Metabolites

1 pages, 131 KB

Open AccessCorrection

Correction: Song et al. Serum Uric Acid and Bone Health in Middle-Aged and Elderly Hypertensive Patients: A Potential U-Shaped Association and Implications for Future Fracture Risk. Metabolites 2025, 15, 15

by Shuaiwei Song, Xintian Cai, Junli Hu, Qing Zhu, Di Shen, Huimin Ma, Yingying Zhang, Rui Ma, Pan Zhou, Wenbo Yang, Jing Hong and Nanfang Li

Metabolites 2026, 16(1), 89; https://doi.org/10.3390/metabo16010089 - 22 Jan 2026

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Abstract

References [...] Full article

(This article belongs to the Special Issue Nutrition and Metabolic Changes in Aging and Age-Related Diseases)

18 pages, 1890 KB

Open AccessSystematic Review

The Effects of High-Intensity Interval Training on Inflammatory Cytokines in Children and Adolescents with Obesity: A Systematic Review and Meta-Analysis

by Meng Cao, Pei Sun, Xiaodong Wang and Mengxian Zhao

Metabolites 2026, 16(1), 88; https://doi.org/10.3390/metabo16010088 - 21 Jan 2026

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Abstract

Background: High-intensity interval training (HIT) is a time-efficient strategy to improve metabolic health in children, but its impact on inflammatory markers is still unclear. Therefore, we conducted a meta-analysis to examine the role of HIT on pro-inflammatory cytokines including C-reactive protein (CRP), [...] Read more.

Background: High-intensity interval training (HIT) is a time-efficient strategy to improve metabolic health in children, but its impact on inflammatory markers is still unclear. Therefore, we conducted a meta-analysis to examine the role of HIT on pro-inflammatory cytokines including C-reactive protein (CRP), interleukin 6 (IL-6), and tumor necrosis factor-alpha (TNF-α) in children with overweight/obesity. Methods: A meta-analysis was conducted following PRISMA guidelines. PubMed, Web of Science, Scopus, and Embase were searched up to 31 July 2025, for studies involving children with overweight/obesity aged 6 to 18 years. Randomized controlled trials and non-randomized controlled trials with outcome measurements that included CRP, IL-6, and TNF-α were included. Random-effects models were used to aggregate a mean effect size (ES) with 95% confidence intervals (CI), and potential moderators were explored. Results: In total, 768 participants from 15 studies were included. HIT significantly improved CRP (574 participants, 13 studies, SMD = −0.63, 95% CI: −1.02 to −0.24, p < 0.01) when compared to control group/pre-intervention. There were no significant effects on IL-6 and TNF-α, and no differences when compared to moderate-intensity training. Subgroup analyses indicated greater effectiveness in intervention duration, work-and-rest ratio, and work time were the significant moderators (p < 0.05). Conclusions: High-intensity interval training is effective for reducing CRP levels in children with obesity. Intervention duration, work-and-rest ratio, and work time can affect the intervention effects of HIT. Full article

(This article belongs to the Special Issue Adipose Thermogenesis and Crosstalk: Signaling Networks in Obesity, Metabolic Disease and Beyond)

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23 pages, 797 KB

Open AccessReview

Metabolic Bone Disease in Captive Flying Foxes: A Conceptual Framework and Future Perspectives

by Diana Faim, Isabel Pires and Filipe Silva

Metabolites 2026, 16(1), 87; https://doi.org/10.3390/metabo16010087 - 21 Jan 2026

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Abstract

In Pteropus spp., metabolic bone disease has been consistently associated with fruit-based diets that are deficient in calcium, vitamin D precursors, and protein, as well as limited ultraviolet B (UVB) exposure, as reported in zoological surveys and clinical observations. Comparative mammalian physiology suggests [...] Read more.

In Pteropus spp., metabolic bone disease has been consistently associated with fruit-based diets that are deficient in calcium, vitamin D precursors, and protein, as well as limited ultraviolet B (UVB) exposure, as reported in zoological surveys and clinical observations. Comparative mammalian physiology suggests that dysregulation of the endocrine axis involving parathyroid hormone (PTH), fibroblast growth factor 23 (FGF23), calcitonin, and calcitriol may contribute to disease development, although direct species-specific endocrine data in flying foxes remain scarce. This narrative review synthesizes current knowledge from published zoological reports, clinical observations, and comparative mammalian physiology regarding the etiology, pathophysiology, and clinical expression of metabolic bone disease in captive flying foxes. Much of the available evidence is derived from juvenile Pteropus vampyrus, and its applicability to other Pteropus species remains to be fully established. The limited availability and consistency of existing data, together with the scarcity of controlled experimental and longitudinal studies, necessarily constrain the conclusions that can be drawn. Nevertheless, this review highlights key nutritional and environmental risk factors and summarizes evidence-informed preventive management strategies to improve skeletal health and welfare in managed Pteropus populations. Full article

(This article belongs to the Special Issue Nutritional and Metabolic Influences on Animal Growth and Reproduction)

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20 pages, 1702 KB

Open AccessArticle

Artificial Neural Network Elucidates the Role of Transport Proteins in Rhodopseudomonas palustris CGA009 During Lignin Breakdown Product Catabolism

by Niaz Bahar Chowdhury, Mark Kathol, Nabia Shahreen and Rajib Saha

Metabolites 2026, 16(1), 86; https://doi.org/10.3390/metabo16010086 - 21 Jan 2026

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Abstract

Background: Rhodopseudomonas palustris is a metabolically versatile bacterium with significant biotechnological potential, including the ability to catabolize lignin and its heterogeneous breakdown products. Understanding the molecular determinants of growth on lignin-derived compounds is essential for advancing lignin valorization strategies under both aerobic [...] Read more.

Background: Rhodopseudomonas palustris is a metabolically versatile bacterium with significant biotechnological potential, including the ability to catabolize lignin and its heterogeneous breakdown products. Understanding the molecular determinants of growth on lignin-derived compounds is essential for advancing lignin valorization strategies under both aerobic and anaerobic conditions. Methods: R. palustris was cultivated on multiple lignin breakdown products (LBPs), including p-coumaryl alcohol, coniferyl alcohol, sinapyl alcohol, p-coumarate, sodium ferulate, and kraft lignin. Condition-specific transcriptomics and proteomics datasets were generated and used as input features to train machine-learning models, with experimentally measured growth rates as the prediction target. Artificial Neural Networks (ANNs), Random Forest (RF), and Support Vector Machine (SVM) models were evaluated and compared. Permutation feature importance analysis was applied to identify genes and proteins most influential for growth. Results: Among the tested models, ANNs achieved the highest predictive performance, with accuracies of 94% for transcriptomics-based models and 96% for proteomics-based models. Feature importance analysis identified the top twenty growth-associated genes and proteins for each omics layer. Integrating transcriptomic and proteomic results revealed eight key transport proteins that consistently influenced growth across LBP conditions. Re-training ANN models using only these eight transport proteins maintained high predictive accuracy, achieving 86% for proteomics and 76% for transcriptomics. Conclusions: This study demonstrates the effectiveness of ANN-based models for predicting growth-associated genes and proteins in R. palustris. The identification of a small set of key transport proteins provides mechanistic insight into lignin catabolism and highlights promising targets for metabolic engineering aimed at improving lignin utilization. Full article

(This article belongs to the Section Cell Metabolism)

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14 pages, 2631 KB

Open AccessArticle

Comparative Analysis of Chemical Constituents in Peppers from Different Regions by Integrated LC-MS and GC-MS Non-Targeted Metabolomics

by Xuefeng Gong, Sihao Hou, Yi Xu, Hong Li, Xin Chen and Zhanfeng Song

Metabolites 2026, 16(1), 85; https://doi.org/10.3390/metabo16010085 - 21 Jan 2026

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Abstract

Background/Objectives: The quality of dried chili peppers is critically influenced by geographical origin, yet the metabolic basis for these differences remains insufficiently explored. This study sought to elucidate the region-specific metabolic profiles and their association with key quality traits in the pepper cultivar [...] Read more.

