgios Sotiroudis, Dionisis Cavouras and Vassilia J. Sinanoglou

Metabolites 2025, 15(5), 321; https://doi.org/10.3390/metabo15050321 - 13 May 2025

Viewed by 712

Abstract

Background/Objectives: Strawberries are highly appreciated for their rich phytochemical composition, but rapid postharvest deterioration limits their shelf life and nutritional quality. This study aimed to investigate the metabolic changes occurring in both strawberry fruits and leaves during storage and to evaluate the NADPH [...] Read more.

Background/Objectives: Strawberries are highly appreciated for their rich phytochemical composition, but rapid postharvest deterioration limits their shelf life and nutritional quality. This study aimed to investigate the metabolic changes occurring in both strawberry fruits and leaves during storage and to evaluate the NADPH oxidase 2 (NOX2) inhibitory potential of strawberry-derived metabolites. Methods: Untargeted LC-MS/MS analysis was conducted on fruit and leaf tissues stored at 8 ± 0.5 °C. A total of 37 metabolites were identified, including organic acids, phenolic acids, flavonoids, and hydroxycinnamic acid derivatives. Multivariate statistical analyses (ANOVA, PLS-DA, and volcano plots) were used to assess temporal and tissue-specific metabolic shifts. Additionally, a machine learning-based predictive model was applied to evaluate the NOX2 inhibitory potential of 24 structurally characterized metabolites. Results: Storage induced significant and tissue-specific metabolic changes. In fruits, malic acid, caffeic acid, and quercetin-3-glucuronide showed notable variations, while ellagic acid aglycone and galloylquinic acid emerged as prominent markers in leaves. The predictive model identified 21 out of 24 metabolites as likely NOX2 inhibitors, suggesting potential antioxidant and anti-inflammatory bioactivity. Conclusions: These findings provide new insights into postharvest biochemical dynamics in both strawberry fruits and leaves. The results highlight the value of leaves as a source of bioactive compounds and support their potential valorization in functional food and nutraceutical applications. Full article

(This article belongs to the Special Issue Metabolic Changes during Pre- and Post-harvest Fruit and Vegetable Decay, Ripening and Senescence)

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15 pages, 1440 KB

Open AccessEditor’s ChoiceArticle

Plasma Metabolic Outliers Identified in Estonian Human Knockouts

by Ketian Yu, Estonian Biobank Research Team, Karol Estrada, Tõnu Esko, Mart Kals, Tiit Nikopensius, Jaanika Kronberg, Urmo Võsa, Arthur Wuster and Lorenzo Bomba

Metabolites 2025, 15(5), 323; https://doi.org/10.3390/metabo15050323 - 13 May 2025

Viewed by 776

Abstract

Background/Objectives: Metabolomics, in combination with genetic data, is a powerful approach to study the biochemical consequences of genetic variation. We assessed the impact of human gene knockouts (KOs) on the metabolite levels of Estonia Biobank (EstBB) participants and integrated the results with electronic [...] Read more.

Background/Objectives: Metabolomics, in combination with genetic data, is a powerful approach to study the biochemical consequences of genetic variation. We assessed the impact of human gene knockouts (KOs) on the metabolite levels of Estonia Biobank (EstBB) participants and integrated the results with electronic health record data. Methods: In 150,000 EstBB genotyped participants, we identified 723 KOs with 152 different predicted loss of function (pLoF) variants in 115 genes. For those KOs and 258 controls, 1387 metabolites were profiled using ultra-high-performance liquid chromatography–tandem mass spectrometry. Results: We identified 48 associations linking rare pLoF variants in 22 genes to 43 metabolites. Out of 48 associations, 27 (56%) were found in genes that cause inborn errors of metabolism. The top associations identified in our analysis included genes and metabolites involved in the degradation pathway of the pyrimidine bases uracil and thymine (DPYD and UPB1). We found DPYD gene KOs to be associated with elevated levels of Uracil, confirming that DPD-deficiency is a leading cause of severe 5-Fluorouracil toxicity. Overall, 54% of reported associations are gene targets of approved drugs or bioactive drug-like compounds. Conclusions: Our findings contribute to assessing the impact of human KOs on metabolite levels and offer insights into gene functions, disease mechanism, and drug target validation. Full article

(This article belongs to the Section Bioinformatics and Data Analysis)

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14 pages, 3108 KB

Open AccessEditor’s ChoiceArticle

Comprehensive Analysis of Small RNA Modifications in Arabidopsis thaliana and Their Dynamics During Seed Germination

by Liu-Cheng Jiang, Meng Men, Xuan-Jun Cui, Ren-Jie Zeng, Shu-Yi Gu, Tian Feng, Chen Zeng, Tiantian Ye, Jun Xiong, Bi-Feng Yuan and Yu-Qi Feng

Metabolites 2025, 15(5), 319; https://doi.org/10.3390/metabo15050319 - 10 May 2025

Viewed by 665

Abstract

Background: Small RNA, defined as RNA molecules of less than 200 nucleotides in length, play pivotal regulatory roles in plant growth, development, and environmental stress responses. However, research on modifications in plant small RNA remains limited. Methods: In this study, we [...] Read more.

Background: Small RNA, defined as RNA molecules of less than 200 nucleotides in length, play pivotal regulatory roles in plant growth, development, and environmental stress responses. However, research on modifications in plant small RNA remains limited. Methods: In this study, we developed a liquid chromatography–tandem mass spectrometry (LC-MS/MS) method for the simultaneous detection of 41 RNA modifications, facilitating the systematic qualification and quantification of modifications in plant small RNA. Results: We identified a total of nine modifications, among which N⁶,N⁶-dimethyladenosine (m^6,6A) is a newly identified modification in plant small RNA. Furthermore, we conducted a quantitative analysis of these modifications in Arabidopsis thaliana during the germination process and observed significant dynamic changes in their abundance from 1 to 5 days post-germination. Notably, the trends in the contents of these modifications exhibited a strong correlation with the reported gene expression levels of the relevant modifying enzymes and demodifying enzymes, suggesting that these modifications may play essential roles during seed germination and are tightly regulated by the genes of the corresponding enzymes. Conclusions: The discovery of these modifications in plant small RNA, coupled with the dynamic changes in their levels during germination, holds great promise for a further understanding of the physiological functions of small RNA modifications and their associated regulatory mechanisms in plant seed germination. Full article

(This article belongs to the Special Issue LC-MS/MS Analysis for Plant Secondary Metabolites)

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20 pages, 3404 KB

Open AccessEditor’s ChoiceArticle

A Data-Driven Approach to Link GC-MS and LC-MS with Sensory Attributes of Chicken Bouillon with Added Yeast-Derived Flavor Products in a Combined Prediction Model

by Simon Leygeber, Carmen Diez-Simon, Justus L. Großmann, Anne-Charlotte Dubbelman, Amy C. Harms, Johan A. Westerhuis, Doris M. Jacobs, Peter W. Lindenburg, Margriet M. W. B. Hendriks, Brenda C. H. Ammerlaan, Marco A. van den Berg, Rudi van Doorn, Roland Mumm, Age K. Smilde, Robert D. Hall and Thomas Hankemeier

Metabolites 2025, 15(5), 317; https://doi.org/10.3390/metabo15050317 - 8 May 2025

Viewed by 1146

Abstract

Background: There is a continuous demand to create new, superior sensory food experiences. In the food industry, yeast-derived flavor products (YPs) are often used as ingredients in foods to create new aromas and taste qualities that are appreciated by consumers. Methods: Chicken bouillon [...] Read more.

Background: There is a continuous demand to create new, superior sensory food experiences. In the food industry, yeast-derived flavor products (YPs) are often used as ingredients in foods to create new aromas and taste qualities that are appreciated by consumers. Methods: Chicken bouillon samples containing diverse YPs were chemically and sensorially characterized using statistical multivariate analyses. The sensory evaluation was performed using quantitative descriptive analysis (QDA) by trained panelists. Thirty-four sensory attributes were scored, including odor, flavor, mouthfeel, aftertaste and afterfeel. Untargeted metabolomic profiles were obtained using stir bar sorptive extraction (SBSE) coupled to GC-MS, RPLC-MS and targeted HILIC-MS. Results: In total, 261 volatiles were detected using GC-MS, from chemical groups of predominantly aldehydes, esters, pyrazines and ketones. Random Forest (RF) modeling revealed volatiles associated with roast odor (2-ethyl-5-methyl pyrazine, 2,3,5-trimethyl-6-isopentyl pyrazine) and chicken odor (2,4-nonadienal, 2,4-decadienal, 2-acetyl furan), which could be predicted by our combined model with R² > 0.5. In total, 2305 non-volatiles were detected for RPLC-MS and 34 for targeted HILIC-MS, where fructose-isoleucine and cyclo-leucine-proline were found to correlate with roast flavor and odor. Furthermore, a list of metabolites (glutamate, monophosphates, methionyl-leucine) was linked to umami-related flavor. This study describes a straightforward data-driven approach for studying foods with added YPs to identify flavor-impacting correlations between molecular composition and sensory perception. It also highlights limitations and preconditions for good prediction models. Overall, this study emphasizes a matrix-based approach for the prediction of food taste, which can be used to analyze foods for targeted flavor design or quality control. Full article

(This article belongs to the Section Food Metabolomics)

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17 pages, 1679 KB

Open AccessEditor’s ChoiceArticle

Peripheral Antinociception Induced by Carvacrol in the Formalin Test Involves the Opioid Receptor-NO-cGMP-K⁺ Channel Pathway

by Mario I. Ortiz, Raquel Cariño-Cortés, Eduardo Fernández-Martínez, Victor Manuel Muñoz-Pérez, Gilberto Castañeda-Hernández and Martha Patricia González-García

Metabolites 2025, 15(5), 314; https://doi.org/10.3390/metabo15050314 - 7 May 2025

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Abstract

Background/Objectives: Carvacrol is a naturally occurring phenolic monoterpene that is one of the main constituents of the essential oils of oregano (Origanum vulgare) and other herbs. Carvacrol has anti-inflammatory and antinociceptive effects. Carvacrol can activate and inhibit several second messengers and [...] Read more.

Background/Objectives: Carvacrol is a naturally occurring phenolic monoterpene that is one of the main constituents of the essential oils of oregano (Origanum vulgare) and other herbs. Carvacrol has anti-inflammatory and antinociceptive effects. Carvacrol can activate and inhibit several second messengers and ionic channels at the systemic level. However, there is no evidence of the peripheral antinociception of carvacrol and its mechanism of action. This study was designed to determine whether the opioid receptor-nitric oxide (NO)-cyclic guanosine monophosphate (cGMP)-K⁺ channel pathway is involved in the local antinociception of carvacrol. Methods: Wistar rats were injected with 1% formalin subcutaneously on the dorsal surface of the right hind paw with the vehicle or carvacrol (100–300 µg/paw). To determine whether the opioid receptor-NO-cGMP-K⁺ channel pathway and a biguanide-dependent mechanism are responsible for the local antinociception induced by carvacrol, the effect of the injection (10 min before the 1% formalin injection) with the corresponding vehicles, metformin, naltrexone, NG-L-nitro-arginine methyl ester (L-NAME), 1 H-(1,2,4)-oxadiazolo (4,2-a) quinoxalin-1-one (ODQ), and K⁺ channel blockers on the antinociception induced by local carvacrol (300 µg/paw) was determined. Results: In both phases of the formalin test, carvacrol produced antinociception. Naltrexone, metformin, L-NAME, ODQ, glibenclamide and glipizide (both ATP-sensitive K⁺ channel blockers), tetraethylammonium and 4-aminopyridine (voltage-gated K⁺ channel blockers), and apamin and charybdotoxin (Ca²⁺-activated K⁺ channel blockers) reversed the carvacrol-induced peripheral antinociception. Conclusions: The local peripheral administration of carvacrol produced significant antinociception and activated the opioid receptor-NO-cGMP-K⁺ channel pathway. Full article

(This article belongs to the Special Issue Exploring Innovations in Secondary Metabolites and Their Effects on Pain, Inflammation and Metabolic Syndrome)

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14 pages, 1467 KB

Open AccessEditor’s ChoiceArticle

Propionyl Carnitine Metabolic Profile: Optimizing the Newborn Screening Strategy Through Customized Cut-Offs

by Maria Lucia Tommolini, Maria Concetta Cufaro, Silvia Valentinuzzi, Ilaria Cicalini, Mirco Zucchelli, Alberto Frisco, Simonetta Simonetti, Michela Perrone Donnorso, Sara Moccia, Ines Bucci, Maurizio Aricò, Vincenzo De Laurenzi, Luca Federici, Damiana Pieragostino and Claudia Rossi

Metabolites 2025, 15(5), 308; https://doi.org/10.3390/metabo15050308 - 6 May 2025

Cited by 1 | Viewed by 1313

Abstract

Background: The advent of tandem mass spectrometry (MS/MS) had an essential role in the expansion of newborn screening (NBS) for different inborn errors of metabolism (IEMs). Nowadays, almost 50 IEMs are screened in Italy. The use of second-tier tests (2-TTs) in NBS minimizes [...] Read more.

