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Impact of Short-Term Liraglutide Therapy on Non-Invasive Markers of Liver Fibrosis in Patients with MASLD
The Long-Term Impact of Preterm Birth on Metabolic Bone Profile and Bone Mineral Density in Childhood
Prediagnostic Plasma Metabolomic Profiles Using NMR for Exfoliation Glaucoma Among US Health Professionals
Human Metabolism of Sirolimus Revisited

Journal Description

Metabolites

Metabolites is an international, peer-reviewed, open access journal of metabolism and metabolomics, published monthly online by MDPI.

Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, Embase, CAPlus / SciFinder, and other databases.
Journal Rank: JCR - Q2 (Biochemistry and Molecular Biology) / CiteScore - Q2 (Endocrinology, Diabetes and Metabolism)
Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 14.4 days after submission; acceptance to publication is undertaken in 3.6 days (median values for papers published in this journal in the first half of 2025).
Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.

Impact Factor: 3.7 (2024); 5-Year Impact Factor: 4.1 (2024)

Imprint Information Journal Flyer Open Access ISSN: 2218-1989

Latest Articles

15 pages, 2026 KB

Open AccessArticle

Multiparametric Evaluation of Drug-Induced Acute Kidney Injury Using Preclinical 7T Magnetic Resonance Imaging in Rat Models

by Tomohiro Natsuyama, Junpei Ueda, Isamu Yabata, Reika Sawaya, Koji Itagaki and Shigeyoshi Saito

Metabolites 2025, 15(9), 593; https://doi.org/10.3390/metabo15090593 (registering DOI) - 7 Sep 2025

Objectives: Acute kidney injury (AKI), characterized by a rapid decline in renal function, affects approximately 13 million new patients annually. Adverse drug reactions have increasingly contributed to renal injury, underscoring the need for methods to directly and quantitatively evaluate renal injury. Methods [...] Read more.

Objectives: Acute kidney injury (AKI), characterized by a rapid decline in renal function, affects approximately 13 million new patients annually. Adverse drug reactions have increasingly contributed to renal injury, underscoring the need for methods to directly and quantitatively evaluate renal injury. Methods: We utilized a drug-induced AKI model using gentamicin overdose, combining 7T magnetic resonance imaging (MRI) relaxation time measurements and blood tests to evaluate pathophysiological changes from multiple perspectives. Ten-week-old Wistar rats received intraperitoneal administration of gentamicin (80 mg/kg) for 7 days. Under respiratory synchronization, T₁, T_1rho, T₂, and T₂* maps were obtained in six control and five disease model rats. Relaxation times in the cortex and medulla were measured separately and compared between groups. Results: Blood tests evaluated Na, K, Cl, blood urea nitrogen, creatinine, and hematocrit levels. Renal tissue damage was evaluated via hematoxylin and eosin (HE) staining. Relaxation time showed significant changes in the cortex, especially in the T₁ (control: 1156.7 ± 140.0, gentamicin: 1550.4 ± 162.1, p < 0.05) and T₂ (control: 42.9 ± 3.4, gentamicin: 53.4 ± 4.8, p < 0.05) maps. Blood tests revealed significant increases in Na, blood urea nitrogen, creatinine, and hematocrit levels in the disease model. A correlation was observed between the T1 map of the renal cortex and each substance. HE staining revealed tissue damage due to renal injury. Conclusions: Multiparametric MRI facilitates quantitative and multidimensional evaluation of renal pathological changes caused by drug-induced AKI. Full article

(This article belongs to the Special Issue Integration of Emerging Technologies in Metabolite Analysis)

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16 pages, 3103 KB

Open AccessArticle

Plasma Lipidomic Alterations in Fontan Circulation Reflect Cardiovascular Functional Reserve

by Arun Surendran, Amir Ravandi and Ashish H. Shah

Metabolites 2025, 15(9), 592; https://doi.org/10.3390/metabo15090592 (registering DOI) - 7 Sep 2025

Background: Fontan circulation is associated with impaired cardiac output, reduced exercise capacity, and systemic metabolic stress. However, the underlying lipidomic alterations remain poorly defined. Methods: Using targeted mass spectrometry, we analyzed 291 lipid species in fasting plasma samples from 20 adults with Fontan [...] Read more.