Background/Objectives: The quality of dried chili peppers is critically influenced by geographical origin, yet the metabolic basis for these differences remains insufficiently explored. This study sought to elucidate the region-specific metabolic profiles and their association with key quality traits in the pepper cultivar ‘Hong Guan 6’. Methods: Fruits harvested from three major cultivation regions in China were analyzed. We quantified fat and capsaicinoid content and employed an integrated LC-MS and GC-MS untargeted metabolomics approach to characterize the metabolite composition. Multivariate statistical analyses were applied to identify differentially abundant metabolites (DAMs) and uncover their related biochemical pathways. Results: Significant regional variations in fat and capsaicinoid content were observed, with peppers from Pengzhou (PZ) exhibiting the highest capsaicin levels. Metabolomic profiling revealed 529 metabolites that were significantly more abundant in PZ samples. These metabolites were enriched in several key pathways, including beta-alanine metabolism, plant hormone signal transduction, and N-glycan biosynthesis. Specifically, elevated levels of β-alanine and malonate in the beta-alanine metabolism pathway were detected in PZ and Anyue (AY) samples, suggesting a potential biochemical mechanism for their enhanced fat synthesis. Conclusions: Our findings demonstrate that geographical origin significantly reprograms the pepper metabolome, directly impacting quality attributes. The results provide crucial insights into the biochemical mechanisms, particularly those involving beta-alanine metabolism, that underpin the differences in critical quality traits such as fat content. Full article

(This article belongs to the Special Issue Advances in Food Sciences: Metabolomics to Unravel the Complexity of Food Metabolites)

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21 pages, 2287 KB

Open AccessArticle

Chemical Attributes of UK-Grown Tea and Identifying Catechin and Metabolite Dynamics in Green and Black Tea Using Metabolomics and Machine Learning

by Amanda J. Lloyd, Jasen Finch, Alina Warren-Walker, Alison Watson, Laura Lyons, MJ Pilar Martinez Martin, Thomas Wilson and Manfred Beckmann

Metabolites 2026, 16(1), 84; https://doi.org/10.3390/metabo16010084 - 21 Jan 2026

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Abstract

The Dartmoor Estate Tea plantation in Devon, UK, benefits from a unique microclimate and diverse soil conditions, which, together with its different processing methods, contribute to the distinctive flavours and chemical profiles of its teas. Objectives: The chemical diversity of Dartmoor tea was [...] Read more.

The Dartmoor Estate Tea plantation in Devon, UK, benefits from a unique microclimate and diverse soil conditions, which, together with its different processing methods, contribute to the distinctive flavours and chemical profiles of its teas. Objectives: The chemical diversity of Dartmoor tea was assessed via samples collected during processing of green and black tea. Methods: Leaf samples were collected during the processing of green and black tea and analysed using Flow Infusion Electrospray Ionisation Mass Spectrometry (FIE-MS). Results: For green tea processing, random forest regression identified features associated with the processing steps, resulting in a total of 272 m/z explanatory features. The analysis of black tea processing (4 h and overnight oxidation prior to roasting) yielded 209 discriminatory m/z features (4 h) and the model for the overnight oxidation and roasting treatments yielded 605 discriminatory m/z features. K-means clustering was performed on the percentage of relative abundance of the discriminatory m/z features. This grouped the discriminatory m/z features into 15 clusters of features showing similar trends across the processing stages. Functional and structural enrichment analysis was performed on each of the clusters and significant metabolic pathways included metabolism and biosynthesis of flavonoids, amino acids and lipids, the Pentose phosphate pathway, and the TCA cycle. Many discriminatory features were putatively classified as catechin-derived flavan-3-ols and flavonol glycosides. Conclusions: This research highlights the complex role that processing plays in shaping tea quality. It provides valuable insights into the metabolic pathways that influence tea production and emphasises how these factors determine the final chemical profile and sensory characteristics of tea. Full article

(This article belongs to the Section Food Metabolomics)

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14 pages, 497 KB

Open AccessArticle

Vitamin D Status in People Living with HIV: Assessment of 25(OH)D Levels and Associated Factors—A Cross-Sectional Study

by Florentina Dumitrescu, Eugenia-Andreea Marcu, Vlad Pădureanu, Livia Dragonu, Ilona-Andreea Georgescu, Lucian Giubelan, Rodica Pădureanu and Sineta Cristina Firulescu

Metabolites 2026, 16(1), 83; https://doi.org/10.3390/metabo16010083 - 21 Jan 2026

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Abstract

Background: Vitamin D deficiency (VDD) is highly prevalent among people living with human immunodeficiency virus (HIV), with reported rates of insufficiency and deficiency substantially higher than in many general-population cohorts. This study aims to assess the prevalence of vitamin D deficiency and to [...] Read more.

Background: Vitamin D deficiency (VDD) is highly prevalent among people living with human immunodeficiency virus (HIV), with reported rates of insufficiency and deficiency substantially higher than in many general-population cohorts. This study aims to assess the prevalence of vitamin D deficiency and to investigate the risk factors contributing to its occurrence among people living with HIV who are receiving antiretroviral therapy (ART) and are registered at the Craiova Regional Center (CRC). Methods: A retrospective study was conducted from May 2024 to August 2024, including individuals with HIV aged 18 years and older who were registered at the CRC. Results: A total of 138 patients were included in the study. The prevalence of vitamin D deficiency (<20 ng/mL) and vitamin D insufficiency (20–29.9 ng/mL) was 36.2% and 33.3%, respectively, with an average vitamin D level of 26.4 ± 9.9 ng/mL. Vitamin D deficiency was associated with obesity (p = 0.0013), high HIV viral load (p = 0.043), low CD4 nadir (<200 cells/mm³, p = 0.006), prolonged ART exposure (p = 0.002), and the use of tenofovir disoproxil fumarate or protease inhibitor-containing regimens (p = 0.034 and p = 0.016, respectively). Conclusions: These findings indicate that monitoring vitamin D levels could be particularly relevant for patients with HIV with higher-risk profiles. However, our study included a relatively small number of participants, so further research in larger cohorts is needed to better understand these patterns. Full article

(This article belongs to the Special Issue Vitamin D Metabolism and Human Health)

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14 pages, 3496 KB

Open AccessArticle

Distinct Metabolic Signatures Linked to High-Resolution Computed Tomography Radiographic Phenotypes in Stable and Progressive Fibrotic Lung Disease

by Girish B. Nair, Faizan Faizee, Zachary Smith, Sayf Al-Katib, Nadia Ashrafi, Ali Yilmaz, Romana Ashrafi Mimi, Sarayu Bhogoju, Vilija Lomeikaite, Juozas Gordevičius, Edward Castillo and Stewart F. Graham

Metabolites 2026, 16(1), 82; https://doi.org/10.3390/metabo16010082 - 19 Jan 2026

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Abstract

Background: This study aimed to identify distinct metabolic signatures associated with disease progression by integrating high-resolution computed tomography (HRCT) visual scoring with comprehensive metabolomic profiling. Materials and Methods: This single-center, cross-sectional study enrolled 60 idiopathic pulmonary fibrosis/interstitial lung disease (IPF/ILD) patients [...] Read more.

Background: This study aimed to identify distinct metabolic signatures associated with disease progression by integrating high-resolution computed tomography (HRCT) visual scoring with comprehensive metabolomic profiling. Materials and Methods: This single-center, cross-sectional study enrolled 60 idiopathic pulmonary fibrosis/interstitial lung disease (IPF/ILD) patients with usual interstitial pneumonia pattern. Participants underwent standardized pulmonary function testing, HRCT imaging, and peripheral blood collection for metabolomic analysis using one-dimensional hydrogen nuclear magnetic resonance spectroscopy and ultra-high-performance liquid chromatography coupled to tandem mass spectrometry. Linear regression analysis integrated radiographic scores with metabolomic profiles, adjusted for multiple covariates. Results: Stable IPF/ILD exhibited moderate negative correlations between the six most significant metabolites and HRCT scores (r = −0.27 to −0.51), along with a high abundance of specific phospholipids (triacylglycerol, monoacylglycerol, phosphatidylglycerol, phosphatidylethanolamine, diacylglycerol), sphingomyelin, ceramide, and acylcarnitine. In contrast, progressive disease showed weak positive correlations between the six most significant metabolites and HRCT scores (r = 0.19–0.26), and moderate negative correlation between specific triacylglycerol species and HRCT scores (r = −0.37–0.4). Furthermore, metabolomic analysis in individuals with progressive disease revealed both high and low abundances of specific phospholipid species (including high and low triacylglycerol species, as well as low levels of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, and phosphatidylinositol), along with high levels of certain sphingomyelin, ceramide, taurine, and purine bases, and low levels of xanthine and lactic acid observed. Conclusions: Integration of systematic HRCT semi-quantitative scoring with metabolomic profiling successfully differentiated stable from progressive IPF/ILD through distinct molecular-radiographic signatures. Full article

(This article belongs to the Special Issue State-of-the-Art NMR-Based Metabolomics and Its Applications)

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31 pages, 1713 KB

Open AccessArticle

In Vitro Antioxidant, Anti-Platelet and Anti-Inflammatory Natural Extracts of Amphiphilic Bioactives from Organic Watermelon Juice and Its By-Products

by Emmanuel Nikolakakis, Anna Ofrydopoulou, Katie Shiels, Sushanta Kumar Saha and Alexandros Tsoupras

Metabolites 2026, 16(1), 81; https://doi.org/10.3390/metabo16010081 - 19 Jan 2026

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Abstract

Background/Objectives: Watermelon (Citrullus lanatus) processing generates substantial quantities of rind, seeds, and residual pulp that are typically discarded despite being rich in polyunsaturated fatty acids, polar lipids, carotenoids, and phenolic compounds. These amphiphilic bioactives are increasingly recognized for their roles in [...] Read more.