Background: The advent of tandem mass spectrometry (MS/MS) had an essential role in the expansion of newborn screening (NBS) for different inborn errors of metabolism (IEMs). Nowadays, almost 50 IEMs are screened in Italy. The use of second-tier tests (2-TTs) in NBS minimizes the false positive rate; nevertheless, the metabolic profile is influenced not only by the genome but also by environmental factors and clinical variables. We reviewed the MS/MS NBS data from over 37,000 newborns (of which 8% required 2-TTs) screened in the Italian Abruzzo region to evaluate the impact of neonatal and maternal variables on propionate-related primary biomarker levels. Methods: Expanded NBS and 2-TT analyses were performed using MS/MS and liquid chromatography–MS/MS methods. We set up layered cut-offs dividing all 37,000 newborns into categories. Statistical analysis was used to create alarm thresholds for NBS-positive samples. Statistically significant differences were found in both neonatal and maternal conditions based on the 2-TTs carried out. According to the stratified cut-offs, only 1.47% of the newborns would have required a 2-TT while still retaining the ability to recognize the true-positive case of methylmalonic acidemia with homocystinuria, which has been identified by NBS. To further support the clinical applicability, we performed an external evaluation considering nine positive cases from an extra-regional neonatal population, confirming the potential of our model. Interestingly, the setting of alarm thresholds and their application would allow for establishing the degree of priority/urgency for 2-TTs. Conclusions: Tailoring NBS by customized cut-offs may enhance the application of precision medicine, focusing on true-positive cases and also reducing analysis costs and times. Full article

(This article belongs to the Section Endocrinology and Clinical Metabolic Research)

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18 pages, 1862 KB

Open AccessEditor’s ChoiceReview

SMARCB1 Deficiency as a Driver of the Hallmarks of Cancer in Rhabdoid Tumours: Novel Insights into Dysregulated Energy Metabolism, Emerging Targets, and Ongoing Clinical Trials

by Abdul L. Shakerdi and Graham P. Pidgeon

Metabolites 2025, 15(5), 304; https://doi.org/10.3390/metabo15050304 - 3 May 2025

Viewed by 2134

Abstract

Background: Rhabdoid tumours (RTs) are aggressive neoplasms most often characterised by biallelic loss of the SMARCB1 gene, encoding a core subunit of the SWI/SNF chromatin-remodelling complex. Despite their relative genetic stability, RTs exhibit a highly malignant phenotype and poor prognosis. Methods: This review [...] Read more.

Background: Rhabdoid tumours (RTs) are aggressive neoplasms most often characterised by biallelic loss of the SMARCB1 gene, encoding a core subunit of the SWI/SNF chromatin-remodelling complex. Despite their relative genetic stability, RTs exhibit a highly malignant phenotype and poor prognosis. Methods: This review explores the mechanisms underlying SMARCB1 aberrations, their role in driving hallmarks of cancer, and emerging therapeutic strategies for RTs. Ongoing clinical trials listed on ClinicalTrials were reviewed to evaluate the translational potential of targeted therapies in SMARCB1-deficient rhabdoid tumours. Results: Loss of SMARCB1 drives multiple cancer hallmarks by disrupting key regulatory pathways. It promotes unchecked cell proliferation through alterations in p16INK4a and Myc signalling. SMARCB1-deficient tumours possess immune-evading capabilities via PD-L1 overexpression and immune checkpoint activation. SMARCB1 deficiency also alters cellular energetics. The nucleotide biosynthesis pathway has been demonstrated to be upregulated in RT organoids, as shown by increased levels of pathway metabolites. Enzymes of the mevalonate pathway such as HMG-CoA reductase and mevalonate kinase are also dysregulated. Targeting glutathione metabolism with eprenetapopt may induce oxidative stress and apoptosis. Widespread epigenetic aberrations, including increased EZH2 activity, are being targeted with inhibitors such as tazemetostat. Conclusions: SMARCB1 loss is a central driver of cancer hallmarks in RTs, enabling proliferation, immune evasion, metabolic reprogramming, and epigenetic dysregulation. Future horizons in RT treatment include immunotherapies, epigenetic modifiers, and gene therapies. The synergy and optimal timing of targeted therapy with conventional treatment requires further characterisation for clinical translation. Full article

(This article belongs to the Special Issue Cancer Metabolomics 2024)

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29 pages, 2365 KB

Open AccessEditor’s ChoiceReview

Caloric Restriction and Sirtuins as New Players to Reshape Male Fertility

by Diana C. A. André, Pedro F. Oliveira, Marco G. Alves and Ana D. Martins

Metabolites 2025, 15(5), 303; https://doi.org/10.3390/metabo15050303 - 2 May 2025

Viewed by 1415

Abstract

Over the years, caloric intake has remained a subject of profound scrutiny. Within the scientific community, there has been rigorous debate to ascertain which path is most ideal for enhancing quality of life and extending the human lifespan. Caloric restriction has been shown [...] Read more.

Over the years, caloric intake has remained a subject of profound scrutiny. Within the scientific community, there has been rigorous debate to ascertain which path is most ideal for enhancing quality of life and extending the human lifespan. Caloric restriction has been shown to be a promising contributor towards longevity and delaying the onset of age-related diseases. This diet consists of a reduction in caloric intake while maintaining essential energy and nutritional requirements to achieve optimal health while avoiding malnutrition. However, the effects of this nutritional regimen on male reproductive health have not yet been comprehensively studied. Nevertheless, such a complex process will certainly be regulated by a variety of metabolic sensors, likely sirtuins. Evidence has been gathered regarding this group of enzymes, and their ability to regulate processes such as chromatin condensation, the cell cycle, insulin signaling, and glucose and lipid metabolism, among many others. Concerning testicular function and male fertility, sirtuins can modulate certain metabolic processes through their interaction with the hypothalamic–pituitary–gonadal axis and mitochondrial dynamics, among many others, which remain largely unexplored. This review explores the impact of caloric restriction on male fertility, highlighting the emerging role of sirtuins as key regulators of male reproductive health through their influence on cellular metabolism. Full article

(This article belongs to the Special Issue The Impact of Environmental Contaminants on Neurodevelopment and Human Metabolism)

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24 pages, 2280 KB

Open AccessEditor’s ChoiceReview

From Biomarker Discovery to Clinical Applications of Metabolomics in Glioblastoma

by Neja Šamec, Gloria Krapež, Cene Skubic, Ivana Jovčevska and Alja Videtič Paska

Metabolites 2025, 15(5), 295; https://doi.org/10.3390/metabo15050295 - 29 Apr 2025

Cited by 1 | Viewed by 1571

Abstract

Background/Objectives: In recent years, interest in studying changes in cancer metabolites has resulted in significant advances in the metabolomics field. Glioblastoma remains the most aggressive and lethal brain malignancy, which presents with notable metabolic reprogramming. Methods: We performed literature research from the PubMed [...] Read more.

Background/Objectives: In recent years, interest in studying changes in cancer metabolites has resulted in significant advances in the metabolomics field. Glioblastoma remains the most aggressive and lethal brain malignancy, which presents with notable metabolic reprogramming. Methods: We performed literature research from the PubMed database and considered research articles focused on the key metabolic pathways altered in glioblastoma (e.g., glycolysis, lipid metabolism, TCA cycle), the role of oncometabolites and metabolic plasticity, and the differential expression of metabolites in glioblastoma. Currently used metabolomics approaches can be either targeted, focusing on specific metabolites and pathways, or untargeted, which involves data-driven exploration of the metabolome and also results in the identification of new metabolites. Data processing and analysis is of great importance and can be improved with the integration of machine learning approaches for metabolite identification. Results: Changes in α/β-glucose, lactate, choline, and 2-hydroxyglutarate were detected in glioblastoma compared with non-tumor tissues. Different metabolites such as fumarate, tyrosine, and leucine, as well as citric acid, isocitric acid, shikimate, and GABA were detected in blood and CSF, respectively. Conclusions: Although promising new technological and bioinformatic approaches help us understand glioblastoma better, challenges associated with biomarker availability, tumor heterogeneity, interpatient variability, standardization, and reproducibility still remain. Metabolomics research, either alone or combined with genomics or proteomics (i.e., multiomics) in glioblastoma, can lead to biomarker identification, tracking of metabolic therapy response, discovery of novel metabolites and pathways, and identification of potential therapeutic targets. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Metabolomics in Health and Disease: Targeted Analysis and Its Trends)

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34 pages, 1818 KB

Open AccessEditor’s ChoiceReview

From Childhood Obesity to Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) and Hyperlipidemia Through Oxidative Stress During Childhood

by Siham Accacha, Julia Barillas-Cerritos, Ankita Srivastava, Frances Ross, Wendy Drewes, Shelly Gulkarov, Joshua De Leon and Allison B. Reiss

Metabolites 2025, 15(5), 287; https://doi.org/10.3390/metabo15050287 - 24 Apr 2025

Cited by 2 | Viewed by 3006

Abstract

Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD), previously known as non-alcoholic fatty liver disease (NAFLD), is rapidly becoming the most prevalent form of chronic liver disease in both pediatric and adult populations. It encompasses a wide spectrum of liver abnormalities, ranging from simple [...] Read more.

Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD), previously known as non-alcoholic fatty liver disease (NAFLD), is rapidly becoming the most prevalent form of chronic liver disease in both pediatric and adult populations. It encompasses a wide spectrum of liver abnormalities, ranging from simple fat accumulation to severe conditions such as inflammation, fibrosis, cirrhosis, and liver cancer. Major risk factors for MASLD include obesity, insulin resistance, type 2 diabetes, and hypertriglyceridemia. Methods: This narrative review employed a comprehensive search of recent literature to identify the latest studies on the relationship between MAFLD and obesity, the health consequences and the latest treatment options to prevent long-term damage to the liver and other organs. Additionally, the article presents perspectives on diagnostic biomarkers. Results: Childhood obesity is linked to a multitude of comorbid conditions and remains a primary risk factor for adult obesity. This abnormal fat accumulation is known to have long-term detrimental effects into adulthood. Scientific evidence unequivocally demonstrates the role of obesity-related conditions, such as insulin resistance, dyslipidemia, and hyperglycemia, in the development and progression of MASLD. Oxidative stress, stemming from mitochondrial dysfunction, is a leading factor in MASLD. This review discusses the interconnections between oxidative stress, obesity, dyslipidemia, and MASLD. Conclusions: Atherogenic dyslipidemia, oxidative stress, inflammation, insulin resistance, endothelial dysfunction, and cytokines collectively contribute to the development of MASLD. Potential treatment targets for MASLD are focused on prevention and the use of drugs to address obesity and elevated blood lipid levels. Full article

(This article belongs to the Special Issue Metabolic Dysregulation in Fatty Liver Disease)

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18 pages, 954 KB

Open AccessEditor’s ChoiceArticle

Alcohol Exposure May Increase Prenatal Choline Needs Through Redirection of Choline into Lipid Synthesis Rather than Methyl Donation

by Hannah G. Petry, Nipun Saini, Susan M. Smith and Sandra M. Mooney

Metabolites 2025, 15(5), 289; https://doi.org/10.3390/metabo15050289 - 24 Apr 2025

Cited by 2 | Viewed by 968

Abstract

Background: Prenatal alcohol exposure (PAE) can reduce fetal growth and cause neurodevelopmental disability. Prenatal choline supplements attenuate PAE-induced behavioral and growth deficits; however, the underlying mechanisms are unknown. Alcohol alters nutrient metabolism and potentially increases nutrient needs. Here, we investigate how alcohol [...] Read more.

Background: Prenatal alcohol exposure (PAE) can reduce fetal growth and cause neurodevelopmental disability. Prenatal choline supplements attenuate PAE-induced behavioral and growth deficits; however, the underlying mechanisms are unknown. Alcohol alters nutrient metabolism and potentially increases nutrient needs. Here, we investigate how alcohol affects choline metabolism in the maternal–fetal dyad and the role of supplemental choline. Methods: Pregnant C57BL/6J mice were assigned to one of four groups: alcohol-exposed (3 g/kg alcohol/day) or control +/− 100 mg/kg choline daily from embryonic day (E)8.5–17.5. We performed an exploratory hypothesis-generating analysis of targeted metabolomics on choline-related metabolites in the maternal liver, plasma, placenta, and fetal brain at E17.5 and Spearman correlation analyses to determine their association with gestational and fetal growth outcomes. Results: Although choline levels were largely unaffected by alcohol or choline, alcohol increased many lipid products in the CDP–choline pathway; this was not normalized by choline. Alcohol increased placental CDP–ethanolamine and reduced the maternal hepatic SAM/SAH ratio as well as dimethylglycine and the serine/glycine ratio across the dyad, suggesting a functional insufficiency in methyl donor pools. These outcomes were rescued by supplemental choline. Correlation analyses among choline metabolites and fetal growth outcomes suggest that maternal plasma methionine, serine, and the serine/glycine ratio may be predictive of maternal–fetal choline status. Conclusions: The increased hepatic lipid synthesis that characterizes chronic alcohol exposure may draw choline into phospholipid biosynthesis at the expense of its use as a methyl donor. We propose that PAE increases choline needs, and that its supplementation is necessary to fulfill these competing demands for lipid and methyl use. Full article

(This article belongs to the Special Issue One-Carbon Metabolism in Pregnant Women, Fetuses, and Infants)

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27 pages, 788 KB

Open AccessEditor’s ChoiceReview

Lipid Metabolism and Statin Therapy in Neurodegenerative Diseases: An Endocrine View

by Antonella Di Sarno, Fiammetta Romano, Rossana Arianna, Domenico Serpico, Mariarosaria Lavorgna, Silvia Savastano, Annamaria Colao and Carolina Di Somma

Metabolites 2025, 15(4), 282; https://doi.org/10.3390/metabo15040282 - 18 Apr 2025

Cited by 1 | Viewed by 1750

Abstract

Background/aim: A growing body of evidence suggests a link between dyslipidemias and neurodegenerative diseases, highlighting the crucial role of lipid metabolism in the health of the central nervous system. The aim of our work was to provide an update on this topic, [...] Read more.