Background: Fontan circulation is associated with impaired cardiac output, reduced exercise capacity, and systemic metabolic stress. However, the underlying lipidomic alterations remain poorly defined. Methods: Using targeted mass spectrometry, we analyzed 291 lipid species in fasting plasma samples from 20 adults with Fontan circulation and 20 age- and sex-matched healthy controls. Results: Forty-eight lipids were significantly altered between groups (p < 0.05), including reductions in total lysophosphatidylcholines (LPC) and total ether-linked LPC [LPC(O)] and elevations in total phosphatidylserines (PS). Notably, LPC(O-22:1) and LPC(O-20:0) were decreased, while PS 40:5 was elevated, with several of these species demonstrating strong correlations (|r| > 0.5, p < 0.001) with the stroke index, cardiac index, and VO₂max. These three lipid species also showed excellent capability in discriminating Fontan patients from healthy controls (AUC > 0.78). Correlation network and pathway enrichment analyses revealed tightly coordinated lipid clusters containing LPC/LPC(O), PE, and PS species as central features of dysregulated Fontan metabolism. Conclusions: These exploratory findings highlight coordinated lipid alterations associated with impaired cardiovascular reserve in Fontan patients. While based on unadjusted p-values and therefore being hypothesis-generating, they provide novel insight into the metabolic landscape of Fontan physiology and warrant validation in larger, independent cohorts. Full article

(This article belongs to the Special Issue Lipid Metabolism Dysregulation in Metabolic Disorders: Unraveling the Molecular Complexity)

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25 pages, 2807 KB

Open AccessArticle

A Holistic Approach to Metabolic Health Assessment—Analysis of Bioimpedance, Blood, and Saliva Biochemistry in Population Studies—A Pilot Study

by Aleksandra Stawiarska, Renata Francik, Anna Mikulec, Marek Zborowski, Urszula Cisoń-Apanasewicz, Ryszard Gajdosz, Iwona Zaczyk, Halina Potok, Agnieszka Radom, Dorota Ogonowska and Elżbieta Rafa

Metabolites 2025, 15(9), 591; https://doi.org/10.3390/metabo15090591 (registering DOI) - 7 Sep 2025

Background: Metabolic syndrome is a multifaceted condition involving lipid and carbohydrate metabolism disorders and hypertension, increasing the risk of cardiovascular disease and type 2 diabetes. Accurate diagnosis and prevention require an interdisciplinary approach that includes both traditional lab tests and modern, non-invasive health [...] Read more.

Background: Metabolic syndrome is a multifaceted condition involving lipid and carbohydrate metabolism disorders and hypertension, increasing the risk of cardiovascular disease and type 2 diabetes. Accurate diagnosis and prevention require an interdisciplinary approach that includes both traditional lab tests and modern, non-invasive health assessments. Methods: This study aimed to evaluate metabolic health in adults from the Małopolska Voivodeship by analyzing the relationships between obesity indicators (BMI, waist circumference) and anthropometric, blood, and salivary biomarkers. Sixty-three participants (36 women, 27 men) aged 40–71 underwent body composition analysis (InBody 770), anthropometric measurements, and biochemical tests of blood and saliva. Assessed parameters included body composition (BMI, BFM, FFM, SMM, PBF, VFA, PA), blood pressure, blood biomarkers (glucose, TG, LDL, HDL, HbA1c, insulin, cortisol), and salivary markers (FRAP, DPPH, urea, amylase activity, protein content, pH, buffering capacity). Results: The results showed a strong correlation between body composition and biochemical markers, but the results of the analyzed salivary biomarkers were inconclusive and, in some cases, contradictory to the findings of other authors. Conclusions: Fat mass, cell integrity, and diastolic pressure were key determinants of waist circumference. Our research confirms the validity of using combined diagnostics, bioimpedance, and blood analysis for a comprehensive assessment of metabolic health and indicates the direction for further research using salivary biomarkers. A holistic approach improves risk assessment and strengthens preventive and therapeutic strategies. However, our pilot study showed that the research requires a larger sample size, especially in order to draw representative conclusions regarding salivary biomarkers and their relationship to metabolic health. Full article

(This article belongs to the Special Issue Metabolic Changes in Diet-Mediated Inflammatory Diseases)

12 pages, 757 KB

Open AccessArticle

The Role of Visfatin/NAMPT in the Pathogenesis of Psoriasis

by Mateusz Matwiejuk, Agnieszka Kulczyńska-Przybik, Bartłomiej Łukaszuk, Hanna Myśliwiec, Piotr Myśliwiec, Adrian Chabowski, Barbara Mroczko and Iwona Flisiak

Metabolites 2025, 15(9), 590; https://doi.org/10.3390/metabo15090590 (registering DOI) - 6 Sep 2025

Introdcution: Psoriasis is a complex, chronic, immunologically, inflammatory, and environmentally mediated disease which may affect not only the skin, but also nails, and joints. This dermatosis is known for hyperproliferation, parakeratosis, dysregulated differentiation of keratinocytes, lack of granular layer of the skin and [...] Read more.