Background/Objectives: Watermelon (Citrullus lanatus) processing generates substantial quantities of rind, seeds, and residual pulp that are typically discarded despite being rich in polyunsaturated fatty acids, polar lipids, carotenoids, and phenolic compounds. These amphiphilic bioactives are increasingly recognized for their roles in modulating oxidative stress, inflammation, and platelet activation; however, the lipid fraction of watermelon by-products remains insufficiently characterized. This study examined organic watermelon juice and its by-products to isolate, characterize, and evaluate extracts enriched in amphiphilic and lipophilic bioactives, with emphasis on their in vitro antioxidant, anti-inflammatory, and antithrombotic properties. Methods: total lipids were extracted using a modified Bligh–Dyer method and fractionated into total amphiphilic compounds (TAC) and total lipophilic compounds (TLC) via counter-current distribution. Phenolic and carotenoid levels were quantified, and antioxidant capacity was assessed using DPPH, ABTS, and FRAP assays. Anti-platelet and anti-inflammatory activities were evaluated against ADP- and PAF-induced platelet aggregation. Structural characterization of polar lipids was performed using ATR–FTIR, and LC–MS was used to determine fatty acid composition and phospholipid structures. Results and Discussion: Carotenoids were primarily concentrated in the TLC fractions with high ABTS values for antioxidant activity, while phenolics mostly in the juice, the TACs of which showed the strongest total antioxidant capacity based on DPPH. TAC fractions of both samples showed also higher FRAP values of antioxidant activity, likely due to greater phenolic content. TAC extracts also exhibited notable inhibition of PAF- and ADP-induced platelet aggregation, associated with their enriched ω-3 PUFA profiles and favorable ω-6/ω-3 ratios based on their LC-MS profiles. Conclusions: Overall, watermelon products (juice) and by-products represent a valuable and sustainable source of amphiphilic bioactives with significant antioxidant, anti-inflammatory, and anti-platelet potential, supporting their future use in functional foods, nutraceuticals, and cosmetic applications. Full article

(This article belongs to the Special Issue Secondary Metabolites and Their Activities: From the Identification to the Biological Investigation)

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19 pages, 3351 KB

Open AccessArticle

Spatial Heterogeneity of Metabolic Response to Drought Stress in Medicago lupulina L. Leaves

by Xinglin Wang, Ning Lv, Yuyun Xu, Xingpan Meng, Yukun Jin, Hongbin Gao, Fei Li, Yin Yi, Lunxian Liu and Tie Shen

Metabolites 2026, 16(1), 80; https://doi.org/10.3390/metabo16010080 - 17 Jan 2026

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Abstract

Background: Drought stress is a primary environmental constraint limiting crop growth and productivity. Current drought-related plant research predominantly focuses on whole-leaf analyses, neglecting the spatial heterogeneity of metabolites within leaf tissues. Methods: This study combined transcriptomic and metabolomic approaches to investigate [...] Read more.

Background: Drought stress is a primary environmental constraint limiting crop growth and productivity. Current drought-related plant research predominantly focuses on whole-leaf analyses, neglecting the spatial heterogeneity of metabolites within leaf tissues. Methods: This study combined transcriptomic and metabolomic approaches to investigate spatially distinct metabolic responses in marginal versus central regions of Medicago lupulina L. leaves under PEG-simulated drought. Results: Findings demonstrated that TCA cycle metabolites exhibited relative stability between leaf margins and centers under drought conditions, suggesting preserved core metabolic functionality in central tissues to sustain stress tolerance. Additionally, shikimic acid displayed a significantly reduced regional gradient in stressed tissues (PEG Margin vs. PEG Center) compared to controls. Phenylalanine, tryptophan, liquiritigenin, isoliquiritigenin, coproporphyrin III, and coproporphyrinogen III itself exhibited significantly increased internal gradient differences in stressed groups compared to control groups. The coordinated upregulation of key biosynthetic genes (e.g., TAT, AST, FNS II) in both the marginal and central regions of stressed leaves indicates a metabolic shift toward the biosynthesis of downstream defensive flavonoids. These metabolites and genes accumulated preferentially in margin regions of stressed leaves, indicative of localized activation of defense-associated metabolic pathways. Conclusions: This study reveals a spatially partitioned metabolic response to drought stress in M. lupulina leaves, where defensive metabolism is preferentially enhanced at the leaf margins while core metabolic homeostasis is maintained. These findings provide new spatial insights into plant drought acclimation and identify potential targets for improving crop resilience through the fine-tuning of local metabolism. Full article

(This article belongs to the Special Issue Metabolomics and Plant Defence, 2nd Edition)

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18 pages, 2211 KB

Open AccessArticle

Metabolomic Signatures of Recovery: A Secondary Analysis of Public Longitudinal LC–MS Datasets Shows Polyphenol-Rich Interventions Attenuate Purine Degradation and Oxidative Stress Following Exhaustive Exercise

by Xuyang Wang, Chang Liu, Yirui Chen, Mengyang Wang, Kai Zhao and Wei Jiang

Metabolites 2026, 16(1), 79; https://doi.org/10.3390/metabo16010079 - 16 Jan 2026

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Abstract

Background: Post-exercise recovery involves coordinated metabolic restoration and redox rebalancing. Although dietary polyphenols have been proposed to facilitate recovery, the metabolic mechanisms underlying their effects—particularly during the recovery phase—remain insufficiently characterized. This study aimed to investigate how polyphenol supplementation modulates post-exercise metabolic recovery [...] Read more.

Background: Post-exercise recovery involves coordinated metabolic restoration and redox rebalancing. Although dietary polyphenols have been proposed to facilitate recovery, the metabolic mechanisms underlying their effects—particularly during the recovery phase—remain insufficiently characterized. This study aimed to investigate how polyphenol supplementation modulates post-exercise metabolic recovery using an integrative metabolomics approach. Methods: We conducted a secondary analysis of publicly available longitudinal human LC–MS metabolomics datasets from exercise intervention studies with polyphenol supplementation. Datasets were obtained from the NIH Metabolomics Workbench and MetaboLights repositories; study-level metadata were used as provided by the original investigators. Global metabolic trajectories were assessed using principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA). Targeted analyses focused on purine degradation intermediates and redox-related metabolites. Correlation-based network and pathway enrichment analyses were applied to characterize recovery-phase metabolic reorganization. Results: Exercise induced a pronounced global metabolic perturbation in both placebo and polyphenol groups. During recovery, polyphenol supplementation was associated with a partial reversion of the metabolome toward the pre-exercise state, whereas placebo samples remained metabolically displaced. Discriminant metabolite analyses identified purine degradation intermediates and oxidative stress-related lipid species as key contributors to group separation during recovery. Polyphenol supplementation attenuated recovery-phase accumulation of hypoxanthine, xanthine, and uric acid and was associated with a sustained suppression of the uric acid-to-hypoxanthine ratio. Network analyses revealed weakened correlations between purine metabolites and oxidative stress markers, along with reduced network centrality of stress-responsive metabolic hubs. Conclusions: These findings indicate that polyphenol supplementation is associated with accelerated metabolic normalization during post-exercise recovery, potentially through modulation of purine-associated oxidative pathways and system-level metabolic network reorganization. Full article

(This article belongs to the Special Issue Metabolic Responses to Exercise and Nutrition: From Molecular Mechanisms to Functional Performance)

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13 pages, 517 KB

Open AccessArticle

Multimatrix Detection and Quantification of the Advanced Glycation End Products Precursor Fructoselysine via UHPLC-HRMS/MS

by Simona Fenizia, Marcello Manfredi, Valentina Antoniotti, Sabrina Tini, Jessica Baima, Flavia Prodam and Elettra Barberis

Metabolites 2026, 16(1), 78; https://doi.org/10.3390/metabo16010078 - 16 Jan 2026

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Abstract

Background: Advanced glycation end products (AGEs) play a pivotal role in various human pathologies, including aging and metabolic diseases, and their formation may have significant physiological consequences for human health. Fructoselysine (FL) is an intermediate in the formation of AGEs, and its accumulation [...] Read more.