Background/aim: A growing body of evidence suggests a link between dyslipidemias and neurodegenerative diseases, highlighting the crucial role of lipid metabolism in the health of the central nervous system. The aim of our work was to provide an update on this topic, with a focus on clinical practice from an endocrinological point of view. Endocrinologists, being experts in the management of dyslipidemias, can play a key role in the prevention and treatment of neurodegenerative conditions, through precocious and effective lipid profile optimization. Methods: The literature was scanned to identify clinical trials and correlation studies on the association between dyslipidemia, statin therapy, and the following neurodegenerative diseases: Alzheimer’s disease (AD), Parkisons’s disease (PD), Multiple sclerosis (MS), and Amyotrophic lateral sclerosis (ALS). Results: Impaired lipid homeostasis, such as that frequently observed in patients affected by obesity and diabetes, is related to neurodegenerative diseases, such as AD, PD, and other cognitive deficits related to aging. AD and related dementias are now a real priority health problem. In the United States, there are approximately 7 million subjects aged 65 and older living with AD and related dementias, and this number is projected to grow to 12 million in the coming decades. Lipid-lowering therapy with statins is an effective strategy in reducing serum low-density lipoprotein cholesterol to normal range concentrations and, therefore, cardiovascular disease risk; moreover, statins have been reported to have a positive effect on neurodegenerative diseases. Conclusions: Several pieces of research have found inconsistent information following our review. There was no association between statin use and ALS incidence. More positive evidence has emerged regarding statin use and AD/PD. However, further large-scale prospective randomized control trials are required to properly understand this issue. Full article

(This article belongs to the Special Issue Lipid Metabolism in Age-Related Diseases)

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17 pages, 1407 KB

Open AccessEditor’s ChoiceArticle

Metabolic Effects of the Cancer Metastasis Modulator MEMO1

by Marziyeh Ghanbarian, Natalia Dolgova, Frederick S. Vizeacoumar, Franco J. Vizeacoumar, Deborah Michel, Anas El-Aneed and Oleg Y. Dmitriev

Metabolites 2025, 15(4), 277; https://doi.org/10.3390/metabo15040277 - 17 Apr 2025

Viewed by 965

Abstract

Background/Objectives: Cancer cells often display altered energy metabolism. In particular, expression levels and activity of the tricarboxylic acid cycle (TCA cycle) enzymes may change in cancer, and dysregulation of the TCA cycle is a frequent hallmark of cancer cell metabolism. MEMO1, a modulator [...] Read more.

Background/Objectives: Cancer cells often display altered energy metabolism. In particular, expression levels and activity of the tricarboxylic acid cycle (TCA cycle) enzymes may change in cancer, and dysregulation of the TCA cycle is a frequent hallmark of cancer cell metabolism. MEMO1, a modulator of cancer metastasis, has been shown to bind iron and regulate iron homeostasis in the cells. MEMO1 knockout changed mitochondrial morphology and iron content in breast cancer cells. Our previous genome-wide analysis of MEMO1 genetic interactions across multiple cancer cell lines revealed that gene sets involved in mitochondrial respiration and the TCA cycle are enriched among the gain-of-function interaction partners of MEMO1. Based on these findings, we measured the TCA cycle metabolite levels in breast cancer cells with varying levels of MEMO1 expression. Methods: ShRNA knockdown assay was performed to test essentiality of key TCA cycle enzymes. TCA metabolites were quantified using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in MDA-MB-231 (high MEMO1), M67-2 (MEMO1 knockdown), and M67-9 (MEMO1 knockout) cells under iron-depleted, basal iron, and iron-supplemented conditions. Results:ACO2 and OGDH knockdowns inhibit cell proliferation, indicating an essential role of the TCA cycle in MDA-MB-231 metabolism. α-Ketoglutarate and citrate levels exhibited an inverse relationship with MEMO1 expression, increasing significantly in MEMO1 knockout cells regardless of iron availability. In contrast, fumarate, malate, and glutamate levels were elevated in MEMO1 knockout cells specifically under low iron conditions, suggesting an iron-dependent effect. Conclusions: Overall, our results indicate that MEMO1 plays a role in regulating the TCA in cancer cells in an iron-dependent manner. Full article

(This article belongs to the Special Issue Reactive Oxygen Species and Energy Metabolic Alterations in Health and Disease)

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16 pages, 1293 KB

Open AccessEditor’s ChoiceArticle

Comprehensive Characterization of Serum Lipids of Dairy Cows: Effects of Negative Energy Balance on Lipid Remodelling

by Zhiqian Liu, Wenjiao Wang, Joanne E. Hemsworth, Coralie M. Reich, Carolyn R. Bath, Monique J. Berkhout, Muhammad S. Tahir, Vilnis Ezernieks, Leah C. Marett, Amanda J. Chamberlain, Mike E. Goddard and Simone J. Rochfort

Metabolites 2025, 15(4), 274; https://doi.org/10.3390/metabo15040274 - 15 Apr 2025

Cited by 1 | Viewed by 824

Abstract

Background: The presence and concentration of lipids in serum of dairy cows have significant implications for both animal health and productivity and are potential biomarkers for several common diseases. However, information on serum lipid composition is rather fragmented, and lipid remodelling during the [...] Read more.

Background: The presence and concentration of lipids in serum of dairy cows have significant implications for both animal health and productivity and are potential biomarkers for several common diseases. However, information on serum lipid composition is rather fragmented, and lipid remodelling during the transition period is only partially understood. Methods: Using a combination of reversed-phase liquid chromatography-mass spectrometry (RP-LC-MS), hydrophilic interaction-mass spectrometry (HILIC-MS), and lipid annotation software, we performed a comprehensive identification and quantification of serum of dairy cows in pasture-based Holstein-Friesian cows. The lipid remodelling induced by negative energy balance was investigated by comparing the levels of all identified lipids between the fresh lactation (5–14 days in milk, DIM) and full lactation (65–80 DIM) stages. Results: We identified 535 lipid molecular species belonging to 19 classes. The most abundant lipid class was cholesteryl ester (CE), followed by phosphatidylcholine (PC), sphingomyelin (SM), and free fatty acid (FFA), whereas the least abundant lipids included phosphatidylserine (PS), phosphatidic acid (PA), phosphatidylglycerol (PG), acylcarnitine (AcylCar), ceramide (Cer), glucosylceramide (GluCer), and lactosylceramide (LacCer). Conclusions: A remarkable increase in most lipids and a dramatic decrease in FFAs, AcylCar, and DHA-containing species were observed at the full lactation compared to fresh lactation stage. Several serum lipid biomarkers for detecting negative energy balance in cows were also identified. Full article

(This article belongs to the Special Issue Effects of Stress on Animal Metabolism)

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23 pages, 3688 KB

Open AccessEditor’s ChoiceArticle

Targeted and Non-Targeted Metabolomic Evaluation of Cerebrospinal Fluid in Early Phase Schizophrenia: A Pilot Study from the Hopkins First Episode Psychosis Project

by George E. Jaskiw, Mark E. Obrenovich, Curtis J. Donskey, Farren B. S. Briggs, Sun Sunnie Chung, Anastasiya I. Kalinina, Austin Bolomey, Lindsay N. Hayes, Kun Yang, Robert H. Yolken and Akira Sawa

Metabolites 2025, 15(4), 275; https://doi.org/10.3390/metabo15040275 - 15 Apr 2025

Viewed by 1512

Abstract

(1) Background: The lack of reliable biomarkers remains a significant barrier to improving outcomes for patients with schizophrenia. While metabolomic analyses of blood, urine, and feces have been explored, results have been inconsistent. Compared to peripheral compartments, cerebrospinal fluid (CSF) more closely reflects [...] Read more.

(1) Background: The lack of reliable biomarkers remains a significant barrier to improving outcomes for patients with schizophrenia. While metabolomic analyses of blood, urine, and feces have been explored, results have been inconsistent. Compared to peripheral compartments, cerebrospinal fluid (CSF) more closely reflects the chemical composition of brain extracellular fluid. Given that brain dysregulation may be more pronounced during the first episode of psychosis (FEP), we hypothesized that metabolomic analysis of CSF from FEP patients could reveal disease-associated biomarkers. (2) Methods: We recruited 15 patients within 24 months of psychosis onset (DSM-4 criteria) and 14 control participants through the Johns Hopkins Schizophrenia Center. CSF samples were analyzed using both non-targeted and targeted liquid chromatography–mass spectrometry. (3) Results: The non-targeted analysis identified lower levels of N-acetylneuraminic acid and N-acetyl-L-aspartic acid in the FEP group, while levels of uric acid were elevated. The targeted analysis focused on indolic and phenolic molecules previously linked to neuropsychiatric disorders. Notably, L-phenylalanine and 4-hydroxycinnamic acid levels were lower in the FEP group, and this difference remained significant after adjusting for age and sex. However, none of the significant differences in analyte levels between the groups survived an adjustment for multiple comparisons. (4) Conclusions: Our intriguing but preliminary associations align with results from other investigational approaches and highlight potential CSF analytes that warrant further study in larger samples. Full article

(This article belongs to the Special Issue Metabolomics in Human Diseases and Health)

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18 pages, 1901 KB

Open AccessEditor’s ChoiceArticle

Comparative Effects of Turmeric Secondary Metabolites Across Resorptive Bone Diseases

by Laura E. Wright, Jennifer B. Frye, Andrew G. Kunihiro, Barbara N. Timmermann and Janet L. Funk

Metabolites 2025, 15(4), 266; https://doi.org/10.3390/metabo15040266 - 11 Apr 2025

Viewed by 1197

Abstract

Background: Turmeric (Curcuma longa L.) rhizomes, whose secondary metabolites include polyphenols and terpenoids, have been used medicinally for millennia. However, modern scientific inquiry has primarily focused on medicinal effects of turmeric’s polyphenolic curcuminoids, including when evaluating turmeric use to maintain bone [...] Read more.

Background: Turmeric (Curcuma longa L.) rhizomes, whose secondary metabolites include polyphenols and terpenoids, have been used medicinally for millennia. However, modern scientific inquiry has primarily focused on medicinal effects of turmeric’s polyphenolic curcuminoids, including when evaluating turmeric use to maintain bone health. Methods: Disease-specific biological effects of turmeric’s major secondary metabolites (polyphenols and/or terpenoids), with or without associated turmeric rhizome-derived polysaccharides, were determined in vivo using pre-clinical models of clinically relevant resorptive bone diseases induced by different mechanisms. These included inflammatory arthritis, cancer-driven osteolytic bone metastases, and hormone deficiency-driven post-menopausal osteoporosis. Results: In the arthritis model, the safety profile of curcuminoids alone was superior. However, curcuminoids and terpenoids each had anti-inflammatory effects and prevented bone resorption, with polysaccharide-containing curcuminoid extracts having greater effect than curcuminoids alone. In the human osteolytic breast cancer bone metastases model, curcuminoid extracts containing polysaccharides tended to yield greater effects in reducing bone osteolysis and tumor progression than curcuminoids alone or more complex extracts. In contrast, only purified curcuminoids prevented bone loss in a post-menopausal osteoporosis model, while polysaccharide-containing curcuminoid extracts were without effect. In vitro metabolite effects on disease-specific mechanistic pathways in synoviocytes, osteoclasts, or breast cancer cells were consistent with documented in vivo outcomes and included differential metabolite-specific effects. Conclusions: In summary, these findings suggest that turmeric’s potential medicinal musculoskeletal effects are complex, pathway- and target-specific, and not limited to curcuminoids, with safety concerns potentially limiting certain uses. Full article

(This article belongs to the Special Issue Identification of Plant Metabolites: Characterization and Biological Activities, 2nd Edition)

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19 pages, 1595 KB

Open AccessEditor’s ChoiceReview

From Inflammation to Infertility: How Oxidative Stress and Infections Disrupt Male Reproductive Health

by Anastasios Potiris, Efthalia Moustakli, Eleni Trismpioti, Eirini Drakaki, Despoina Mavrogianni, Alkis Matsas, Athanasios Zikopoulos, Antonios Sfakianakis, Ioannis Tsakiridis, Themistoklis Dagklis, Athanasios Zachariou, Panagiotis Christopoulos, Ekaterini Domali, Peter Drakakis and Sofoklis Stavros

Metabolites 2025, 15(4), 267; https://doi.org/10.3390/metabo15040267 - 11 Apr 2025

Cited by 10 | Viewed by 3750

Abstract

Background/Objectives: Inflammation, infections, and oxidative stress (OS) all have an impact on male infertility, which is a complicated, multifaceted illness. OS affects motility and fertilization capability. It accomplishes this through damaging sperm DNA, oxidizing proteins, and triggering lipid peroxidation. These effects occur due [...] Read more.

Background/Objectives: Inflammation, infections, and oxidative stress (OS) all have an impact on male infertility, which is a complicated, multifaceted illness. OS affects motility and fertilization capability. It accomplishes this through damaging sperm DNA, oxidizing proteins, and triggering lipid peroxidation. These effects occur due to an imbalance between reactive oxygen species (ROS) and antioxidant defenses. Methods: This review aims to evaluate the impact of oxidative stress and inflammation on male infertility by assessing recent literature. Results: Pro-inflammatory cytokines, like TNF-α and IL-6, interfere with spermatogenesis and promote oxidative damage. Additionally, infections caused by pathogens like Escherichia coli and Chlamydia trachomatis alter the reproductive microenvironment, leading to sperm dysfunction and inflammation. Conclusions: Early detection and targeted treatment are essential due to the intricate interactions among these elements. Microbiota-modulating techniques, antimicrobial therapies, anti-inflammatory drugs, and antioxidants are therapeutic approaches that may help reduce oxidative damage and enhance male fertility. Full article

(This article belongs to the Special Issue Advancements in Reproductive Medicine: Unlocking the Secrets of the Ovary and Sperm for Fertility and Beyond)

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23 pages, 6197 KB

Open AccessEditor’s ChoiceArticle

Combined Effects of Rhodiola Rosea and Caffeine Supplementation on Straight Punch Explosive Power in Untrained and Trained Boxing Volunteers: A Synergistic Approach

by Biaoxu Tao, Hao Sun, Huixin Li, Zhiqin Xu, Yuan Xu, Liqi Chen, Chengzhe Ma, Xiaoyu Zhang, Longqi Yu, Shanjun Bao and Chang Liu

Metabolites 2025, 15(4), 262; https://doi.org/10.3390/metabo15040262 - 10 Apr 2025

Cited by 1 | Viewed by 2830

Abstract

Objectives: This study aimed to investigate the effects of combined supplementation with Rhodiola rosea (RHO) and caffeine (CAF) on the explosive power and sustained output capacity of lead and rear straight punches in both untrained and trained volunteers, with a focus on potential [...] Read more.