Introdcution: Psoriasis is a complex, chronic, immunologically, inflammatory, and environmentally mediated disease which may affect not only the skin, but also nails, and joints. This dermatosis is known for hyperproliferation, parakeratosis, dysregulated differentiation of keratinocytes, lack of granular layer of the skin and impaired apoptosis of keratinocytes. Methods Fifty patients with psoriasis and twenty-eight healthy individuals were enrolled in the study. Serum samples were collected both from the psoriatic patients and patients with an inguinal hernia, who served as the control group. Visfatin levels were measured by enzyme-linked immunosorbent assay. Various proteins have been well described as key contributors to the complex pathogenesis of psoriasis. Results: In our study, we found that serum visfatin levels were significantly higher in the psoriatic group compared to the control group. Interestingly, we observed a positive and statistically significant correlation between serum visfatin levels and HDL-C concentrations in patients with psoriasis. Discussion: An elevated HDL-C level in psoriatic serum might be a sign of a compensatory response to systemic inflammation, or a marker of metabolic dysfunction, or an early prognostic signal in disease progression. However, no significant correlations were found between visfatin levels and the Psoriasis Area and Severity Index (PASI) score. Conclusions: In summary, our findings indicate that visfatin levels are significantly altered in the serum of patients with psoriasis compared to the control group and it could be a pivotal point of understanding the pathogenesis of psoriasis and a new way of implementing therapeutic procedures. Full article

(This article belongs to the Special Issue Psoriasis and Metabolic Syndrome)

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53 pages, 3155 KB

Open AccessReview

The Power of Lignans: Plant Compounds with Multifaceted Health-Promoting Effects

by Marta Burgberger, Justyna Mierziak, Beata Augustyniak, Wioleta Wojtasik and Anna Kulma

Metabolites 2025, 15(9), 589; https://doi.org/10.3390/metabo15090589 - 4 Sep 2025

Lignans are plant-derived biphenolic compounds with multiple hydroxyl groups, which, upon ingestion, are metabolized by gut microbiota into enterolignans—enterolactone and enterodiol. These mammalian metabolites exhibit structural similarity to estradiol, enabling lignans to modulate hormonal balance and exert estrogen-like effects. A growing body of [...] Read more.

Lignans are plant-derived biphenolic compounds with multiple hydroxyl groups, which, upon ingestion, are metabolized by gut microbiota into enterolignans—enterolactone and enterodiol. These mammalian metabolites exhibit structural similarity to estradiol, enabling lignans to modulate hormonal balance and exert estrogen-like effects. A growing body of evidence highlights their broad spectrum of health-promoting properties, including antioxidant, anti-inflammatory, and hormone-regulating effects. Lignans have shown potential in alleviating menopausal symptoms, preventing estrogen-dependent cancers, and mitigating conditions such as cardiovascular disease, diabetes, and metabolic syndrome. Additionally, their antimicrobial activity against bacteria, fungi, and viruses is being increasingly recognized. This review provides a comprehensive and up-to-date synthesis of current knowledge. It uniquely integrates the latest insights into lignan biosynthesis, gut microbiota-mediated metabolism, and clinically relevant outcomes. Importantly, this review incorporates recent findings from prospective cohort studies and meta-analyses and sheds light on emerging therapeutic applications, including antifungal activity—an area rarely covered in earlier literature. By presenting a holistic perspective, this review advances our understanding of lignans as multifaceted compounds with significant potential in preventive and therapeutic health strategies. Full article

(This article belongs to the Section Plant Metabolism)

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22 pages, 1349 KB

Open AccessArticle

Fruit Quality Characterization and Comprehensive Evaluation of 30 Chionanthus retusus Accessions

by Muge Niu, Jinnan Wang, Baoqiang Huang, Hui Tian, Maotong Sun, Jihong Li, Jing Ren and Cuishuang Liu

Metabolites 2025, 15(9), 588; https://doi.org/10.3390/metabo15090588 - 3 Sep 2025

Objectives: Research on kernel oil content and secondary metabolites in Chionanthus retusus was conducted to evaluate its potential as an oil crop. Methods: Fruits from 30 individual trees were collected to analyze morphological traits, oil content, and the composition of fatty acids, phytosterols, [...] Read more.