Background: Advanced glycation end products (AGEs) play a pivotal role in various human pathologies, including aging and metabolic diseases, and their formation may have significant physiological consequences for human health. Fructoselysine (FL) is an intermediate in the formation of AGEs, and its accumulation has been associated with detrimental health effects. Although several chromatographic methods have been developed for AGEs detection and quantification, no mass spectrometry-based approach has previously been established to quantify FL in different human biological matrices. Methods: In this study, we present a novel UHPLC-HRMS/MS method for the identification and quantification of this compound in various biological matrices, including plasma, feces, and urine. Results: The method demonstrates excellent linearity, accuracy, and precision, with limit of detection (LOD) of 0.02 µM and limit of quantification (LOQ) of 0.06 µM. Recovery rates ranged from 95% to 109% and intra- and inter-day relative standard deviations (RSDs) were below 10%, indicating robust analytical performance. The validated method was successfully applied to quantify FL in plasma, feces, and urine samples from healthy individuals. Additionally, given the known association between AGEs and diabetes, we analyzed a small cohort of prediabetic patients and observed elevated circulating levels of FL compared to healthy controls. Conclusions: This study introduces a sensitive and reliable method for the specific detection and quantification of FL in biological samples and provides new insights into early molecular changes associated with prediabetic condition to improve early diagnosis in aging related diseases. Full article

(This article belongs to the Special Issue Lipid Metabolism in Age-Related Diseases: 2nd Edition)

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14 pages, 1060 KB

Open AccessArticle

Genomic-Driven Identification of Conserved Biosynthetic Gene Clusters in Cladosporium limoniforme: The Case of the DHN-Melanin Pathway

by Angela Rojas-Coll, José-Ignacio Valencia, Javier Tognarelli and Guillermo Fernández-Bunster

Metabolites 2026, 16(1), 77; https://doi.org/10.3390/metabo16010077 - 16 Jan 2026

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Abstract

Background: Endolichenic fungi represent an emerging source of bioactive secondary metabolites; however, the genomic basis of their chemical diversity remains largely poorly characterized. Specifically, the metabolic capabilities of Cladosporium limoniforme have not been explored at the genomic level. Objectives: This study [...] Read more.

Background: Endolichenic fungi represent an emerging source of bioactive secondary metabolites; however, the genomic basis of their chemical diversity remains largely poorly characterized. Specifically, the metabolic capabilities of Cladosporium limoniforme have not been explored at the genomic level. Objectives: This study aimed to characterize the biosynthetic potential of C. limoniforme by presenting its first whole-genome sequence and conducting a comparative analysis of its biosynthetic gene clusters (BGCs), with a specific focus on the evolutionary conservation of the DHN-melanin pathway. Methods: Genome mining was performed using antiSMASH and fungiSMASH tools. Comparative genomics involved heatmap-based distribution analysis across the Cladosporium genus, synteny profiling using Clinker to assess gene order conservation, and Maximum Likelihood phylogenetic analysis of the polyketide synthase (T1PKS) domain. Results: We identified 26 putative BGCs, revealing a largely untapped metabolic repertoire. Comparative analysis demonstrated a high degree of conservation for the metachelin C (siderophore) and 1,3,6,8-tetrahydroxynaphthalene (T4HN) clusters across the genus. Notably, synteny and phylogenetic analyses showed that while C. limoniforme retains a conserved, ancestral T1PKS core essential for stress survival, it exhibits a significant reduction in accessory genes compared to plant-pathogenic congeners. Conclusions: These findings support a “metabolic streamlining” hypothesis driven by the endolichenic lifestyle, where the fungus retains essential protective machinery while shedding costly accessory genes unnecessary in the buffered lichen niche. This study establishes C. limoniforme as a valuable genomic resource for future biotechnological research. Full article

(This article belongs to the Special Issue Comprehensive Insights into Metabolic Pathways: Genome-Scale Modeling Techniques)

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22 pages, 867 KB

Open AccessArticle

A Major Update and Improved Validation Functionality in the mwtab Python Library and the Metabolomics Workbench File Status Website

by P. Travis Thompson and Hunter N. B. Moseley

Metabolites 2026, 16(1), 76; https://doi.org/10.3390/metabo16010076 - 15 Jan 2026

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Abstract

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, [...] Read more.

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to the mwTab file format and an earnest effort to use MW datasets in meta-analyses, the mwtab Python package has been updated. Methods: Updates include better error handling for batch processing, better parsing to read more files without error, and extensive improvements to the validation capabilities of the package. These updates also required our mwFileStatusWebsite to be updated and improved. Results: We used the enhanced validation features of the mwtab package to evaluate all available datasets in MW to facilitate improved curation, FAIRness of the repository, and reuse for meta-analyses. Conclusions: Version 2.0.0 of the mwtab Python package is now officially released and freely available on GitHub and the Python Package Index (PyPI) under a Clear Berkeley Software Distribution (BSD) license, with documentation available on GitHub. The updated mwFileStatusWebsite is also officially in its 2.0.0 version. Full article

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

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20 pages, 1028 KB

Open AccessReview

Lactic Acid in Tumour Biology

by Cristina Cruz and Ignasi Barba

Metabolites 2026, 16(1), 75; https://doi.org/10.3390/metabo16010075 - 15 Jan 2026

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Abstract

Lactic acid accumulates in the tumour microenvironment (TME) at concentrations reaching up to 40 mM. Initially, lactic acid was considered merely a metabolic by-product of aerobic glycolysis, a phenomenon commonly referred to as the Warburg effect and observed in the majority of tumours. [...] Read more.

Lactic acid accumulates in the tumour microenvironment (TME) at concentrations reaching up to 40 mM. Initially, lactic acid was considered merely a metabolic by-product of aerobic glycolysis, a phenomenon commonly referred to as the Warburg effect and observed in the majority of tumours. Recent evidence, however, has demonstrated that lactic acid is not merely a waste product; rather, it plays a pivotal role in tumour biology. High plasma lactic acid levels correlate with increased metastatic potential and lower survival rates. Elevated lactic acid levels in the TME have been shown to suppress antitumour immune responses, facilitate both metastasis and cellular senescence, and might modulate gene expression through novel epigenetic mechanisms such as histone lactylation. This review aims to summarize current knowledge on the multifaceted impact of elevated lactic acid in the TME on tumour progression and biology. Full article

(This article belongs to the Special Issue Mechanistic Insights into Metabolic Interactions with the Tumor Microenvironment)

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15 pages, 108518 KB

Open AccessReview

From Sunlight to Signaling: Evolutionary Integration of Vitamin D and Sterol Metabolism

by Marianna Raczyk and Carsten Carlberg

Metabolites 2026, 16(1), 74; https://doi.org/10.3390/metabo16010074 - 14 Jan 2026

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Abstract

Background/Objectives: This review integrates evolutionary, metabolic, genetic, and nutritional perspectives to explain how sterol-derived vitamin D pathways shape human physiology and inter-individual variability in vitamin D status. Methods: The literature on sterol and vitamin D metabolism across animals, plants, fungi, and algae was [...] Read more.

Background/Objectives: This review integrates evolutionary, metabolic, genetic, and nutritional perspectives to explain how sterol-derived vitamin D pathways shape human physiology and inter-individual variability in vitamin D status. Methods: The literature on sterol and vitamin D metabolism across animals, plants, fungi, and algae was synthesized with data from metabolomics databases, genome-wide association studies, RNA-seq resources (including GTEx), structural biology, and functional genomics. Results: Vitamin D₂ and vitamin D₃ likely emerged early in evolution as non-enzymatic photochemical sterol derivatives and were later co-opted into a tightly regulated endocrine system in vertebrates. In humans, cytochrome P450 enzymes coordinate vitamin D activation and degradation and intersect with oxysterol production, thereby linking vitamin D signaling to cholesterol and bile acid metabolism. Tissue-specific gene expression and regulatory genetic variants, particularly in the genes DHCR7, CYP2R1, CYP27B1, and CYP27A1, contribute to population-level differences in vitamin D status and metabolic outcomes. Structural analyses reveal selective, high-affinity binding of 1,25-dihydroxyvitamin D₃ to VDR, contrasted with broader, lower-affinity ligand recognition by LXRs. Dietary patterns modulate nuclear receptor signaling through distinct yet convergent ligand sources, including cholesterol-derived oxysterols, oxidized phytosterols, and vitamin D₂ versus vitamin D₃. Conclusions: Sterol and vitamin D metabolism constitute an evolutionarily conserved, adaptable network shaped by UV exposure, enzymatic control, genetic variation, and diet. This framework explains inter-individual variability in vitamin D biology and illustrates how evolutionary and dietary modulation of sterol-derived ligands confers functional flexibility to nuclear receptor signaling in human health. Full article

(This article belongs to the Special Issue Vitamin D Metabolism and Human Health)

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14 pages, 2988 KB

Open AccessArticle

Region-Specific Lipid Alterations Around the 28-Year Transition as Early Indicators of Skin Aging

by Meiting Yi, Qian Jiao, Jianbiao He, Huiliang Li, Yangyang Fang, Youjie He, Huaming He and Yan Jia

Metabolites 2026, 16(1), 73; https://doi.org/10.3390/metabo16010073 - 13 Jan 2026

Viewed by 319

Abstract

Background: Early molecular changes on the facial skin surface during early adulthood remain insufficiently characterized. We integrated biophysical readouts with untargeted skin surface lipid (SSL) profiling to identify region-dependent, age-associated features in women with combination skin. Methods: Eighty healthy Chinese women [...] Read more.