Objectives: This study aimed to investigate the effects of combined supplementation with Rhodiola rosea (RHO) and caffeine (CAF) on the explosive power and sustained output capacity of lead and rear straight punches in both untrained and trained volunteers, with a focus on potential synergistic effects. Methods: randomized, double-blind, placebo-controlled design was employed, enrolling 96 participants (48 untrained, 48 trained). Participants were stratified and randomly assigned to the control (CTR), CAF, RHO, or CAF+RHO group. All subjects completed an 8-week standardized boxing training program (twice per week). Punch performance was assessed using professional boxing equipment and a biomechanical testing system, evaluating lead and rear straight punches, ground reaction force (GRF), and a 30 s continuous punching test. Results: the CAF+RHO group showed significant improvements in both untrained and trained volunteers. Com-pared to the RHO group, this group demonstrated higher lead punch velocity, shorter bi-lateral peak force time during rear punches, and more punches in the 30 s test (p < 0.05). Compared to the CAF group, the CAF+RHO group exhibited greater rear punch force, higher bilateral peak force during lead punches, increased forefoot peak force in rear punches, and improved 30 s power output (p < 0.05). The CAF+RHO group also outperformed the CTR group across all parameters (p < 0.05). Conclusions: Combined supple mentation with CAF and RHO significantly enhances both explosive power and sustained output in boxing performance. This may result from improved energy metabolism efficiency and neuromuscular coordination, providing a promising nutritional strategy for high-intensity intermittent exercise. Full article

(This article belongs to the Section Nutrition and Metabolism)

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8 pages, 1174 KB

Open AccessEditor’s ChoiceArticle

Kinetics of Manganese Peroxidase Using Simple Phenolic Compounds as Substrates

by Madeline G. Gruenberg, Jonathan J. Halvorson and Michael A. Schmidt

Metabolites 2025, 15(4), 254; https://doi.org/10.3390/metabo15040254 - 9 Apr 2025

Cited by 1 | Viewed by 816

Abstract

Background/Objectives: Secondary metabolites encompass diverse groups of compounds; one such group is phenolics, which include small phenols up to larger polyphenols such as lignin and tannins. Smaller compounds such as phenolic acids can serve as substrates for soil microbes and enzymes. The specific [...] Read more.

Background/Objectives: Secondary metabolites encompass diverse groups of compounds; one such group is phenolics, which include small phenols up to larger polyphenols such as lignin and tannins. Smaller compounds such as phenolic acids can serve as substrates for soil microbes and enzymes. The specific interaction between plant secondary metabolites (PSMs) and soil enzymes determines whether the products of these reactions contribute to the formation of soil organic matter (SOM) or are degraded into small organic molecules. Methods: Here, we monitored the activity of a redox active soil enzyme, manganese peroxidase (MnP), with three small phenolic compounds. The compounds used in this study were pyrogallol, gallic acid, and benzoic acid. Results: Based on the kinetic parameters determined, pyrogallol and gallic acid are both substrates for MnP with different products and kinetics. Conclusion: Pyrogallol reacts faster and produces a more stable quinone than gallic acid. Benzoic acid is not a substrate for MnP. Full article

(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)

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17 pages, 1220 KB

Open AccessEditor’s ChoiceArticle

Serum Amino Acid Profiles in Dogs with a Congenital Portosystemic Shunt

by Robert Kyle Phillips, Amanda B. Blake, Michael S. Tivers, Alex Chan, Patricia E. Ishii, Jan S. Suchodolski, Jörg M. Steiner and Jonathan A. Lidbury

Metabolites 2025, 15(4), 258; https://doi.org/10.3390/metabo15040258 - 9 Apr 2025

Viewed by 1033

Abstract

Background/Objectives: A functional liver is vital for normal protein metabolism. Alterations of circulating amino acid (AA) concentrations have previously been reported in dogs with hepatocellular carcinoma, chronic hepatitis, and hepatocutaneous syndrome. The purpose of this study was to compare serum AA profiles [...] Read more.

Background/Objectives: A functional liver is vital for normal protein metabolism. Alterations of circulating amino acid (AA) concentrations have previously been reported in dogs with hepatocellular carcinoma, chronic hepatitis, and hepatocutaneous syndrome. The purpose of this study was to compare serum AA profiles between dogs with a congenital portosystemic shunt (CPSS) and healthy control dogs. Methods: Serum samples were collected from 50 dogs with an extrahepatic congenital portosystemic shunt (eCPSS) and 10 dogs with an intrahepatic congenital portosystemic shunt (iCPSS) at time of surgical intervention and from 21 healthy control dogs. Serum AA and other nitrogenous compounds were measured with a dedicated amino acid analyzer. The concentration of each AA was compared between groups using a Kruskal–Wallis test followed by Dunn’s multiple comparisons tests, as appropriate. The Benjamini–Hochberg procedure was used to control for false discovery. Significance was set at q < 0.05. Results: Compared to healthy controls, dogs with a CPSS had significantly increased serum concentrations of ammonia, asparagine, glutamic acid, histidine, phenylalanine, serine, and tyrosine and had significantly decreased concentrations of isoleucine, leucine, threonine, urea, and valine. There were no significant differences in serum AA concentrations between dogs with an eCPSS and dogs with an iCPSS. Conclusions: Dogs with a CPSS had altered serum AA concentrations compared to healthy control dogs, including decreased branched-chain amino acids (BCAAs) and increased aromatic amino acids (AAAs). In summary, serum AA profiles can differentiate dogs with a CPSS from healthy dogs but not dogs with an eCPSS from dogs with an iCPSS. Full article

(This article belongs to the Special Issue Proteomics and Metabolomics in Veterinary and Animal Health)

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16 pages, 1461 KB

Open AccessEditor’s ChoiceArticle

Impact of Tributyltin (TBT) on Energy Metabolism and Redox Homeostasis in Blue Crab Callinectes sapidus

by Leonardo Airton Ressel Simões, Rafaella Sanfelice Normann, Daniela Drosdowski, Bruna Selau, Marjoriane de Amaral, Alex Sander da Rosa Araujo and Anapaula Sommer Vinagre

Metabolites 2025, 15(4), 253; https://doi.org/10.3390/metabo15040253 - 8 Apr 2025

Cited by 1 | Viewed by 925

Abstract

Background/Objectives: Tributyltin (TBT), a potent biocide used in antifouling paints, is highly toxic to aquatic environments, causing oxidative stress, endocrine dysfunction, and metabolic disorders in aquatic organisms, including crustaceans. The blue crab Callinectes sapidus is an economically and ecologically important species in [...] Read more.

Background/Objectives: Tributyltin (TBT), a potent biocide used in antifouling paints, is highly toxic to aquatic environments, causing oxidative stress, endocrine dysfunction, and metabolic disorders in aquatic organisms, including crustaceans. The blue crab Callinectes sapidus is an economically and ecologically important species in several countries worldwide and is considered an invasive species in Europe. Methods: This study evaluated the effects of 7 days of exposure to environmentally relevant TBT concentrations (100 and 1000 ng.L⁻¹) on the intermediary metabolism and oxidative balance of the blue crab Callinectes sapidus. After exposure, hemolymph samples were analyzed to determine glucose, lactate, total protein, and cholesterol levels. In tissue samples, concentrations of triglycerides, glycogen, total glutathione (GSH), reactive oxygen species (ROS), sulfhydryls, lipid peroxidation (LPO), and glutathione S-transferase (GST) activity were assessed. Results: In the hemolymph, glucose and lactate levels increased, while the total cholesterol, triglycerides, and total proteins decreased in all exposed groups. The GST activity increased in exposed tissues, while the total GSH and sulfhydryl content decreased. The ROS concentration increased in response to higher TBT concentrations. Conclusions: These findings highlight the toxicity of TBT and show that 7 days of exposure to environmentally relevant concentrations disrupts the metabolic homeostasis and oxidative balance in C. sapidus. Additionally, this study demonstrates that C. sapidus is sensitive to TBT exposure and has potential as a model species for ecotoxicological studies. Full article

(This article belongs to the Special Issue Metabolic and Endocrine Adaptations in Aquatic Animals)

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18 pages, 3524 KB

Open AccessEditor’s ChoiceArticle

Untargeted Metabolomics Reveals Acylcarnitines as Major Metabolic Targets of Resveratrol in Breast Cancer Cells

by Isabella G. Falcone and Blake R. Rushing

Metabolites 2025, 15(4), 250; https://doi.org/10.3390/metabo15040250 - 5 Apr 2025

Cited by 2 | Viewed by 1080

Abstract

Background/Objectives: Millions of new diagnoses of breast cancer are made each year, with many cases having poor prognoses and limited treatment options, particularly for some subtypes such as triple-negative breast cancer. Resveratrol, a naturally occurring polyphenol, has demonstrated many anticancer properties in breast [...] Read more.

Background/Objectives: Millions of new diagnoses of breast cancer are made each year, with many cases having poor prognoses and limited treatment options, particularly for some subtypes such as triple-negative breast cancer. Resveratrol, a naturally occurring polyphenol, has demonstrated many anticancer properties in breast cancer studies. However, the mechanism of action of this compound remains elusive, although prior evidence suggests that this compound may work through altering cancer cell metabolism. Our objective for the current study was to perform untargeted metabolomics analysis on resveratrol-treated breast cancer cells to identify key metabolic targets of this compound. Methods: MCF-7 and MDA-MB-231 breast cancer cells were treated with varying doses of resveratrol and extracted for mass spectrometry-based untargeted metabolomics. Data preprocessing and filtering of metabolomics data from MCF-7 samples yielded 4751 peaks, with 312 peaks matched to an in-house standards library and 3459 peaks matched to public databases. Results: Pathway analysis in MetaboAnalyst identified significant (p < 0.05) metabolic pathways affected by resveratrol treatment, particularly those involving steroid, fatty acid, amino acid, and nucleotide metabolism. Evaluation of standard-matched peaks revealed acylcarnitines as a major target of resveratrol treatment, with long-chain acylcarnitines exhibiting a 2–5-fold increase in MCF-7 cells and a 5–13-fold increase in MDA-MB-231 cells when comparing the 100 µM treated cells to vehicle-treated cells (p < 0.05, VIP > 1). Notably, doses below 10 µM showed an opposite effect, possibly indicating a biphasic effect of resveratrol due to a switch from anti-oxidant to pro-oxidant effects as dose levels increase. Conclusions: These findings suggest that resveratrol induces mitochondrial metabolic reprogramming in breast cancer cells in a dose-dependent manner. The biphasic response indicates a potential optimal dosage for therapeutic effectiveness. Further research is warranted to explore the mechanisms underlying these metabolic alterations and their implications for precision nutrition strategies in cancer treatment. Full article

(This article belongs to the Collection Advances in Metabolomics)

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16 pages, 652 KB

Open AccessEditor’s ChoiceArticle

Uncovering Non-Invasive Biomarkers in Paediatric Severe Acute Asthma Using Targeted Exhaled Breath Analysis

by Sarah van den Berg, Annabel S. Zaat, Isabel F. van der Poel, Yoni E. van Dijk, Simone Hashimoto, Niels W. P. Rutjes, Suzanne W. J. Terheggen-Largo, Bart E. van Ewijk, Claudia Gagliani, Fleur L. Sondaal, Job B. M. van Woensel, Anke-Hilse Maitland-van der Zee, Paul Brinkman, Susanne J. H. Vijverberg and Berber Kapitein

Metabolites 2025, 15(4), 247; https://doi.org/10.3390/metabo15040247 - 3 Apr 2025

Viewed by 960

Abstract

Background: Severe acute asthma (SAA) in children can be life-threatening. There has been a significant rise in paediatric intensive care unit (PICU) admissions due to SAA over the past two decades. While asthma is a heterogeneous disease, its underlying pathophysiological pathways remain underexplored. [...] Read more.

Background: Severe acute asthma (SAA) in children can be life-threatening. There has been a significant rise in paediatric intensive care unit (PICU) admissions due to SAA over the past two decades. While asthma is a heterogeneous disease, its underlying pathophysiological pathways remain underexplored. This study aimed to assess the value of non-invasive targeted exhaled breath metabolomics analysis to better characterise SAA. Methods: Breath samples from 17 children admitted to the PICU with SAA (cases) and 27 children with controlled severe asthma (controls) were analysed using thermal desorption gas chromatography–mass spectrometry (TD-GC-MS). Results: A targeted volatile organic compound (VOC) analysis identified 25 compounds, of which 16 were shared between groups. Four VOCs were significantly more often present in SAA, and nine VOCs exhibited higher concentrations in SAA. Longitudinal analysis of VOCs from follow-up samples of 10 cases showed no significant temporal differences, reinforcing the reproducibility of identified biomarkers. Conclusions: This study exemplifies the potential of exhaled breath analysis to provide insights into the molecular background of SAA. Breath metabolomics may enable early recognition of severe asthma attacks and preventive therapeutic interventions in children with severe asthma. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Technology for Metabolic Profiling)

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21 pages, 997 KB

Open AccessEditor’s ChoiceReview

Polymorphisms Involved in Insulin Resistance and Metabolic Inflammation: Influence of Nutrients and Dietary Interventions

by Graziela Biude Silva Duarte, Gabriela de Freitas Laiber Pascoal and Marcelo Macedo Rogero

Metabolites 2025, 15(4), 245; https://doi.org/10.3390/metabo15040245 - 2 Apr 2025

Cited by 1 | Viewed by 1463

Abstract

Insulin resistance (IR) is a metabolic disorder characterized by an impaired response to insulin. This condition is associated with excess adiposity and metabolic inflammation, contributing to an increased risk for related chronic diseases. Single-nucleotide polymorphisms (SNPs) can affect genes related to metabolic pathways [...] Read more.