Objectives: Research on kernel oil content and secondary metabolites in Chionanthus retusus was conducted to evaluate its potential as an oil crop. Methods: Fruits from 30 individual trees were collected to analyze morphological traits, oil content, and the composition of fatty acids, phytosterols, and tocopherols. Correlation, cluster, and principal component analyses were performed on the resulting data. Results: The mean fresh fruit weight, dry fruit weight, dry kernel weight, and kernel percentage were 77.02 g, 24.33 g, 12.22 g, and 51.14%, respectively. Kernel oil content averaged 35.83%, comprising seven fatty acids with oleic acid as the predominant component. Total phytosterol content reached 279.58 mg/100 g oil, with β-sitosterol being the major constituent among seven detected sterols. Total tocopherols were 571.13 μg/g oil, dominated by γ-tocopherol, indicating a potential antioxidant capacity. These components may reduce the demand for synthetic antioxidant food additives. A significant positive correlation was observed between kernel dry weight and oil content (r = 0.760, p < 0.01), supporting kernel dry weight as a key phenotypic indicator for high-oil breeding. Fruit quality traits did not cluster by geographic origin, whereas secondary metabolite profiles showed origin-based clustering. For breeding oil-producing C. retusus, select seeds with superior provenances based on secondary metabolites and cultivate them under optimal conditions to develop varieties with plump fruit, thereby boosting yield. Accessions WS-4 and WS-3 were identified as promising germplasm resources for oil production. Conclusions: The abundant oleic acid, β-sitosterol, and γ-tocopherol in C. retusus kernels highlight its potential as a woody oilseed crop. Full article

(This article belongs to the Special Issue LC-MS/MS Analysis for Plant Secondary Metabolites, 2nd Edition)

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21 pages, 1109 KB

Open AccessArticle

Herbal Weight Loss Supplements Induce Metabolomic In Vitro Changes Indicative of Oxidative Stress

by Emily C. Davies, Garth L. Maker, Ian F. Musgrave and Samantha Lodge

Metabolites 2025, 15(9), 587; https://doi.org/10.3390/metabo15090587 - 1 Sep 2025

Background/Objectives: The prevalence of obesity continues to rise globally, and with this an increase in the use of herbal weight loss supplements (WLS). At present, there is limited evidence to support the efficacy and safety of WLS, and there have been growing [...] Read more.

Background/Objectives: The prevalence of obesity continues to rise globally, and with this an increase in the use of herbal weight loss supplements (WLS). At present, there is limited evidence to support the efficacy and safety of WLS, and there have been growing reports of adverse events associated with their use. We aimed to determine those WLS that caused toxicity in vitro and to use ¹H nuclear magnetic spectroscopy (NMR) to examine the metabolomic changes induced by these WLS in human hepatic and intestinal cells. Materials and Methods: This study used in vitro methods and ¹H NMR spectroscopy to analyse the metabolomic changes in vitro of WLS available for purchase in Australia. Ten WLS were selected, nine WLS caused significant toxicity in HepG2 human liver cells, and of these, six met the criteria for ¹H NMR analysis, which was based on a 25–50% reduction in cell viability. Results: All 10 WLS caused a significant reduction in viability of Caco-2 human intestinal cells, with seven selected for metabolic profiling. Orthogonal partial least squares discriminant analysis (O-PLS-DA) of ¹H NMR spectral data was used to characterise the metabolites that differed between the untreated and treated cells and the fold changes of the metabolites were determined. The results showed alterations to key metabolites such as amino acids, glucose, carboxylic acids, and amines in all treatment groups compared to untreated controls across both cell lines. Conclusions: Collectively, these biochemical changes represent disturbances to intracellular proteins, energy metabolism, and membrane lipids suggestive of oxidative stress. This study highlights the need for further investigations into the actions of these WLS in vivo, and, as these products were regulated by the Therapeutic Goods Administration (TGA) at the time of purchase, this study suggests improved pre-market screening to ensure consumer health is protected. Full article