Background: Early molecular changes on the facial skin surface during early adulthood remain insufficiently characterized. We integrated biophysical readouts with untargeted skin surface lipid (SSL) profiling to identify region-dependent, age-associated features in women with combination skin. Methods: Eighty healthy Chinese women were stratified into 22–28 years (n = 40) and 29–35 years (n = 40). Sebum was measured on the cheek and forehead; cheek elasticity, hydration (CM), transepidermal water loss (TEWL), pH, and tone indices were assessed under standardized conditions. SSLs from both regions were profiled by UPLC–QTOF–MS. Differential features were prioritized using OPLS-DA (VIP > 1) with univariate screening (p < 0.05; fold change > 2 or <0.5). Results: TEWL, CM, and pH were comparable between age groups, whereas the older group showed lower cheek elasticity and reduced sebum. Lipidomics revealed clearer remodeling on the cheek than the forehead: 30 and 59 differential SSL features were identified in the cheek and forehead, respectively. Cheek changes in the older group were characterized by lower ceramides (including acylceramides), TG/DG and long-chain fatty acids, alongside relatively higher cholesteryl esters. Conclusions: Conventional barrier indices remained largely stable across this age window, while cheek SSL profiles captured earlier molecular shifts, providing candidates for targeted validation and longitudinal follow-up. Full article

(This article belongs to the Special Issue The Role of Lipid Metabolism in Health and Disease)

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15 pages, 772 KB

Open AccessArticle

High Ratio of Dietary Palmitic Acid to DHA + EPA Induces Glucose Metabolic Disorder Through Endocrine and Transcriptional Regulation in Large Yellow Croaker (Larimichthys crocea)

by Qi Wang, Huaicheng Ge, Zhixiang Gu, Hao Chen, Hua Mu, Kangsen Mai and Wenbing Zhang

Metabolites 2026, 16(1), 72; https://doi.org/10.3390/metabo16010072 - 13 Jan 2026

Viewed by 291

Abstract

Background/Objectives: Replacing fish oil with vegetable oil is an important measure for aquaculture to relieve the pressure of fish oil, but it is also easy to cause the growth decline and metabolic disorder of farmed animals, mainly due to the change in [...] Read more.

Background/Objectives: Replacing fish oil with vegetable oil is an important measure for aquaculture to relieve the pressure of fish oil, but it is also easy to cause the growth decline and metabolic disorder of farmed animals, mainly due to the change in dietary fatty acids. This study investigated the regulatory effects of dietary fatty acid composition on glucose metabolism in large yellow croaker (Larimichthys crocea) with an initial weight of 30.51 ± 0.16 g. Methods: Three isonitrogenous (~43% crude protein) and isolipid (~11% crude lipid) diets were formulated as follows: control (CON, DHA/EPA-rich oil as primary lipid), moderate palmitic acid (MPA, 50% of DHA+EPA-rich oil was replaced by glyceryl palmitate), and high palmitic acid (HPA, 100% of DHA+EPA-rich oil was replaced by glyceryl palmitate). Results: After 10 weeks of feeding, the HPA significantly reduced the liver/muscle glycogen contents, increased the liver lipid content, decreased the serum leptin/insulin level, and increased the adiponectin level. The levels of DHA and EPA in liver were decreased significantly. Transcriptionally, HPA upregulated hepatic glucokinase (gk, glycolysis) but down-regulated glycogen synthase (gys) and insulin/irs2 (insulin pathway) while inhibiting muscle ampk and leptin receptor (lepr). Conclusions: This study showed that high dietary PA/(DHA + EPA) impacted glycolipid homeostasis through endocrine and transcriptional regulation, leading to increased crude lipid and decreased glycogen levels, which provides a theoretical basis for scientific aquatic feed fatty acid formulation. Full article

(This article belongs to the Special Issue Nutrition, Metabolism and Physiology in Aquatic Animals)

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10 pages, 1412 KB

Open AccessArticle

Cystatin C Mirrors Fibrosis Burden in Metabolic Syndrome: Insights from the Metabolic Dysfunction-Associated Fibrosis-5 Score

by Musa Salmanoğlu, Sinan Kazan, Elif Yıldırım Ayaz, Süleyman Kılıç, Elif Kazan and Sena Ulu

Metabolites 2026, 16(1), 71; https://doi.org/10.3390/metabo16010071 - 13 Jan 2026

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Abstract

Background: Metabolic syndrome (MetS) comprises interrelated metabolic abnormalities that collectively confer increased risk of cardiovascular disease and hepatic morbidity. The MAF-5 score is a non-invasive prognostic marker of liver fibrosis and mortality, while Cystatin C (CysC) is a sensitive indicator of renal function [...] Read more.

Background: Metabolic syndrome (MetS) comprises interrelated metabolic abnormalities that collectively confer increased risk of cardiovascular disease and hepatic morbidity. The MAF-5 score is a non-invasive prognostic marker of liver fibrosis and mortality, while Cystatin C (CysC) is a sensitive indicator of renal function that also reflects inflammation, atherosclerosis, and metabolic dysfunction. Although both MetS and CysC have been widely studied, their potential interplay via MAF-5 remains unclear. We aimed to investigate the relationship between MAF-5 scores and CysC levels in MetS patients for the first time. Materials and Methods: Adults (≥18 years) with MetS were included in this study. MAF-5 scores (based on waist circumference, BMI, diabetes status, AST, and platelet count) and CysC levels were recorded. The MAF-5–CysC relationship was assessed via Pearson correlation. Participants were grouped into MAF-5 quartiles, and continuous variables were compared using ANOVA with Bonferroni-corrected pairwise tests. Results: We included 347 MetS patients (54.8% female, median age 54 years). The median MAF-5 score was 1.25, and MAF-5 correlated positively with CysC (r = 0.357, p < 0.001). CysC levels differed significantly across MAF-5 quartiles (Q1 = 0.96, Q2 = 0.99, Q3 = 1.06, Q4 = 1.09; p < 0.001), with Q4 showing higher values than Q1 and Q2. Conclusions: A significant correlation was found between MAF-5 scores and CysC in patients with MetS. CysC levels differed significantly across MAF-5 quartiles, suggesting a potential link between systemic inflammation, liver fibrosis, and CysC. These results highlight shared inflammatory and fibrotic pathways, underlying metabolic dysfunction. Clinically, combined assessment of MAF-5 and CysC may improve risk stratification, identifying patients at higher risk for hepatic fibrosis and adverse outcomes. Full article

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

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12 pages, 2360 KB

Open AccessArticle

Synovial Joint Fluid Metabolomic Profiles and Pathways Differentiate Osteoarthritis, Rheumatoid Arthritis, and Psoriatic Arthritis

by Ozan Kaplan, Rositsa Karalilova, Zguro Batalov, Konstantin Batalov, Maria Kazakova, Victoria Sarafian, Emine Koç, Mustafa Çelebier and Feza Korkusuz

Metabolites 2026, 16(1), 70; https://doi.org/10.3390/metabo16010070 - 12 Jan 2026

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Abstract

Background: Distinguishing between osteoarthritis (OA), rheumatoid arthritis (RA), and psoriatic arthritis (PsA) remains challenging despite different underlying mechanisms. Synovial fluid reflects metabolic changes within affected joints, yet comprehensive metabolomic comparisons across these conditions are limited. We aimed to identify disease-specific metabolic signatures in [...] Read more.