Insulin resistance (IR) is a metabolic disorder characterized by an impaired response to insulin. This condition is associated with excess adiposity and metabolic inflammation, contributing to an increased risk for related chronic diseases. Single-nucleotide polymorphisms (SNPs) can affect genes related to metabolic pathways which are related to IR and the individual response to nutrients and dietary patterns, affecting metabolic inflammation and insulin sensitivity. This narrative review explores the current evidence on interactions between genetic variants and dietary factors, specifically their effects in modulating IR and metabolic inflammation. A comprehensive search of the literature was conducted in PubMed, Google Scholar, and Web of Science, and a total of 95 articles were reviewed. The key findings reveal that SNPs in the TCF7L2, ADIPOQ, and TNF genes significantly influence metabolic responses and modulate the effects of the Mediterranean diet on biomarkers of inflammation and IR. Genotype-dependent variations in IR and inflammation biomarkers were observed in the response to different diets for SNPs in the TCF7L2, ADIPOQ, and TNF genes. Additionally, polygenic risk scores (PRSs) can also predict the response to the intake of nutrients and specific diets, and offer a promising tool for assessing genetic predisposition to IR. This review underscores the pivotal role of an individual’s genetic background in the effects of their nutrient intake and in the responses to dietetic interventions, thereby laying the foundation for personalized and effective nutritional strategies tailored to each individual’s necessity in mitigating IR and its associated risk factors for chronic diseases. Full article

(This article belongs to the Special Issue Bioactive Food Ingredients in Prevention and Alleviation of Metabolic Diseases)

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28 pages, 4577 KB

Open AccessEditor’s ChoiceArticle

Cell-Free DNA (cfDNA) Regulates Metabolic Remodeling in the ES-2 Ovarian Carcinoma Cell Line, Influencing Cell Proliferation, Quiescence, and Chemoresistance in a Cell-of-Origin-Specific Manner

by Isabel Lemos, Catarina Freitas-Dias, Ana Hipólito, José Ramalho, Fabrizio Carteni, Luís G. Gonçalves, Stefano Mazzoleni and Jacinta Serpa

Metabolites 2025, 15(4), 244; https://doi.org/10.3390/metabo15040244 - 2 Apr 2025

Cited by 1 | Viewed by 967

Abstract

Background: The cell-free DNA (cfDNA) is an extracellular fragmented DNA found in body fluids in physiological and pathophysiological contexts. In cancer, cfDNA has been pointed out as a marker for disease diagnosis, staging, and prognosis; however, little is known about its biological role. [...] Read more.

Background: The cell-free DNA (cfDNA) is an extracellular fragmented DNA found in body fluids in physiological and pathophysiological contexts. In cancer, cfDNA has been pointed out as a marker for disease diagnosis, staging, and prognosis; however, little is known about its biological role. Methods: The role of cfDNA released by ES-2 ovarian cancer cells was investigated, along with the impact of glucose bioavailability and culture duration in the cfDNA-induced phenotype. The effect of cfDNA on ES-2 cell proliferation was evaluated by proliferation curves, and cell migration was assessed through wound healing. We explored the impact of different cfDNA variants on ES-2 cells’ metabolic profile using nuclear magnetic resonance (NMR) spectroscopy and cisplatin resistance through flow cytometry. Moreover, we assessed the protein levels of DNA-sensitive Toll-like receptor 9 (TLR9) by immunofluorescence and its colocalization with lysosome-associated membrane protein 1 (LAMP1). Results: This study demonstrated that despite inducing similar effects, different variants of cfDNA promote different effects on cells derived from the ES-2 cell line. We observed instant reactions of adopting the metabolic profile that brings back the cell functioning of more favorable culture conditions supporting proliferation and resembling the cell of origin of the cfDNA variant, as observed in unselected ES-2 cells. However, as a long-term selective factor, certain cfDNA variants induced quiescence that favors the chemoresistance of a subset of cancer cells. Conclusions: Therefore, different tumoral microenvironments may generate cfDNA variants that will impact cancer cells differently, orchestrating the disease fate. Full article

(This article belongs to the Special Issue Insights into Tumor Cell Metabolism and Epigenetics)

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18 pages, 741 KB

Open AccessEditor’s ChoiceArticle

A 30-Day Randomized Crossover Human Study on the Safety and Tolerability of a New Micellar Berberine Formulation with Improved Bioavailability

by Afoke Ibi, Chuck Chang, Yun Chai Kuo, Yiming Zhang, Min Du, Yoon Seok Roh, Roland Gahler, Mary Hardy and Julia Solnier

Metabolites 2025, 15(4), 240; https://doi.org/10.3390/metabo15040240 - 1 Apr 2025

Cited by 1 | Viewed by 7561

Abstract

Background/Objectives: Berberine is a naturally occurring compound found in several plants and has been traditionally used for its various health benefits. However, its poor bioavailability limits its therapeutic potential. Berberine LipoMicel^® is a novel micellar formulation of berberine, microencapsulated within an emulsified [...] Read more.

Background/Objectives: Berberine is a naturally occurring compound found in several plants and has been traditionally used for its various health benefits. However, its poor bioavailability limits its therapeutic potential. Berberine LipoMicel^® is a novel micellar formulation of berberine, microencapsulated within an emulsified matrix, designed to enhance bioavailability and bioactivity. This study aims to evaluate its safety, ensuring that improved bioavailability does not introduce new safety concerns. Methods: To assess its safety, a randomized, double-blind, placebo-controlled crossover study with a minimum 4-week washout period was conducted in 19 healthy participants over 30 days. The participants received 1000 mg of the treatment daily (i.e., 2 capsules/d), and their capillary blood was analyzed every week to monitor for changes in established safety markers related to liver and kidney function, including aspartate aminotransferase (AST), alanine aminotransferase (ALT), total bilirubin (TB), creatinine, fasting glucose (GLU), HbA1c, and various electrolytes. Additionally, potential side effects were recorded through the collection of weekly health questionnaires to determine treatment tolerability. Results: Compared to placebo, no statistically significant changes in any of the safety markers related to liver or kidney health were detected. Within-group analysis revealed a significant reduction of total cholesterol (TC) in females after 30 days of Berberine LipoMicel^® treatment. Although not significant, both male and female participants showed a noticeable improvement in the mean AST, potentially signaling a hepatoprotective effect. As for tolerability, no adverse events were reported by any of the participants. Conclusions: Based on these findings, despite higher bioavailability of berberine in a newly formulated delivery system (LipoMicel^®), the treatment was found to be safe and well tolerated by human participants, with no significant deviations in blood chemistry that would indicate safety concerns over a period of 30 days. Full article

(This article belongs to the Special Issue Metabolic Insights into Natural Health Products and Dietary Supplements for Human Health)

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15 pages, 2770 KB

Open AccessEditor’s ChoiceArticle

Influence of Amino Acids on Quorum Sensing-Related Pathways in Pseudomonas aeruginosa PAO1: Insights from the GEM iJD1249

by Javier Alejandro Delgado-Nungaray, Luis Joel Figueroa-Yáñez, Eire Reynaga-Delgado, Mario Alberto García-Ramírez, Karla Esperanza Aguilar-Corona and Orfil Gonzalez-Reynoso

Metabolites 2025, 15(4), 236; https://doi.org/10.3390/metabo15040236 - 29 Mar 2025

Cited by 1 | Viewed by 1141

Abstract

Background/objectives: Amino acids (AAs) play a critical role in diseases such as cystic fibrosis where Pseudomonas aeruginosa PAO1 adapts its metabolism in response to host-derived nutrients. The adaptation influences virulence and complicates antibiotic treatment mainly for the antimicrobial resistance context. D- and L-AAs [...] Read more.

Background/objectives: Amino acids (AAs) play a critical role in diseases such as cystic fibrosis where Pseudomonas aeruginosa PAO1 adapts its metabolism in response to host-derived nutrients. The adaptation influences virulence and complicates antibiotic treatment mainly for the antimicrobial resistance context. D- and L-AAs have been analyzed for their impact on quorum sensing (QS), a mechanism that regulates virulence factors. This research aimed to reconstruct the genome-scale metabolic model (GEM) of P. aeruginosa PAO1 to investigate the metabolic roles of D- and L-AAs in QS-related pathways. Methods: The updated GEM, iJD1249, was reconstructed by using protocols to integrate data from previous models and refined with well-standardized in silico media (LB, M9, and SCFM) to improve flux balance analysis accuracy. The model was used to explore the metabolic impact of D-Met, D-Ala, D-Glu, D-Ser, L-His, L-Glu, L-Arg, and L-Ornithine (L-Orn) at 5 and 50 mM in QS-related pathways, focusing on the effects on bacterial growth and carbon flux distributions. Results: Among the tested AAs, D-Met was the only one that did not enhance the growth rate of P. aeruginosa PAO1, while L-Arg and L-Orn increased fluxes in the L-methionine biosynthesis pathway, influencing the metH gene. These findings suggest a differential metabolic role for D-and L-AAs in QS-related pathways. Conclusions: Our results shed some light on the metabolic impact of AAs on QS-related pathways and their potential role in P. aeruginosa virulence. Future studies should assess D-Met as a potential adjuvant in antimicrobial strategies, optimizing the concentration in combination with antibiotics to maximize its therapeutic effectiveness. Full article

(This article belongs to the Special Issue Biostatistics and Bioinformatics in Metabolomics Research: From Study Design and Analytics to Clinical Insights and Public Health Implications)

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19 pages, 11976 KB

Open AccessEditor’s ChoiceArticle

Metabolome Profiling and Predictive Modeling of Dark Green Leaf Trait in Bunching Onion Varieties

by Tetsuya Nakajima, Mari Kobayashi, Masato Fuji, Kouei Fujii, Mostafa Abdelrahman, Yasumasa Matsuoka, Jun’ichi Mano, Muneo Sato, Masami Yokota Hirai, Naoki Yamauchi and Masayoshi Shigyo

Metabolites 2025, 15(4), 226; https://doi.org/10.3390/metabo15040226 - 26 Mar 2025

Viewed by 1494

Abstract

Background: The dark green coloration of bunching onion leaf blades is a key determinant of market value, nutritional quality, and visual appeal. This trait is regulated by a complex network of pigment interactions, which not only determine coloration but also serve as critical [...] Read more.

Background: The dark green coloration of bunching onion leaf blades is a key determinant of market value, nutritional quality, and visual appeal. This trait is regulated by a complex network of pigment interactions, which not only determine coloration but also serve as critical indicators of plant growth dynamics and stress responses. This study aimed to elucidate the mechanisms regulating the dark green trait and develop a predictive model for accurately assessing pigment composition. These advancements enable the efficient selection of dark green varieties and facilitate the establishment of optimal growth environments through plant growth monitoring. Methods: Seven varieties and lines of heat-tolerant bunching onions were analyzed, including two commercial

F_{1}

cultivars, along with two purebred varieties and three

F_{1}

hybrid lines bred in Yamaguchi Prefecture. The analysis was conducted on visible spectral reflectance data (400–700 nm at 20 nm intervals) and pigment compounds (chlorophyll a, chlorophyll b and pheophytin a, lutein, and

β

-carotene), whereas primary and secondary metabolites were assessed by using widely targeted metabolomics. In addition, a random forest regression model was constructed by using spectral reflectance data and pigment compound contents. Results: Principal component analysis based on spectral reflectance data and the comparative profiling of 186 metabolites revealed characteristic metabolite accumulation associated with each green color pattern. The “green” group showed greater accumulation of sugars, the “gray green” group was characterized by the accumulation of phenolic compounds, and the “dark green” group exhibited accumulation of cyanidins. These metabolites are suggested to accumulate in response to environmental stress, and these differences are likely to influence green coloration traits. Furthermore, among the regression models for estimating pigment compound contents, the one for chlorophyll a content achieved high accuracy, with an

R^{2}

value of 0.88 in the test dataset and 0.78 in Leave-One-Out Cross-Validation, demonstrating its potential for practical application in trait evaluation. However, since the regression model developed in this study is based on data obtained from greenhouse conditions, it is necessary to incorporate field trial results and reconstruct the model to enhance its adaptability. Conclusions: This study revealed that cyanidin is involved in the characteristics of dark green varieties. Additionally, it was demonstrated that chlorophyll a can be predicted using visible spectral reflectance. These findings suggest the potential for developing markers for the dark green trait, selecting high-pigment-accumulating varieties, and facilitating the simple real-time diagnosis of plant growth conditions and stress status, thereby enabling the establishment of optimal environmental conditions. Future studies will aim to elucidate the genetic factors regulating pigment accumulation, facilitating the breeding of dark green varieties with enhanced coloration traits for summer cultivation. Full article

(This article belongs to the Special Issue Metabolomics in Plant Natural Products Research)

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15 pages, 1075 KB

Open AccessEditor’s ChoiceArticle

Green Extraction Method: Microwave-Assisted Water Extraction Followed by HILIC-HRMS Analysis to Quantify Hydrophilic Compounds in Plants

by Alexandra Louis, Jean François Chich, Hadrien Chepca, Isabelle Schmitz, Philippe Hugueney and Alessandra Maia-Grondard

Metabolites 2025, 15(4), 223; https://doi.org/10.3390/metabo15040223 - 25 Mar 2025

Viewed by 579

Abstract

Background: Hydrophilic compounds, such as amino acids, organic acids and sugars, among others, are present in large amounts in plant cells. The analysis and quantification of these major hydrophilic compounds are particularly relevant in plant science because they have a considerable impact on [...] Read more.