(This article belongs to the Special Issue Metabolic Signatures in Human Health and Disease)

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12 pages, 424 KB

Open AccessReview

Investigating the Utility of Dopamine in Agricultural Practices: A Review

by Wael M. Semida, Kareem Khalafallah Abdeltawab, Ashraf Sh. Osman and Mohamed H. H. Roby

Metabolites 2025, 15(9), 586; https://doi.org/10.3390/metabo15090586 - 31 Aug 2025

Background/Objectives: Dopamine (DA), a chemical commonly associated with neuroscience and human physiology, has been the subject of growing interest in the field of agriculture due to its potential applications. Methods: This comprehensive review examines the multifaceted role of dopamine in agricultural [...] Read more.

Background/Objectives: Dopamine (DA), a chemical commonly associated with neuroscience and human physiology, has been the subject of growing interest in the field of agriculture due to its potential applications. Methods: This comprehensive review examines the multifaceted role of dopamine in agricultural practices, elucidating its chemical characteristics, biological activities, and diverse applications. The review examines the chemical properties and physiological functions of dopamine in plants, highlighting the unique characteristics that make it suitable for agricultural applications. A significant portion of the review is dedicated to analyzing the biological activities of dopamine, particularly its antioxidant properties, and exploring the underlying mechanisms. The review also delves into the potential of dopamine to enhance crop growth, yield, and quality and investigates the influence of dopamine on plant physiology and metabolism. Results: Furthermore, the review provides a forward-looking perspective on the prospects of dopamine in agriculture, identifying emerging trends and areas of innovation that hold promise for sustainable and resilient farming systems. Conclusions: In summary, this review consolidates the current knowledge surrounding dopamine’s potential in agriculture, underscoring its versatility as a natural tool for growth enhancement and environmental sustainability, and offering valuable insights for researchers, practitioners, and policymakers seeking innovative approaches to address the challenges of modern agriculture. Full article

(This article belongs to the Section Plant Metabolism)

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40 pages, 14652 KB

Open AccessArticle

Ecballium elaterium (L.) A. Rich. (Squirting Cucumber) Plants Cultured Under Different Temperatures: Anatomical and Biochemical Modifications of Their Leaves and the Bioactivity of Leaf Extracts

by Aikaterina L. Stefi, Maria Chalkiadaki, Emily Bashari, Konstantina Mitsigiorgi, Paweł Szczeblewski, Danae Papageorgiou, Dimitrios Gkikas, Dido Vassilacopoulou, Nikolaos S. Christodoulakis and Maria Halabalaki

Metabolites 2025, 15(9), 585; https://doi.org/10.3390/metabo15090585 - 31 Aug 2025

Background/Objectives: Ecballium elaterium is a widely distributed species and is one of the earliest recorded in traditional medicine. With global temperatures rising, this study aimed to investigate the changes in E. elaterium plantlets subjected to thermal stress. The goal was to understand how [...] Read more.

Background/Objectives: Ecballium elaterium is a widely distributed species and is one of the earliest recorded in traditional medicine. With global temperatures rising, this study aimed to investigate the changes in E. elaterium plantlets subjected to thermal stress. The goal was to understand how thermal stress affects morphology, physiology, and bioactive metabolite production, both for ecological adaptation and potential therapeutic applications. Methods: Seedlings were cultivated under controlled conditions and subjected to either the control temperature (22 °C) or the heat stress temperature (35 °C) for one week. Morphological and anatomical traits were assessed, along with physiological parameters such as chlorophyll content, malondialdehyde (MDA), hydrogen peroxide (H₂O₂), L-proline, soluble sugars, and total phenolic content. Methanolic leaf extracts from both groups were analyzed via LC-HRMS/MS and examined in vitro for cytotoxic activity against three human cancer cell lines: MCF-7 (breast), DU-145 (prostate), and SH-SY5Y (neuroblastoma). Results: Heat stress reduced dry mass and stomatal density but increased the diameter of the root transition zone, indicating anatomical adaptation. Leaves exhibited elevated oxidative stress markers and altered metabolite accumulation, while the roots showed a more integrated stress response. LC-HRMS/MS profiling revealed significant shifts in Cucurbitacin composition. Extracts from heat-stressed plants displayed stronger cytotoxicity, particularly toward DU-145 and SH-SY5Y cells, correlating with higher levels of glycosylated Cucurbitacins. Conclusions: E. elaterium demonstrates organ-specific thermotolerance mechanisms, with heat stress enhancing the production of bioactive metabolites. These stress-induced phytochemicals, especially Cucurbitacins, hold promise for future cancer research and therapeutic applications. Full article