Background: Distinguishing between osteoarthritis (OA), rheumatoid arthritis (RA), and psoriatic arthritis (PsA) remains challenging despite different underlying mechanisms. Synovial fluid reflects metabolic changes within affected joints, yet comprehensive metabolomic comparisons across these conditions are limited. We aimed to identify disease-specific metabolic signatures in synovial fluid that could improve differential diagnosis and reveal therapeutic targets. Methods: We collected synovial fluid from 39 patients (20 OA, 5 RA, and 14 PsA) during routine knee arthrocentesis between January 2023 and February 2024. Following metabolite extraction, we performed untargeted metabolomic profiling using quadrupole time-of-flight liquid chromatography–mass spectrometry (Q-TOF LC/MS). Data underwent multivariate statistical analysis, including principal component analysis (PCA) and partial least squares–discriminant analysis (PLS-DA), to identify discriminatory metabolites. Results: While unsupervised analysis showed overlap between groups, supervised PLS-DA achieved clear metabolic separation. RA samples showed elevated itaconic acid, indicating inflammatory macrophage activation, and increased O-acetylserine, suggesting altered one-carbon metabolism. Hypoxanthine was decreased, which reflected severe metabolic stress. PsA exhibited the unique elevation of 4,4-dimethylcholestane and 2-oxoarginine. These metabolites have previously been unreported in this disease. OA demonstrated increased hippuric acid and indoleacetic acid, which are both gut microbiota products, supporting the gut–joint axis hypothesis. Conclusions: Each arthritis type displayed distinct metabolic fingerprints in synovial fluid. Candidate discriminatory metabolites, including gut-derived metabolites in OA and specific lipid alterations in PsA, open new diagnostic and therapeutic avenues. Given the limited RA sample size (n = 5), RA-related results should be viewed as exploratory and requiring validation in larger independent cohorts. These metabolites may, after rigorous validation in larger and independent cohorts, contribute to multi-metabolite biomarker panels for earlier diagnosis and to the rational design of targeted therapeutics addressing disease-specific metabolic disruptions. Full article

(This article belongs to the Special Issue Research on Metabolic Biomarkers in Different Diseases)

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29 pages, 4302 KB

Open AccessArticle

Discrimination of Bipolar Disorder and Schizophrenia Patients Based on LC-HRMS Lipidomics

by Milan R. Janković, Nataša Avramović, Zoran Miladinović, Milka B. Jadranin, Marija Takić, Gordana Krstić, Aleksandra Gavrilović, Čedo Miljević, Maja Pantović, Zorana Andrić, Savvas Radević, Danica Savić, Stefan Lekić, Vele Tešević and Boris Mandić

Metabolites 2026, 16(1), 69; https://doi.org/10.3390/metabo16010069 - 12 Jan 2026

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Abstract

Background/Objectives: Schizophrenia (SCH) and bipolar disorder (BD) share overlapping symptoms and genetic factors, making differential diagnosis challenging and often leading to misdiagnosis. This study aimed to identify potential lipid biomarkers of serum capable of distinguishing BD from SCH. Methods: Lipid profiles of serum [...] Read more.

Background/Objectives: Schizophrenia (SCH) and bipolar disorder (BD) share overlapping symptoms and genetic factors, making differential diagnosis challenging and often leading to misdiagnosis. This study aimed to identify potential lipid biomarkers of serum capable of distinguishing BD from SCH. Methods: Lipid profiles of serum from 30 SCH and 31 BD patients were analyzed in triplicates using liquid chromatography–high-resolution mass spectrometry (LC-HRMS). Chemometric analysis was applied, including class and gender identifiers. Orthogonal partial least squares (OPLS) models with 1000 cross-validations were used to validate feature subsets. Results: The chemometric analysis included the most relevant metabolites in the comparison between all samples of SCH and BD patients, identifying five key biomarkers (LPC 16:0, SM 33:1, SM 32:1, compound C30H58O3, and PC 30:0) with VIP scores > 1 for distinguishing BD from SCH. Gender-specific models revealed five biomarkers in males (SM 32:1, SM 33:1, PC 32:1, PC 30:0, and FA 16:1) and two in females (LPC 16:0 and C30H58O3). These biomarkers primarily belonged to glycerophospholipids (GPs) and sphingophospholipids (SPs). Conclusions: Comparative lipid profiling between SCH and BD, including gender-specific subgroups, enabled identification of potential diagnosis-specific biomarkers. Elevated levels of GPs and SPs in SCH patients suggest lipid metabolism differences that may support improved diagnostic accuracy and personalized treatment strategies. Full article

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

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15 pages, 2833 KB

Open AccessArticle

Untargeted Metabolomics Unravel the Effect of SlPBB2 on Tomato Fruit Quality and Associated Plant Metabolism

by Cuicui Wang, Lihua Jin, Daqi Fu and Weina Tian

Metabolites 2026, 16(1), 68; https://doi.org/10.3390/metabo16010068 - 12 Jan 2026

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Abstract

Background: Proteasomes are protein complexes that mediate proteolysis to degrade unneeded or damaged proteins, and they play an indispensable role in plant growth and development. However, their regulatory effects on tomato fruit quality and the underlying metabolic mechanisms remain largely elusive. This [...] Read more.

Background: Proteasomes are protein complexes that mediate proteolysis to degrade unneeded or damaged proteins, and they play an indispensable role in plant growth and development. However, their regulatory effects on tomato fruit quality and the underlying metabolic mechanisms remain largely elusive. This study aimed to elucidate the metabolic regulatory mechanisms of proteasomes in tomato fruits through untargeted metabolome analysis. Methods: An untargeted metabolomics approach was employed to profile the metabolic changes in tomato fruits. Metabolites were detected and identified under both positive and negative ion modes. Metabolic profiles were compared between wild-type (WT) tomato fruits and SlPBB2 RNA interference (SlPBB2-RNAi) lines. Specifically, the SlPBB2-RNAi line refers to a transgenic tomato line constructed via Agrobacterium-mediated transformation, where the expression of the proteasome component gene SlPBB2 was stably downregulated by RNA interference technology to clarify its regulatory role in fruit metabolism. KEGG enrichment analysis was performed to annotate the functions of differential metabolites. Results: A total of 568 and 333 metabolites were identified in positive and negative ion modes, respectively. Comparative analysis revealed 43 differentially abundant metabolites between WT and SlPBB2-RNAi fruits, including D-glucose, pyruvic acid, leucine, and naringenin. KEGG enrichment analysis further identified key metabolites involved in the carbon fixation pathway of photosynthetic organisms, with L-malic acid being a prominent representative. Reduced accumulation of D-glucose and pyruvic acid in SlPBB2-RNAi fruits suggested the inhibition of the citrate cycle, a core pathway in cellular energy metabolism. This metabolic perturbation was associated with decreased chlorophyll content in SlPBB2-RNAi plants, implying impaired photosynthetic carbon fixation and energy metabolism. Conclusions: This study uncovers the metabolic regulatory role of SlPBB2-mediated proteasome function in tomato fruits, providing novel insights into the link between proteasomal activity and fruit metabolic homeostasis from a metabolomic perspective. These findings offer new theoretical foundations for developing strategies to improve tomato nutritional quality. Full article

(This article belongs to the Special Issue Metabolic Changes During Pre- and Post-Harvest Fruit and Vegetable Decay, Ripening and Senescence—2nd Edition)

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13 pages, 2350 KB

Open AccessArticle

Metabolomic Subtyping and Machine Learning-Based Diagnosis Reveal Clinical Heterogeneity in Silicosis

by Jia Si, Hangju Zhu, Xinyu Ji, An-Dong Li, Ye Li, Shidan Wang, Yizhou Yang, Jianye Guo, Xinyu Li, Xiaocheng Peng, Ming Xu, Baoli Zhu, Yuanfang Chen and Lei Han

Metabolites 2026, 16(1), 67; https://doi.org/10.3390/metabo16010067 - 12 Jan 2026

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Abstract

Background/Objectives: Silicosis remains a major occupational health concern worldwide and is characterized by notable clinical heterogeneity in terms of disease progression and complications. However, the underlying metabolic mechanisms contributing to this heterogeneity remain poorly understood. Methods: We conducted a case–control study involving 156 [...] Read more.