Background: Hydrophilic compounds, such as amino acids, organic acids and sugars, among others, are present in large amounts in plant cells. The analysis and quantification of these major hydrophilic compounds are particularly relevant in plant science because they have a considerable impact on the quality of plant-derived products and on plant–pathogen relationships. Our objective was to develop and validate a complete analysis workflow combining a water-based extraction procedure with a fast separation using hydrophilic interaction liquid chromatography coupled to high-resolution mass spectrometry (HILIC-HRMS) for quantitative analysis of hydrophilic compounds in plant tissues. Results: Water-based microwave-assisted extraction (MAE) methods for hydrophilic compounds were compared using HILIC-HRMS. The newly developed method involved 20 s MAE time followed by a 10 min HILIC-HRMS analysis. This bioanalytical method was validated for 24 polar metabolites, including amino acids, organic acids, and sugars, to ensure the reliability of analytical results: selectivity, limits of detection and quantification, calibration range and precision. Depending on the compounds, quantification limit was as low as 0.10 µM up to 4.50 µM. Between-run RSDs evaluated on Vitis vinifera and Arabidopsis samples were all below 20% except for three compounds. Conclusions: A water-based MAE method, coupled with HILIC-HRMS, was developed for the absolute quantification of free amino acids, organic acids, and sugars in plant tissues. Its effectiveness was demonstrated in both lignified plants, such as Vitis vinifera, and non-lignified plants, such as Arabidopsis. This method is suitable for medium- to high-throughput analysis of key polar metabolites from small amounts of plant material. Full article

(This article belongs to the Section Plant Metabolism)

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53 pages, 1912 KB

Open AccessFeature PaperEditor’s ChoiceReview

Endoplasmic Reticulum Stress and Its Role in Metabolic Reprogramming of Cancer

by Salvatore Zarrella, Maria Rosaria Miranda, Verdiana Covelli, Ignazio Restivo, Sara Novi, Giacomo Pepe, Luisa Tesoriere, Manuela Rodriquez, Alessia Bertamino, Pietro Campiglia, Mario Felice Tecce and Vincenzo Vestuto

Metabolites 2025, 15(4), 221; https://doi.org/10.3390/metabo15040221 - 24 Mar 2025

Cited by 3 | Viewed by 2527

Abstract

Background/Objectives: Endoplasmic reticulum (ER) stress occurs when ER homeostasis is disrupted, leading to the accumulation of misfolded or unfolded proteins. This condition activates the unfolded protein response (UPR), which aims to restore balance or trigger cell death if homeostasis cannot be achieved. In [...] Read more.

Background/Objectives: Endoplasmic reticulum (ER) stress occurs when ER homeostasis is disrupted, leading to the accumulation of misfolded or unfolded proteins. This condition activates the unfolded protein response (UPR), which aims to restore balance or trigger cell death if homeostasis cannot be achieved. In cancer, ER stress plays a key role due to the heightened metabolic demands of tumor cells. This review explores how metabolomics can provide insights into ER stress-related metabolic alterations and their implications for cancer therapy. Methods: A comprehensive literature review was conducted to analyze recent findings on ER stress, metabolomics, and cancer metabolism. Studies examining metabolic profiling of cancer cells under ER stress conditions were selected, with a focus on identifying potential biomarkers and therapeutic targets. Results: Metabolomic studies highlight significant shifts in lipid metabolism, protein synthesis, and oxidative stress management in response to ER stress. These metabolic alterations are crucial for tumor adaptation and survival. Additionally, targeting ER stress-related metabolic pathways has shown potential in preclinical models, suggesting new therapeutic strategies. Conclusions: Understanding the metabolic impact of ER stress in cancer provides valuable opportunities for drug development. Metabolomics-based approaches may help identify novel biomarkers and therapeutic targets, enhancing the effectiveness of antitumor therapies. Full article

(This article belongs to the Special Issue NMR-Metabolomics in Peptide and Antibody Drug Discovery)

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17 pages, 3145 KB

Open AccessEditor’s ChoiceReview

Secondary Metabolites from Croton Species and Their Biological Activity on Cell Cycle Regulators

by Jorge Augusto Alamillo-Vásquez, Claudia-Anahí Pérez-Torres, Enrique Ibarra-Laclette, Feliza Ramón-Farías, Pilar Nicasio-Torres and Fulgencio Alatorre-Cobos

Metabolites 2025, 15(4), 216; https://doi.org/10.3390/metabo15040216 - 23 Mar 2025

Cited by 1 | Viewed by 1573

Abstract

Plant-based traditional medicine integrates beliefs, knowledge, and practices to prevent and treat multiple diseases. Croton is a large and worldwide-spread genus belonging to Euphorbiaceae, a family well known for comprising many species with medicinal properties due to its high diversity of phytochemical constituents [...] Read more.

Plant-based traditional medicine integrates beliefs, knowledge, and practices to prevent and treat multiple diseases. Croton is a large and worldwide-spread genus belonging to Euphorbiaceae, a family well known for comprising many species with medicinal properties due to its high diversity of phytochemical constituents with biological activities. Among the various benefits of Croton species in traditional medicine, its use in cancer treatment has recently received significant attention from the scientific community. This review provides a general overview of different studies on the Croton genus in the research for alternative cancer treatments and the impact of its secondary metabolite catalog on cell cycle targets. Our analysis indicates that just under 30 secondary metabolites have been identified so far in latex and extracts obtained from leaves, twigs, or bark from 22 different Croton species. Based on standard assays using cell lines or human platelets, these molecules show multiple biological activities mainly compromising cell viability and cell cycle progression, supporting the ethnobotanical use of Croton species for cancer treatment. Several studies indicate that Croton metabolites target CDK–cyclin complexes and signaling routes that trigger apoptosis; however, further studies are needed to better understand the molecular mechanisms underlying Croton metabolites’ effects and their accurate future applications in cancer treatment. Full article

(This article belongs to the Special Issue Phytochemicals and Pharmacological Significance of Plant Secondary Metabolites in Medicine)

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20 pages, 15032 KB

Open AccessEditor’s ChoiceArticle

Multi-Omics Profiling Reveals Glycerolipid Metabolism-Associated Molecular Subtypes and Identifies ALDH2 as a Prognostic Biomarker in Pancreatic Cancer

by Jifeng Liu, Shurong Ma, Dawei Deng, Yao Yang, Junchen Li, Yunshu Zhang, Peiyuan Yin and Dong Shang

Metabolites 2025, 15(3), 207; https://doi.org/10.3390/metabo15030207 - 18 Mar 2025

Cited by 1 | Viewed by 1387

Abstract

Background: The reprogramming of lipid metabolism, especially glycerolipid metabolism (GLM), plays a key role in cancer progression and response to therapy. However, the role and molecular characterization of GLM in pancreatic cancer (PC) remain unclear. Methods: A pan-cancer analysis of glycerolipid [...] Read more.

Background: The reprogramming of lipid metabolism, especially glycerolipid metabolism (GLM), plays a key role in cancer progression and response to therapy. However, the role and molecular characterization of GLM in pancreatic cancer (PC) remain unclear. Methods: A pan-cancer analysis of glycerolipid metabolism-related genes (GMRGs) was first conducted to assess copy-number variants, single-nucleotide variations, methylation, and mRNA expression. Subsequently, GLM in PC was characterized using lipidomics, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomic analysis. A cluster analysis based on bulk RNA sequencing data from 930 PC samples identified GLM-associated subtypes, which were then analyzed for differences in prognosis, biological function, immune microenvironment, and drug sensitivity. To prioritize prognostically relevant GMRGs in PC, we employed a random forest (RF) algorithm to rank their importance across 930 PC samples. Finally, the key biomarker of PC was validated using PCR and immunohistochemistry. Results: Pan-cancer analysis identified molecular features of GMRGs in cancers, while scRNA-seq, spatial transcriptomics, and lipidomics highlighted GLM heterogeneity in PC. Two GLM-associated subtypes with significant prognostic, biofunctional, immune microenvironmental, and drug sensitivity differences were identified in 930 PC samples. Finally, ALDH2 was identified as a novel prognostic biomarker in PC and validated in a large number of datasets and clinical samples. Conclusions: This study highlights the crucial role of GLM in PC and defines a new PC subtype and prognostic biomarker. These findings establish a novel avenue for studying prognostic prediction and precision medicine in PC patients. Full article

(This article belongs to the Special Issue New Analytical Techniques and Applications of Metabolomics and Lipidomics)

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14 pages, 2223 KB

Open AccessEditor’s ChoiceArticle

Metal Ion Reduction, Chelation, and Cytotoxicity of Selected Bicyclic Monoterpenes and Their Binary Mixtures

by Karolina Wojtunik-Kulesza, Marcela Dubiel and Katarzyna Klimek

Metabolites 2025, 15(3), 199; https://doi.org/10.3390/metabo15030199 - 13 Mar 2025

Cited by 1 | Viewed by 742

Abstract

Background/Objectives: Bicyclic monoterpenes are one of the most common groups of secondary plant metabolites found in Nature. Their wide spectrum of biological activity can be used in the prevention and in the treatment of various diseases, including so-called ‘diseases of civilization’. Their [...] Read more.

Background/Objectives: Bicyclic monoterpenes are one of the most common groups of secondary plant metabolites found in Nature. Their wide spectrum of biological activity can be used in the prevention and in the treatment of various diseases, including so-called ‘diseases of civilization’. Their potential for synergistic interactions may influence the biological activities of more complex mixtures. Methods: This study investigated the ability of selected bicyclic monoterpenes and their binary mixtures to reduce Fe(III) and Cu(II) and chelate Fe(II) and assessed their cytotoxic activity against BJ and HepG2 cell lines. Results: The obtained results did not reveal synergistic interactions towards the biological activities, but binary mixtures proved to be safe in relation to the tested cell lines. Among the tested single monoterpenes, the most effective were 3-carene and β-pinene, with the latter exhibiting the greatest ability to decrease cell viability (CC₅₀ for BJ and HepG2 cells was about 1.08 and 1.85 mM, respectively). Conclusions: The results revealed that both single compounds and binary mixtures demonstrate the ability to reduce selected metal ions and chelate Fe(II) ions. Synergistic interactions were not observed, but an increase in the activity of selected binary mixtures was recorded. Based on cell culture experiments, the monoterpenes and their binary mixtures can be considered safe at a concentration lower than 1 mM and close to 0.313 mM, respectively. Full article

(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)

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29 pages, 3266 KB

Open AccessEditor’s ChoiceReview

Ceramide as a Promising Tool for Diagnosis and Treatment of Clinical Diseases: A Review of Recent Advances

by Xueping Shen, Rui Feng, Rui Zhou, Zhaoyang Zhang, Kaiyong Liu and Sheng Wang

Metabolites 2025, 15(3), 195; https://doi.org/10.3390/metabo15030195 - 11 Mar 2025

Cited by 2 | Viewed by 3446

Abstract

Background/Objectives: Ceramide, a sphingolipid metabolite, has emerged as a key player in various physiological and pathological processes. Changes in ceramide levels are associated with the occurrence and development of various diseases, highlighting its potential as a biomarker of various clinical diseases. Methods: The [...] Read more.

Background/Objectives: Ceramide, a sphingolipid metabolite, has emerged as a key player in various physiological and pathological processes. Changes in ceramide levels are associated with the occurrence and development of various diseases, highlighting its potential as a biomarker of various clinical diseases. Methods: The biosynthesis and metabolism of ceramide are discussed, along with its functions in cell signaling, apoptosis, and inflammation. This study further examines the potential of ceramide as a biomarker for disease diagnosis and treatment. Results: This article highlights the involvement of ceramide in several diseases, including cardiovascular diseases, dermatosis, cancer, neurodegenerative disorders and metabolic syndromes. For each disease, the potential of ceramide as a biomarker for disease diagnosis and prognosis is explored, and the feasibility of therapeutic strategies targeting ceramide metabolism are reviewed. Additionally, the challenges and future directions in the field of ceramide research are addressed. Conclusions: This review article provides an overview of the recent advances in understanding the role of ceramide in clinical diseases and its potential as a diagnostic and therapeutic tool. Full article

(This article belongs to the Special Issue Mass Spectrometry-Based Metabolomics in Health and Disease: Targeted Analysis)

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19 pages, 1710 KB

Open AccessEditor’s ChoiceReview

Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science

by Christina F. Butowski, Yash Dixit, Marlon M. Reis and Chunlong Mu

Metabolites 2025, 15(3), 185; https://doi.org/10.3390/metabo15030185 - 10 Mar 2025

Cited by 3 | Viewed by 2437

Abstract

Microbiome science has greatly expanded our understanding of the diverse composition and function of gut microorganisms over the past decades. With its rich microbial composition, the microbiome hosts numerous functionalities essential for metabolizing food ingredients and nutrients, resulting in the production of active [...] Read more.

Microbiome science has greatly expanded our understanding of the diverse composition and function of gut microorganisms over the past decades. With its rich microbial composition, the microbiome hosts numerous functionalities essential for metabolizing food ingredients and nutrients, resulting in the production of active metabolites that affect food fermentation or gut health. Most of these processes are mediated by microbial enzymes such as carbohydrate-active enzymes and amino acid metabolism enzymes. Metatranscriptomics enables the capture of active transcripts within the microbiome, providing invaluable functional insights into metabolic activities. Given the inter-kingdom complexity of the microbiome, metatranscriptomics could further elucidate the activities of fungi, archaea, and bacteriophages in the microbial ecosystem. Despite its potential, the application of metatranscriptomics in food and nutrition sciences remains limited but is growing. This review highlights the latest advances in food science (e.g., flavour formation and food enzymology) and nutrition science (e.g., dietary fibres, proteins, minerals, and probiotics), emphasizing the integration of metatranscriptomics with other technologies to address key research questions. Ultimately, metatranscriptomics represents a powerful tool for uncovering the microbiome activity, particularly in relation to active metabolic processes. Full article

(This article belongs to the Special Issue Gut Microbiome and Host Metabolism)

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41 pages, 4980 KB

Open AccessEditor’s ChoiceArticle

Untargeted Metabolomics and Targeted Phytohormone Profiling of Sweet Aloes (Euphorbia neriifolia) from Guyana: An Assessment of Asthma Therapy Potential in Leaf Extracts and Latex

by Malaika Persaud, Ainsely Lewis, Anna Kisiala, Ewart Smith, Zeynab Azimychetabi, Tamanna Sultana, Suresh S. Narine and R. J. Neil Emery

Metabolites 2025, 15(3), 177; https://doi.org/10.3390/metabo15030177 - 5 Mar 2025

Cited by 1 | Viewed by 1723

Abstract

Background/Objectives: Euphorbia neriifolia is a succulent plant from the therapeutically rich family of Euphorbia comprising 2000 species globally. E. neriifolia is used in Indigenous Guyanese asthma therapy. Methods: To investigate E. neriifolia’s therapeutic potential, traditionally heated leaf, simple leaf, and latex extracts [...] Read more.