(This article belongs to the Section Plant Metabolism)

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17 pages, 3479 KB

Open AccessArticle

Selective Knockdown of Ceramide Synthases Reveals Opposite Roles of Different Ceramide Species in Cardiac Homeostasis

by Alexandra M. Wiley, Melissa A. Krueger, Jessica O. Becker, Matthew Karasu, Nona Sotoodehnia, Jason G. Umans, Andrew N. Hoofnagle, Sina A. Gharib, Rheem A. Totah and Rozenn N. Lemaitre

Metabolites 2025, 15(9), 584; https://doi.org/10.3390/metabo15090584 - 31 Aug 2025

Background/Objectives: Sphingolipids are a class of lipids that play important structural and functional roles in the cell. Specific ceramide species are distinguishable through the fatty acid that is acylated to the sphingosine backbone, leading to distinct biological activities. Generally, long-chain (LC) ceramides (16:0 [...] Read more.

Background/Objectives: Sphingolipids are a class of lipids that play important structural and functional roles in the cell. Specific ceramide species are distinguishable through the fatty acid that is acylated to the sphingosine backbone, leading to distinct biological activities. Generally, long-chain (LC) ceramides (16:0 and 18:0) drive metabolic dysfunction resulting in the progression of different disease states, while very long-chain (VLC) ceramides (22:0 and 24:0) are thought to be either beneficial against disease progression or benign. In this study, we sought to alter the cellular composition of LC and VLC ceramides in ventricular HCMs to investigate how alterations in these lipids can affect the transcriptome of otherwise healthy HCMs. Methods: Here, we used specific siRNA to knockdown the ceramide synthases responsible for the production of LC and VLC ceramides in ventricular HCMs and investigated the changes in the transcriptome of HCMs with CERS2 or CERS5/6 silenced compared to control conditions. Results: Knocking down CERS2 led to an increase in cell death as well as widespread reductions in cellular VLC sphingolipids. Additionally, we demonstrated that VLC sphingolipid species may play a protective role in maintaining cardiovascular function and that reducing these lipids may contribute to cardiac dysfunction. Similarly, knocking down CERS5 and CERS6 led to reduced LC ceramides and also resulted in profound changes in gene transcription. Interestingly, multiple genes and pathways were affected in the opposite direction when compared to the changes observed with the CERS2 knockdown. Conclusions: Taken together, our results suggest pathways through which VLC ceramides may contribute to cardiac protection, and pathways where LC ceramides may promote HCM stress and the development of cardiac disease. Full article

(This article belongs to the Special Issue Lipid Biomarkers and Cardiometabolic Diseases—2nd Edition)

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13 pages, 671 KB

Open AccessReview

Metabolic Signatures in Lean MASLD: Current Insights and Future Directions

by Ambrin Farizah Babu

Metabolites 2025, 15(9), 583; https://doi.org/10.3390/metabo15090583 - 31 Aug 2025

Lean metabolic dysfunction-associated steatotic liver disease (lean MASLD) challenges longstanding views that link hepatic steatosis primarily to obesity. Emerging as a distinct and under-recognized clinical entity, lean MASLD affects individuals with a normal body mass index (BMI), yet carries risks of cardiovascular disease, [...] Read more.

Lean metabolic dysfunction-associated steatotic liver disease (lean MASLD) challenges longstanding views that link hepatic steatosis primarily to obesity. Emerging as a distinct and under-recognized clinical entity, lean MASLD affects individuals with a normal body mass index (BMI), yet carries risks of cardiovascular disease, hepatocellular carcinoma, and liver-related mortality comparable to obesity-associated MASLD. The absence of overt metabolic dysfunction complicates diagnosis, revealing critical limitations in current screening frameworks centered on BMI. This review synthesizes evolving clinical insights and epidemiological trends in lean MASLD, and delineates its unique pathophysiological mechanisms. Recent advances in metabolomics have uncovered disease-specific disruptions in lipid and amino acid metabolism, bile acid signaling, and gut microbiota-derived metabolites. By integrating evidence from metabolic, genetic, and epigenetic domains, we identified promising biomarkers, and therapeutic targets that may support earlier detection and precision-guided treatment strategies. Full article