Background/Objectives: Silicosis remains a major occupational health concern worldwide and is characterized by notable clinical heterogeneity in terms of disease progression and complications. However, the underlying metabolic mechanisms contributing to this heterogeneity remain poorly understood. Methods: We conducted a case–control study involving 156 silicosis patients and 132 silica-exposed controls. The plasma samples were analyzed via untargeted metabolomics based on liquid chromatography–mass spectrometry (LC-MS/MS). To explore disease subtypes and potential biomarkers, we applied non-negative matrix factorization (NMF) clustering, weighted gene co-expression network analysis (WGCNA), and machine learning approaches. Results: A total of 860 differentially abundant metabolites, including elevated pathogen-associated compounds, were identified in silicosis patients. Unsupervised NMF clustering revealed two distinct metabolic subtypes with different clinical features. Patients in the NMF2 subgroup had a 5.3-fold greater risk of pulmonary infections (p = 0.026) than those in the NMF1 subgroup. Metabolomic analysis revealed that NMF2 was enriched in arachidonic acid and unsaturated fatty acid metabolism pathways, with prominent LysoPC accumulation, suggesting inflammation-related lipid peroxidation. In contrast, NMF1 was characterized by increased spermidine biosynthesis and urea cycle activity, along with suppressed saturated fatty acid metabolism and reduced LysoPC processing, potentially affecting membrane integrity and promoting fibrosis. A machine learning-derived dual-metabolite panel, tyrosocholic acid and PI (20:4/0:0), achieved AUC values above 0.85 for both silicosis detection and subtype classification. Conclusions: These findings highlight metabolic heterogeneity in silicosis and suggest clinically relevant subtypes, providing a foundation for improved stratification, early detection, and targeted interventions. Full article

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

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13 pages, 7859 KB

Open AccessArticle

Itaconate Promotes Cold Adaptation and Myocardial Protection by Enhancing Brown Adipose Tissue Metabolism

by Zilong Geng, Xing Liu, Xiao Cheng, Shizhan Xu, Jin Zhang, Ao Tan, Shun Song and Shasha Zhang

Metabolites 2026, 16(1), 66; https://doi.org/10.3390/metabo16010066 - 12 Jan 2026

Viewed by 293

Abstract

Background/Objectives: Itaconic acid (ITA) is an immunometabolite with anti-inflammatory and metabolic regulatory functions, but its cellular source and role in brown adipose tissue (BAT) remain unclear. This study aims to reveal the expression patterns of the key ITA synthesis gene Irg1 in BAT [...] Read more.

Background/Objectives: Itaconic acid (ITA) is an immunometabolite with anti-inflammatory and metabolic regulatory functions, but its cellular source and role in brown adipose tissue (BAT) remain unclear. This study aims to reveal the expression patterns of the key ITA synthesis gene Irg1 in BAT at different developmental stages and to investigate the effects of cold exposure and exogenous ITA on BAT metabolic function and cardioprotection. Methods: Single-cell RNA sequencing was used to analyze the gene expression profiles of stromal vascular fraction (SVF) cells in BAT from P7 neonatal and adult mice. Bioinformatic methods were applied to identify cell types expressing Irg1. Cold exposure (4 °C) and exogenous ITA treatment were employed to evaluate BAT morphology, and the ITA content in BAT was detected using gas chromatography–triple quadrupole mass spectrometry, UCP1 protein expression, and body temperature changes. A transverse aortic constriction (TAC) surgery model was established to induce cardiac dysfunction, and BAT excision was performed to explore the BAT-dependent effects of ITA on myocardial hypertrophy, fibrosis, and cardiac function. Results: In P7 neonatal mouse BAT, Irg1 was predominantly expressed in a subset of interferon-responsive activated macrophages (macrophage27), while in adult mice, it was mainly expressed in neutrophils and a functionally similar macrophage subset (macrophage25). Cold exposure significantly suppressed Irg1 expression in neutrophils but did not affect its expression in macrophages, also resulting in a significant decrease in ITA content in BAT. Exogenous ITA significantly enhanced BAT thermogenesis under cold conditions, which manifested as reduced lipid droplets, upregulated UCP1 expression, and increased body temperature. In the TAC model, ITA treatment markedly improved cardiac function, attenuated myocardial hypertrophy and fibrosis, and these protective effects were significantly diminished after BAT excision. Conclusions: ITA promotes cold adaptation and ameliorates cardiac injury by enhancing BAT metabolic function, and its effects depend on the presence of BAT. This study provides new insights for the treatment of metabolic cardiovascular diseases. Full article

(This article belongs to the Special Issue Exploring Pathological Mechanisms in Obesity, Diabetes, and Metabolic Syndrome: 2nd Edition)

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17 pages, 1926 KB

Open AccessArticle

Optical and Microdialysis Monitoring of Succinate Prodrug Treatment in a Rotenone-Induced Model of Mitochondrial Dysfunction in Swine

by Alistair Lewis, Rodrigo M. Forti, Tiffany S. Ko, Eskil Elmér, Meagan J. McManus, Arjun G. Yodh, Todd J. Kilbaugh and Wesley B. Baker

Metabolites 2026, 16(1), 65; https://doi.org/10.3390/metabo16010065 - 11 Jan 2026

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Abstract

Background/Objectives: Mitochondrial dysfunction is a major cause of brain injury in patients with primary mitochondrial disease. New mitochondrial therapeutics and non-invasive tools for efficacy monitoring are urgently needed. To these ends, succinate prodrug NV354 (methyl 3-[(2-acetylaminoethylthio)carbonyl]propionate) and diffuse optical techniques are promising. In [...] Read more.

Background/Objectives: Mitochondrial dysfunction is a major cause of brain injury in patients with primary mitochondrial disease. New mitochondrial therapeutics and non-invasive tools for efficacy monitoring are urgently needed. To these ends, succinate prodrug NV354 (methyl 3-[(2-acetylaminoethylthio)carbonyl]propionate) and diffuse optical techniques are promising. In this proof-of-concept study, we characterize NV354’s effects on microdialysis metrics of cerebral metabolism in a swine model of mitochondrial dysfunction and assess the associations of diffuse optical metrics with mitochondrial dysfunction and metabolic improvement. Methods: One-month-old swine received a four-hour co-infusion of rotenone with either the succinate prodrug NV354 (n = 5) or placebo (n = 5). Rotenone is a mitochondrial complex I inhibitor. Before and during co-infusion, cerebral metabolism was probed with microdialysis and diffuse optics. Microdialysis acquired interstitial lactate and pyruvate levels invasively, while diffuse optics measured changes in oxygen extraction fraction (OEF) and oxidized cytochrome-c-oxidase concentration (oxCCO). Results: Interstitial lactate continually increased in the placebo group (p < 0.01), but lactate levels plateaued in the NV354 group (p = 0.90). oxCCO also increased in the placebo group (p = 0.05), but OEF remained constant (p = 0.80). In the NV354 group, oxCCO increased (p < 0.01) while OEF decreased (p < 0.01). Conclusions: Microdialysis results suggest that NV354 treatment can increase oxygen metabolism in large animals with mitochondrial dysfunction. The optical oxCCO metric was also sensitive to metabolic changes induced by rotenone and NV354 administration. Full article

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

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20 pages, 5995 KB

Open AccessArticle

Co-Metabolic Network Reveals the Metabolic Mechanism of Host–Microbiota Interplay in Colorectal Cancer

by Han-Wen Wang, Wang Li, Qi-Jun Ma, Hong-Yu Zhang, Yuan Quan and Qiang Zhu

Metabolites 2026, 16(1), 64; https://doi.org/10.3390/metabo16010064 - 11 Jan 2026

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Abstract

Background: Colorectal cancer (CRC) is a malignancy that ranks among the top three in terms of both global mortality and incidence. Although numerous studies have demonstrated that gut microbes are implicated in CRC pathogenesis, the precise mechanisms underlying host–microbiota metabolic crosstalk remain poorly [...] Read more.

Background: Colorectal cancer (CRC) is a malignancy that ranks among the top three in terms of both global mortality and incidence. Although numerous studies have demonstrated that gut microbes are implicated in CRC pathogenesis, the precise mechanisms underlying host–microbiota metabolic crosstalk remain poorly understood. Objective: This study aims to identify and delineate key co-metabolites and their associated metabolic pathways that modulate the biomass of CRC-related gut bacteria within healthy individuals, through the construction of host–gut microbiota co-metabolic network models. We seek to elucidate the underlying mechanisms of metabolic interplay between the host and CRC-related gut microbiota, thereby offering novel perspectives on the microbial involvement in the initiation and progression of CRC. Methods: We coupled a colon tissue-specific host Genome-Scale Metabolic Model (GEM), which utilized transcriptomic data from healthy human colon tissues, with 12 CRC-associated pro-/anti-carcinogenic gut bacterial GEMs to construct a co-metabolic network. Through a comparative analysis of the network structure and systemic methods (including Flux Sampling and metabolic difference analysis), we simulated scenarios of constrained host co-metabolite supply. Finally, metabolic subsystem enrichment analysis was employed to elucidate the specific molecular mechanisms by which key co-metabolites affect microbial function. Results: The 17 key co-metabolites identified include chloride ions, zinc ions, and acetate. Among these, thirteen metabolites (e.g., ferric iron, succinate, and acetate) were confirmed by literature to be associated with CRC. All 17 key co-metabolites were found to significantly modulate the biomass of CRC-associated gut bacteria. These regulatory effects primarily influence microbial function through core pathways such as glycerophospholipid metabolism and folate metabolism. Conclusion: This research provides a systemic perspective for elucidating the mechanisms of host–gut microbiota metabolic interplay in CRC, thereby complementing the existing theoretical framework concerning microbial regulation by the host genetic background. Full article