Background/Objectives: Euphorbia neriifolia is a succulent plant from the therapeutically rich family of Euphorbia comprising 2000 species globally. E. neriifolia is used in Indigenous Guyanese asthma therapy. Methods: To investigate E. neriifolia’s therapeutic potential, traditionally heated leaf, simple leaf, and latex extracts were evaluated for phytohormones and therapeutic compounds. Full scan, data-dependent acquisition, and parallel reaction monitoring modes via liquid chromatography Orbitrap mass spectrometry were used for screening. Results: Pathway analysis of putative features from all extracts revealed a bias towards the phenylpropanoid, terpenoid, and flavonoid biosynthetic pathways. A total of 850 compounds were annotated using various bioinformatics tools, ranging from confidence levels 1 to 3. Lipids and lipid-like molecules (34.35%), benzenoids (10.24%), organic acids and derivatives (12%), organoheterocyclic compounds (12%), and phenylpropanoids and polyketides (10.35%) dominated the contribution of compounds among the 13 superclasses. Semi-targeted screening revealed 14 out of 16 literature-relevant therapeutic metabolites detected, with greater upregulation in traditional heated extracts. Targeted screening of 39 phytohormones resulted in 25 being detected and quantified. Simple leaf extract displayed 4.4 and 45 times greater phytohormone levels than traditional heated leaf and latex extracts, respectively. Simple leaf extracts had the greatest nucleotide and riboside cytokinin and acidic phytohormone levels. In contrast, traditional heated extracts exhibited the highest free base and glucoside cytokinin levels and uniquely contained methylthiolated and aromatic cytokinins while lacking acidic phytohormones. Latex samples had trace gibberellic acid levels, the lowest free base, riboside, and nucleotide levels, with absences of aromatic, glucoside, or methylthiolated cytokinin forms. Conclusions: In addition to metabolites with possible therapeutic value for asthma treatment, we present the first look at cytokinin phytohormones in the species and Euphorbia genus alongside metabolite screening to present a comprehensive assessment of heated leaf extract used in Indigenous Guyanese asthma therapy. Full article

(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)

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14 pages, 3470 KB

Open AccessEditor’s ChoiceArticle

Predicting the Pathway Involvement of Compounds Annotated in the Reactome Knowledgebase

by Erik D. Huckvale and Hunter N. B. Moseley

Metabolites 2025, 15(3), 161; https://doi.org/10.3390/metabo15030161 - 1 Mar 2025

Cited by 1 | Viewed by 929

Abstract

Background/Objectives: Pathway annotations of non-macromolecular (relatively small) biomolecules facilitate biological and biomedical interpretation of metabolomics datasets. However, low pathway annotation levels of detected biomolecules hinder this type of interpretation. Thus, predicting the pathway involvement of detected but unannotated biomolecules has a high potential [...] Read more.

Background/Objectives: Pathway annotations of non-macromolecular (relatively small) biomolecules facilitate biological and biomedical interpretation of metabolomics datasets. However, low pathway annotation levels of detected biomolecules hinder this type of interpretation. Thus, predicting the pathway involvement of detected but unannotated biomolecules has a high potential to improve metabolomics data analysis and omics integration. Past publications have only made use of the Kyoto Encyclopedia of Genes and Genomes-derived datasets to develop machine learning models to predict pathway involvement. However, to our knowledge, the Reactome knowledgebase has not been utilized to develop these types of predictive models. Methods: We created a dataset ready for machine learning using chemical representations of all pathway-annotated compounds available from the Reactome knowledgebase. Next, we trained and evaluated a multilayer perceptron binary classifier using combined metabolite-pathway paired feature vectors engineered from this new dataset. Results: While models trained on a prior corresponding KEGG dataset with 502 pathways scored a mean Matthew’s correlation coefficient (MCC) of 0.847 and a 0.0098 standard deviation, the models trained on the Reactome dataset with 3985 pathways demonstrated improved performance with a mean MCC of 0.916, but with a higher standard deviation of 0.0149. Conclusions: These results indicate that the pathways in Reactome can also be effectively predicted, greatly increasing the number of human-defined pathways available for prediction. Full article

(This article belongs to the Section Bioinformatics and Data Analysis)

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15 pages, 1023 KB

Open AccessEditor’s ChoiceReview

The Functions of Major Gut Microbiota in Obesity and Type 2 Diabetes

by Siman Liu, Zhipeng Tao, Mingyu Qiao and Limin Shi

Metabolites 2025, 15(3), 167; https://doi.org/10.3390/metabo15030167 - 1 Mar 2025

Cited by 1 | Viewed by 1940

Abstract

Background: Gut microbiomes play a vital role in maintaining whole-body metabolic homeostasis. It has gained significant attention in recent years due to advancements in genome sequencing technologies and a deeper understanding of its relationship with obesity. However, the specific ways in which different [...] Read more.

Background: Gut microbiomes play a vital role in maintaining whole-body metabolic homeostasis. It has gained significant attention in recent years due to advancements in genome sequencing technologies and a deeper understanding of its relationship with obesity. However, the specific ways in which different microorganisms directly or indirectly influence host obesity, as well as the underlying mechanisms, remain uncertain because of the complexity of gut microbiota composition. Methods: In this review, we summarize the roles of the major gut microbiota phyla such as Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia in obesity and type 2 diabetes based on studies published in the past five years on PubMed and Google Scholar. The current therapeutic strategies associated with gut microbiota are also explored from clinical trials, and challenges and future directions are discussed. Results and Conclusions: This review will provide a deeper understanding of the functions of major gut microbiota in obesity and type 2 diabetes, which could lead to more individualized and effective treatments for metabolic diseases. Full article

(This article belongs to the Special Issue Targeting Microbiota and Metabolites for Prevention and Treatment of Human Diseases)

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21 pages, 5553 KB

Open AccessEditor’s ChoiceArticle

Identification of Bioactive Metabolites of Capirona macrophylla by Metabolomic Analysis, Molecular Docking, and In Vitro Antiparasitic Assays

by Joseph Evaristo, Elise de Laia, Bruna Tavares, Esdras Mendonça, Larissa Grisostenes, Caroline Rodrigues, Welington do Nascimento, Carolina Garcia, Sheila Guterres, Fábio Nogueira, Fernando Zanchi and Geisa Evaristo

Metabolites 2025, 15(3), 157; https://doi.org/10.3390/metabo15030157 - 26 Feb 2025

Cited by 1 | Viewed by 1464

Abstract

Capirona macrophylla is a Rubiaceae known as “mulateiro”. Ethnobotanical extracts have been used for skin treatment and in the management of leishmaniasis and malaria. Objectives: The metabolites in aqueous extracts from wood bark, leaves, and stems were identified, and their in silico docking [...] Read more.

Capirona macrophylla is a Rubiaceae known as “mulateiro”. Ethnobotanical extracts have been used for skin treatment and in the management of leishmaniasis and malaria. Objectives: The metabolites in aqueous extracts from wood bark, leaves, and stems were identified, and their in silico docking and in vitro cellular efficacy against Leishmania amazonensis and Plasmodium falciparum were evaluated. Methods: The extracts were analyzed by UHPLC/HRMSⁿ using untargeted metabolomics approach with MSDial, MSFinder, and GNPS software for metabolite identification and spectra clustering. The most abundant metabolites underwent molecular docking using AutoDock via PyRx, targeting the dihydroorotate dehydrogenase from Leishmania and P. falciparum, and evaluated through molecular dynamics simulations using Gromacs. In vitro biological assays were conducted on 60 HPLC-fractions against these parasites. Results: Metabolomics analysis identified 5100 metabolites in ESI+ and 2839 in ESI− spectra among the “mulateiro” samples. GNPS clustering highlighted large clusters of quercetin and chlorogenic acid groups. The most abundant metabolites were isofraxidin, scopoletin, 5(S)-5-carboxystrictosidine, loliolide, quercetin, quinic acid, caffeoylquinic acid (and isomers), chlorogenic acid, neochlorogenic acid, tryptophan, N-acetyltryptophan, epicatechin, procyanidin, and kaempferol-3-O-robinoside-7-O-rhamnoside. Molecular docking pointed to 3,4-dicaffeoylquinic acid and kaempferol as promising inhibitors. The in vitro assays yielded four active HPLC-fractions against L. amazonensis with IC50 values ranging from 175.2 μg/mL to 194.8 μg/mL, and fraction G29 showed an IC50 of 119.8 μg/mL against P. falciparum. Conclusions: The ethnobotanical use of “mulateiro” wood bark tea as an antimalarial and antileishmanial agent was confirmed through in vitro assays. We speculate that these activities are attributed to linoleic acids and quinic acids. Full article

(This article belongs to the Special Issue Advanced Metabolic Profiling via Gas Chromatography–Mass Spectrometry and Liquid Chromatography–Mass Spectrometry)

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22 pages, 5013 KB

Open AccessEditor’s ChoiceArticle

Polar Metabolite Profiles Distinguish Between Early and Severe Sub-Maintenance Nutritional States of Wild Bighorn Sheep

by Galen O’Shea-Stone, Brian Tripet, Jennifer Thomson, Robert Garrott and Valérie Copié

Metabolites 2025, 15(3), 154; https://doi.org/10.3390/metabo15030154 - 24 Feb 2025

Viewed by 1217

Abstract

Background: Understanding the metabolic adaptations of wild bighorn sheep (Ovis c. canadensis) to nutritional stress is crucial for their conservation. Methods: This study employed ¹H nuclear magnetic resonance (NMR) metabolomics to investigate the biochemical responses of these animals to varying [...] Read more.

Background: Understanding the metabolic adaptations of wild bighorn sheep (Ovis c. canadensis) to nutritional stress is crucial for their conservation. Methods: This study employed ¹H nuclear magnetic resonance (NMR) metabolomics to investigate the biochemical responses of these animals to varying sub-maintenance nutritional states. Serum samples from 388 wild bighorn sheep collected between 2014 and 2017 from December (early sub-maintenance) through March (severe sub-maintenance) across Wyoming and Montana were analyzed. Multivariate statistics and machine learning analyses were employed to identify characteristic metabolic patterns and metabolic interactions between early and severe sub-maintenance nutritional states. Results: Significant differences were observed in the levels of 15 of the 49 quantified metabolites, including formate, thymine, glucose, choline, and others, pointing to disruptions in one-carbon, amino acid, and central carbon metabolic pathways. These metabolites may serve as indicators of critical physiological processes such as nutritional intake, immune function, energy metabolism, and protein catabolism, which are essential for understanding how wild bighorn sheep adapt to nutritional stress. Conclusions: This study has generated valuable insights into molecular networks underlying the metabolic resilience of wild bighorn sheep, highlighting the potential for using specific biochemical markers to evaluate nutritional and energetic states in free-ranging ungulates. These insights may help wildlife managers and ecologists compare populations across different times in seasonal cycles, providing information to assess the adequacy of seasonal ranges and support conservation efforts. This research strengthens our understanding of metabolic adaptations to environmental stressors in wild ruminants, offering a foundation for improving management practices to maintain healthy bighorn sheep populations. Full article

(This article belongs to the Section Animal Metabolism)

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11 pages, 1992 KB

Open AccessEditor’s ChoiceArticle

Classification of Packaged Vegetable Soybeans Based on Freshness by Metabolomics Combined with Convolutional Neural Networks

by Yoshio Makino, Yuta Kurokawa, Kenji Kawai and Takashi Akihiro

Metabolites 2025, 15(3), 145; https://doi.org/10.3390/metabo15030145 - 21 Feb 2025

Viewed by 703

Abstract

Background/Objectives: Effectiveness of modified atmosphere (MA) packaging for the preservation of the freshness of vegetable soybeans was confirmed by using metabolomics combined with convolutional neural networks (CNNs). Methods: Stored under a low O₂, high CO₂ environment, the vegetable soybeans’ freshness [...] Read more.

Background/Objectives: Effectiveness of modified atmosphere (MA) packaging for the preservation of the freshness of vegetable soybeans was confirmed by using metabolomics combined with convolutional neural networks (CNNs). Methods: Stored under a low O₂, high CO₂ environment, the vegetable soybeans’ freshness was tracked through changes in hue angle on the surface of the crops and metabolite levels compared to those stored under normoxia. Results: MA packaging slowed respiration and reduced pectin decomposition, succinic acid oxidation, and fatty acid consumption, all linked to freshness maintenance. Using 62 key metabolite concentrations as inputs, CNNs classified vegetable soybean freshness into seven categories with 92.9% accuracy, outperforming traditional linear discriminant analysis by 14.3%. Conclusions: These findings demonstrate MA packaging’s effectiveness in extending freshness of vegetable soybeans by monitoring specific metabolic changes. This will contribute to the advancement of research aimed at elucidating the relationship between freshness and metabolism in horticultural crops. Full article

(This article belongs to the Special Issue Metabolic Changes during Pre- and Post-harvest Fruit and Vegetable Decay, Ripening and Senescence)

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29 pages, 1618 KB

Open AccessEditor’s ChoiceReview

From Microbes to Metabolites: Advances in Gut Microbiome Research in Type 1 Diabetes

by Lente Blok, Nordin Hanssen, Max Nieuwdorp and Elena Rampanelli

Metabolites 2025, 15(2), 138; https://doi.org/10.3390/metabo15020138 - 19 Feb 2025

Cited by 2 | Viewed by 3179

Abstract

Background: Type 1 diabetes (T1D) is a severe chronic T-cell mediated autoimmune disease that attacks the insulin-producing beta cells of the pancreas. The multifactorial nature of T1D involves both genetic and environmental components, with recent research focusing on the gut microbiome as a [...] Read more.