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

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3 pages, 149 KB

Open AccessEditorial

New Analytical Techniques and Applications of Metabolomics and Lipidomics

by Chunxiu Hu, Xianzhe Shi and Xinyu Liu

Metabolites 2026, 16(1), 63; https://doi.org/10.3390/metabo16010063 - 11 Jan 2026

Viewed by 281

Abstract

Metabolomics and lipidomics have emerged as essential tools in systems biology, providing comprehensive insights into small-molecule metabolites and lipids within biological systems [...] Full article

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

12 pages, 1698 KB

Open AccessArticle

Enhancing Caffeic Acid Production in Escherichia coli Through Heterologous Enzyme Combinations and Semi-Rational Design

by Qing Luo, Weihao Wang, Qingjing Huang, Chuan Wang, Lixiu Yan, Jun Kang, Jiamin Zhang and Jie Cheng

Metabolites 2026, 16(1), 62; https://doi.org/10.3390/metabo16010062 - 9 Jan 2026

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Abstract

Background/Objectives: Caffeic acid is a hydroxycinnamic acid that has a wide range of applications in the medical field. The synthesis of caffeic acid using microbial fermentation technology is an environmentally friendly method. Methods: By engaging various enzymes, specifically 4-hydroxyphenylacetate 3-monooxygenase (HpaB), sourced from [...] Read more.

Background/Objectives: Caffeic acid is a hydroxycinnamic acid that has a wide range of applications in the medical field. The synthesis of caffeic acid using microbial fermentation technology is an environmentally friendly method. Methods: By engaging various enzymes, specifically 4-hydroxyphenylacetate 3-monooxygenase (HpaB), sourced from diverse bacterial strains, we successfully engineered a functional version of this enzyme within Escherichia coli, enabling the production of caffeic acid. In addition to the two common tyrosine ammonia lyases (TAL) and HpaC, different combinations of HpaB demonstrated varying abilities in converting the substrate L-tyrosine into the desired product, caffeic acid. Results: Under shake-flask culture conditions, the highest yield of caffeic acid was achieved with an enzyme mixture containing HpaB from Escherichia coli, reaching 75.88 mg/L. Enhancing the activity of the rate-limiting enzyme through engineering could potentially increase caffeic acid titer. This study aims to conduct a semi-rational design of HpaB through structure-based approaches to screen for mutants that can enhance the production of caffeic acid. Initially, the predicted three-dimensional structure of HpaB was generated using AlphaFold2, and subsequent analysis was conducted to pinpoint the critical mutation sites within the substrate-binding pocket. Five key amino acid residues (R113, Y117, H155, S210 and Y461) located in the vicinity of the flavin adenine dinucleotide binding domain in HpaB from Escherichia coli could be instrumental in modulating enzyme activity. Subsequently, the mutant S210G/Y117A was obtained by iterative saturation mutagenesis, which increased the titer of caffeic acid by 1.68-fold. The caffeic acid titer was further improved to 2335.48 mg/L in a 5 L fermenter. The findings show that the yield of caffeic acid was significantly enhanced through the integration of semi-rational design and fermentation process optimization. Full article

(This article belongs to the Special Issue SynBio-Driven Metabolic Engineering: From Novel Tools to Real-World Applications)

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26 pages, 3472 KB

Open AccessArticle

Changes in the Metabolome of Different Tissues in Response to Streptozotocin Diabetes and Mildronate Exposure: A Metabolomic Assessment

by David Hauton, Dragana Savic, John Walsby-Tickle, Damian Tyler and James S. O. McCullagh

Metabolites 2026, 16(1), 61; https://doi.org/10.3390/metabo16010061 - 9 Jan 2026

Viewed by 315

Abstract

Background: Uncontrolled diabetes is characterised by a loss of blood glucose control and increased oxidation of fatty acids to produce ATP. Use of metabolic inhibitors to blunt fatty acid oxidation and restore glucose metabolism is a poorly studied intervention for diabetes. Methods: [...] Read more.

Background: Uncontrolled diabetes is characterised by a loss of blood glucose control and increased oxidation of fatty acids to produce ATP. Use of metabolic inhibitors to blunt fatty acid oxidation and restore glucose metabolism is a poorly studied intervention for diabetes. Methods: Steptozotocin-induced diabetes was developed in Wistar male rats. A subset was supplemented with mildronate (100 mg/kg—14 days). Exploiting liquid chromatography-mass spectrometry for workflows including ion exchange-, C18-reverse phase- and HILIC-based chromatography methods, metabolite levels were quantified in plasma liver and brain tissue. Using both untargeted and targeted metabolomic analysis changes to the global tissue metabolome and individual metabolic pathways were estimated. Results: We document that an inhibitor of carnitine synthesis, mildronate, decreased plasma (50% p < 0.01) carnitine abundance and decreased plasma glucose concentration by one-third compared to streptozotocin (STZ)-treated rats (p < 0.001). Targeted metabolomic analysis of the liver showed decreased alpha-ketoglutarate abundance (35% p < 0.05) by STZ diabetes that was further decreased following mildronate treatment (50% p < 0.05). For both beta-hydroxybutyrate and succinate levels, STZ diabetes increased hepatic abundance by 50% (p < 0.05 for both), which was restored to control levels by mildronate (p < 0.05 for both). In contrast, brain TCA intermediate abundances were unaffected by either STZ diabetes or mildronate (NS for all). STZ diabetes also decreased abundance of pentose phosphate pathway (PPP) metabolites in the liver (glucose-6-phosphate, 6-phosphogluconolactone, 6-phosphogluconate 50% for all; p < 0.05), which was not restored by mildronate treatment. However, brain PPP metabolite abundance was unchanged by STZ diabetes or mildronate (NS for all). However, mildronate treatment did not affect the increased abundance of brain sorbitol, sorbitol-6-phosphate and glucose-6-phosphate as a result of STZ diabetes. Conclusions: Together, these observations highlight the potential role that metabolic inhibitors, like mildronate, may play in restoring blood glucose for diabetic patients, without a direct effect of tissues that represent obligate consumers of glucose (e.g., brain) whilst manipulating fat oxidation in tissues such as the liver. Full article

(This article belongs to the Section Cell Metabolism)

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41 pages, 1893 KB

Open AccessReview

Mitochondrial Redox Vulnerabilities in Triple-Negative Breast Cancer: Integrative Perspectives and Emerging Therapeutic Strategies

by Alfredo Cruz-Gregorio

Metabolites 2026, 16(1), 60; https://doi.org/10.3390/metabo16010060 - 9 Jan 2026

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Abstract

Breast cancer is a significant public health concern, with triple-negative breast cancer (TNBC) being the most aggressive subtype characterized by considerable heterogeneity and the absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression. Currently, there [...] Read more.

Breast cancer is a significant public health concern, with triple-negative breast cancer (TNBC) being the most aggressive subtype characterized by considerable heterogeneity and the absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression. Currently, there are no practical alternatives to chemotherapy, which is associated with a poor prognosis. Therefore, developing new treatments for TNBC is an urgent need. Reactive oxygen species (ROS) and redox adaptation play central roles in TNBC biology. Targeting the redox state has emerged as a promising therapeutic approach, as it is vital to the survival of tumors, including TNBC. Although TNBC does not produce high levels of ROS compared to ER- or PR-positive breast cancers, it relies on mitochondria and oxidative phosphorylation (OXPHOS) to sustain ROS production and create an environment conducive to tumor progression. As a result, novel treatments that can modulate redox balance and target organelles essential for redox homeostasis, such as mitochondria, could be promising for TNBC, an area not yet reviewed in the current scientific literature, thus representing a critical gap. This review addresses that gap by synthesizing current evidence on TNBC biology and its connections to redox state and mitochondrial metabolism, with a focus on innovative strategies such as metal-based compounds (e.g., copper, gold), redox nanoparticles that facilitate anticancer drug delivery, mitochondrial-targeted therapies, and immunomodulatory peptides like GK-1. By integrating mechanistic insights into the redox state with emerging therapeutic approaches, I aim to highlight new redox-centered opportunities to improve TNBC treatments. Moreover, this review uniquely integrates mitochondrial metabolism, redox imbalance, and emerging regulated cell-death pathways, including ferroptosis, cuproptosis, and disulfidptosis, within the context of TNBC metabolic heterogeneity, highlighting translational vulnerabilities and subtype-specific therapeutic opportunities. Full article

(This article belongs to the Special Issue Mitochondrial Metabolism, Redox State and Immunology in Cancer)

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Metabolites, Volume 16, Issue 1 (January 2026) – 89 articles

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