Background: Type 1 diabetes (T1D) is a severe chronic T-cell mediated autoimmune disease that attacks the insulin-producing beta cells of the pancreas. The multifactorial nature of T1D involves both genetic and environmental components, with recent research focusing on the gut microbiome as a crucial environmental factor in T1D pathogenesis. The gut microbiome and its metabolites play an important role in modulating immunity and autoimmunity. In recent years, studies have revealed significant alterations in the taxonomic and functional composition of the gut microbiome associated with the development of islet autoimmunity and T1D. These changes include reduced production of short-chain fatty acids, altered bile acid and tryptophan metabolism, and increased intestinal permeability with consequent perturbations of host (auto)immune responses. Methods/Results: In this review, we summarize and discuss recent observational, mechanistic and etiological studies investigating the gut microbiome in T1D and elucidating the intricate role of gut microbes in T1D pathogenesis. Moreover, we highlight the recent advances in intervention studies targeting the microbiota for the prevention or treatment of human T1D. Conclusions: A deeper understanding of the evolution of the gut microbiome before and after T1D onset and of the microbial signals conditioning host immunity may provide us with essential insights for exploiting the microbiome as a prognostic and therapeutic tool. Full article

(This article belongs to the Special Issue The Role of Gut Microbes in Metabolism Regulation: 2nd Edition)

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12 pages, 740 KB

Open AccessEditor’s ChoiceArticle

Deep Learning-Based Molecular Fingerprint Prediction for Metabolite Annotation

by Hoi Yan Katharine Chau, Xinran Zhang and Habtom W. Ressom

Metabolites 2025, 15(2), 132; https://doi.org/10.3390/metabo15020132 - 14 Feb 2025

Viewed by 1603

Abstract

Background/Objectives: Liquid chromatography coupled with mass spectrometry (LC-MS) is a commonly used platform for many metabolomics studies. However, metabolite annotation has been a major bottleneck in these studies in part due to the limited publicly available spectral libraries, which consist of tandem mass [...] Read more.

Background/Objectives: Liquid chromatography coupled with mass spectrometry (LC-MS) is a commonly used platform for many metabolomics studies. However, metabolite annotation has been a major bottleneck in these studies in part due to the limited publicly available spectral libraries, which consist of tandem mass spectrometry (MS/MS) data acquired from just a fraction of known compounds. Application of deep learning methods is increasingly reported as an alternative to spectral matching due to their ability to map complex relationships between molecular fingerprints and mass spectrometric measurements. The objectives of this study are to investigate deep learning methods for molecular fingerprint based on MS/MS spectra and to rank putative metabolite IDs according to similarity of their known and predicted molecular fingerprints. Methods: We trained three types of deep learning methods to model the relationships between molecular fingerprints and MS/MS spectra. Prior to training, various data processing steps, including scaling, binning, and filtering, were performed on MS/MS spectra obtained from National Institute of Standards and Technology (NIST), MassBank of North America (MoNA), and Human Metabolome Database (HMDB). Furthermore, selection of the most relevant m/z bins and molecular fingerprints was conducted. The trained deep learning models were evaluated on ranking putative metabolite IDs obtained from a compound database for the challenges in Critical Assessment of Small Molecule Identification (CASMI) 2016, CASMI 2017, and CASMI 2022 benchmark datasets. Results: Feature selection methods effectively reduced redundant molecular and spectral features prior to model training. Deep learning methods trained with the truncated features have shown comparable performances against CSI:FingerID on ranking putative metabolite IDs. Conclusion: The results demonstrate a promising potential of deep learning methods for metabolite annotation. Full article

(This article belongs to the Special Issue Machine Learning in Metabolomics: Unlocking the Future of Data Analysis)

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18 pages, 1123 KB

Open AccessEditor’s ChoiceArticle

Development of a Dispersive Liquid–Liquid Microextraction Method for Quantification of Volatile Compounds in Wines Using Gas Chromatography–Mass Spectrometry

by Dinesha Katugampala Appuhamilage, Rebecca E. Jelley, Emma Sherman, Lisa I. Pilkington, Farhana R. Pinu and Bruno Fedrizzi

Metabolites 2025, 15(2), 129; https://doi.org/10.3390/metabo15020129 - 13 Feb 2025

Cited by 2 | Viewed by 1172

Abstract

Background/Objectives: This study reports the development of a straightforward, efficient, and cost-effective dispersive liquid–liquid microextraction (DLLME) method for the gas chromatography–mass spectrometry (GC-MS) analysis of volatile compounds present in wine. Methods: Four critical parameters were optimised using a D-optimal design to [...] Read more.

Background/Objectives: This study reports the development of a straightforward, efficient, and cost-effective dispersive liquid–liquid microextraction (DLLME) method for the gas chromatography–mass spectrometry (GC-MS) analysis of volatile compounds present in wine. Methods: Four critical parameters were optimised using a D-optimal design to maximise extraction outcomes of the targeted analytes from a 10 mL sample, while minimising interference from other compounds. The analytical characteristics of the method were assessed using 36 target compounds. Results: The method provided satisfactory linearity (correlation coefficients > 0.990), good repeatability for both for intra- and inter-day measurements (RSD < 10.3%), and suitable recoveries of target analytes from both model (83–110%) and real matrices (80–120%). The validated method was subsequently applied to analyse the aroma profile of 30 New Zealand Pinot noir (PN) wine samples. Conclusions: This study contributes to the advancement of analytical techniques available to both industry and researchers to explore the complex aroma profiles of wines. Full article

(This article belongs to the Special Issue Metabolomics in Plant Natural Products Research)

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34 pages, 3911 KB

Open AccessEditor’s ChoiceReview

Polyphenols, Alkaloids, and Terpenoids Against Neurodegeneration: Evaluating the Neuroprotective Effects of Phytocompounds Through a Comprehensive Review of the Current Evidence

by Enzo Pereira de Lima, Lucas Fornari Laurindo, Vitor Cavallari Strozze Catharin, Rosa Direito, Masaru Tanaka, Iris Jasmin Santos German, Caroline Barbalho Lamas, Elen Landgraf Guiguer, Adriano Cressoni Araújo, Adriana Maria Ragassi Fiorini and Sandra Maria Barbalho

Metabolites 2025, 15(2), 124; https://doi.org/10.3390/metabo15020124 - 13 Feb 2025

Cited by 19 | Viewed by 5434

Abstract

Neurodegenerative diseases comprise a group of chronic, usually age-related, disorders characterized by progressive neuronal loss, deformation of neuronal structure, or loss of neuronal function, leading to a substantially reduced quality of life. They remain a significant focus of scientific and clinical interest due [...] Read more.

Neurodegenerative diseases comprise a group of chronic, usually age-related, disorders characterized by progressive neuronal loss, deformation of neuronal structure, or loss of neuronal function, leading to a substantially reduced quality of life. They remain a significant focus of scientific and clinical interest due to their increasing medical and social importance. Most neurodegenerative diseases present intracellular protein aggregation or their extracellular deposition (plaques), such as α-synuclein in Parkinson’s disease and amyloid beta (Aβ)/tau aggregates in Alzheimer’s. Conventional treatments for neurodegenerative conditions incur high costs and are related to the development of several adverse effects. In addition, many patients are irresponsive to them. For these reasons, there is a growing tendency to find new therapeutic approaches to help patients. This review intends to investigate some phytocompounds’ effects on neurodegenerative diseases. These conditions are generally related to increased oxidative stress and inflammation, so phytocompounds can help prevent or treat neurodegenerative diseases. To achieve our aim to provide a critical assessment of the current literature about phytochemicals targeting neurodegeneration, we reviewed reputable databases, including PubMed, EMBASE, and COCHRANE, seeking clinical trials that utilized phytochemicals against neurodegenerative conditions. A few clinical trials investigated the effects of phytocompounds in humans, and after screening, 13 clinical trials were ultimately included following PRISMA guidelines. These compounds include polyphenols (flavonoids such as luteolin and quercetin, phenolic acids such as rosmarinic acid, ferulic acid, and caffeic acid, and other polyphenols like resveratrol), alkaloids (such as berberine, huperzine A, and caffeine), and terpenoids (such as ginkgolides and limonene). The gathered evidence underscores that quercetin, caffeine, ginkgolides, and other phytochemicals are primarily anti-inflammatory, antioxidant, and neuroprotective, counteracting neuroinflammation, neuronal oxidation, and synaptic dysfunctions, which are crucial aspects of neurodegenerative disease intervention in various included conditions, such as Alzheimer’s and other dementias, depression, and neuropsychiatric disorders. In summary, they show that the use of these compounds is related to significant improvements in cognition, memory, disinhibition, irritability/lability, aberrant behavior, hallucinations, and mood disorders. Full article

(This article belongs to the Special Issue Plants and Plant-Based Foods for Metabolic Disease Prevention)

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17 pages, 7353 KB

Open AccessEditor’s ChoiceArticle

Multifluid Metabolomics Identifies Novel Biomarkers for Irritable Bowel Syndrome

by Daniel Kirk, Panayiotis Louca, Ilias Attaye, Xinyuan Zhang, Kari E. Wong, Gregory A. Michelotti, Mario Falchi, Ana M. Valdes, Frances M. K. Williams and Cristina Menni

Metabolites 2025, 15(2), 121; https://doi.org/10.3390/metabo15020121 - 12 Feb 2025

Cited by 2 | Viewed by 2088

Abstract

Background/Objectives: Irritable bowel syndrome (IBS) is a complex disorder affecting 10% of the global population, but the underlying mechanisms remain poorly understood. By integrating multifluid metabolomics, we aimed to identify metabolite markers of IBS in a large population-based cohort. Methods: We [...] Read more.

Background/Objectives: Irritable bowel syndrome (IBS) is a complex disorder affecting 10% of the global population, but the underlying mechanisms remain poorly understood. By integrating multifluid metabolomics, we aimed to identify metabolite markers of IBS in a large population-based cohort. Methods: We included individuals from TwinsUK with and without IBS, ascertained using the Rome III criteria, and analysed serum (232 cases, 1707 controls), urine (185 cases, 1341 controls), and stool (186 cases, 1284 controls) metabolites (Metabolon Inc.). Results: After adjusting for covariates, and multiple testing, 44 unique metabolites (25 novel) were associated with IBS, including lipids, amino acids, and xenobiotics. Androsterone sulphate, a sulfated steroid hormone precursor, was associated with lower odds of IBS in both urine (0.69 [95% confidence interval = 0.56–0.85], p = 2.34 × 10⁻⁴) and serum (0.75 [0.63–0.90], p = 1.54 × 10⁻³. Moreover, suberate (C8-DC) was associated with higher odds of IBS in serum (1.36 [1.15–1.61]; p = 1.84 × 10⁻⁴) and lower odds of IBS in stool (0.76 [0.63–0.91]; p = 2.30 × 10⁻³). On the contrary, 32 metabolites appeared to be fluid-specific, including indole, 13-HODE + 9-HODE, pterin, bilirubin (E,Z or Z,Z), and urolithin. The remaining 10 metabolites were associated with IBS in one fluid with suggestive evidence (p < 0.05) in another fluid. Finally, we identified androgenic signalling, dicarboxylates, haemoglobin, and porphyrin metabolism to be significantly over-represented in individuals with IBS compared to controls. Conclusions: Our results highlight the utility of a multi-fluid approach in IBS research, revealing distinct metabolic signatures across biofluids. Full article

(This article belongs to the Special Issue Advances in Metabolomics and Multi-Omics Integration)

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31 pages, 5603 KB

Open AccessEditor’s ChoiceArticle

Oregano Young Plants Cultured at Low Temperature Reveal an Enhanced Healing Effect of Their Extracts: Anatomical, Physiological and Cytotoxicity Approach

by Aikaterina L. Stefi, Maria Chalkiadaki, Katerina Dimitriou, Konstantina Mitsigiorgi, Dimitrios Gkikas, Danae Papageorgiou, Georgia C. Ntroumpogianni, Dido Vassilacopoulou, Maria Halabalaki and Nikolaos S. Christodoulakis

Metabolites 2025, 15(2), 103; https://doi.org/10.3390/metabo15020103 - 7 Feb 2025

Cited by 1 | Viewed by 1933

Abstract

Background: The germination and early development of Origanum vulgare L. subsp. hirtum (Link) Ietswaart (Greek oregano) were studied to assess the plant’s response to different temperatures. Methods: After germination, seedlings were cultivated in control (25 °C) and cold (15 °C) chambers with standard [...] Read more.

Background: The germination and early development of Origanum vulgare L. subsp. hirtum (Link) Ietswaart (Greek oregano) were studied to assess the plant’s response to different temperatures. Methods: After germination, seedlings were cultivated in control (25 °C) and cold (15 °C) chambers with standard growth parameters. Comparative analyses of plant morphology and leaf anatomy were conducted to identify structural modifications induced by different temperatures. Physiological evaluations, including photosynthetic pigment measurements, phenolic content, and antioxidant activity, were performed to assess differences between the plants grown under the two temperature conditions. Methanolic extracts from the leaves were tested for cytotoxicity on MCF-7 breast adenocarcinoma cells and SH-SY5Y neuroblastoma cells, as well as on nine microbial strains. Additionally, biomarkers from the leaves affected by temperature changes were determined using LC-HRMS/MS analysis. Results: Comparative analyses revealed distinct structural and physiological modifications under cold conditions. The methanolic extracts from plants grown at 15 °C exhibited notably higher cytotoxic activity in both cell lines but demonstrated no activity against microbial strains. The results highlight the influence of low temperature on enhancing the bioactive properties of Greek oregano. Conclusions: The findings provide valuable insights into the environmental adaptability of oregano, demonstrating the impact of low temperature on its bioactive properties. The therapeutic potential of methanolic extracts cultured at 15 °C is imprinted in cytotoxicity in SH-SY5Y and MCF-7 cells and the absence of any activity against microbial strains. Full article

(This article belongs to the Special Issue Advances in Secondary Metabolites: Phytochemical Analysis and Bioactivity Assays)

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