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

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18 pages, 1532 KB

Open AccessArticle

Metabolomic Signatures and Predictive Utility of LOXL1-Associated Genetic Risk Scores for Exfoliation Syndrome/Glaucoma in US Cohorts

by Namuunaa Juramt, Oana A. Zeleznik, Louis R. Pasquale, Janey L. Wiggs and Jae H. Kang

Metabolites 2025, 15(9), 582; https://doi.org/10.3390/metabo15090582 - 30 Aug 2025

Background: Exfoliation syndrome (XFS) is a form of deleterious ocular aging mediated by genetic and environmental factors that frequently produces glaucoma (XFG). We aimed to develop a genetic risk score (GRS), assess its clinical utility, and identify metabolites/metabolite classes associated with a high [...] Read more.

Background: Exfoliation syndrome (XFS) is a form of deleterious ocular aging mediated by genetic and environmental factors that frequently produces glaucoma (XFG). We aimed to develop a genetic risk score (GRS), assess its clinical utility, and identify metabolites/metabolite classes associated with a high GRS. Methods: For 39,472 Nurses’ Health Studies (NHS, 1980–2018; NHS2, 1989–2019) and Health Professionals Follow-up Study (1986–2018) participants aged ≥ 40 years reporting eye exams and no baseline glaucoma, we formed an eight-single nucleotide polymorphism Genetic Risk Score (GRS8) using loci with genome-wide associations with XFS. We estimated relative risks (RR) for incident XFG suspect (XFGS)/XFG (n = 118 cases) and Harrell’s C statistics. Among 7547 participants with plasma metabolites measured via liquid chromatography-mass spectrometry, we evaluated the relation between GRS8 and 427 individual metabolites and 20 metabolite classes, adjusting for multiple comparisons. Results: Higher GRS8 was associated with XFGS/XFG (GRS8 RR_{Quintile(Q)5vs.Q1} = 3.82, 95% CI: 1.76, 8.29). GRS8 significantly (p = 0.04) improved model prediction from C-index of 88% (95% CI: 0.84, 0.92) to 93% (95% CI: 0.91, 0.95) when added to a basic risk model including age, sex, period at risk, intraocular pressure, and glaucoma family history. Metabolite class analyses revealed positive associations of bile acids and inverse associations of fatty acyls with GRS8 (adjusted p < 0.001). Conclusions: XFS GRS8 improved XFGS/XFG prediction, and a higher XFS GRS8 was associated with altered levels of fatty acyl and bile acid metabolite classes. Full article

(This article belongs to the Special Issue Metabolomics of the Eye and Adnexa)

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41 pages, 2467 KB

Open AccessReview

Crosstalk Between Skeletal Muscle and Proximal Connective Tissues in Lipid Dysregulation in Obesity and Type 2 Diabetes

by Nataša Pollak, Efua Gyakye Janežič, Žiga Šink and Chiedozie Kenneth Ugwoke

Metabolites 2025, 15(9), 581; https://doi.org/10.3390/metabo15090581 - 30 Aug 2025

Background/Objectives: Obesity and type 2 diabetes mellitus (T2DM) profoundly disrupt lipid metabolism within local microenvironments of skeletal muscle and its associated connective tissues, including adipose tissue, bone, and fascia. However, the role of local communication between skeletal muscle and its proximal connective tissues [...] Read more.

Background/Objectives: Obesity and type 2 diabetes mellitus (T2DM) profoundly disrupt lipid metabolism within local microenvironments of skeletal muscle and its associated connective tissues, including adipose tissue, bone, and fascia. However, the role of local communication between skeletal muscle and its proximal connective tissues in propagating metabolic dysfunction is incompletely understood. This narrative review synthesizes current evidence on these local metabolic interactions, highlighting novel insights and existing gaps. Methods: We conducted a comprehensive literature analysis of primary research published in the last decade, sourced from PubMed, Web of Science, and ScienceDirect. Studies were selected for relevance to skeletal muscle, adipose tissue, fascia, and bone lipid metabolism in the context of obesity and T2DM, with emphasis on molecular, cellular, and paracrine mechanisms of local crosstalk. Findings were organized into thematic sections addressing physiological regulation, pathological remodeling, and inter-organ signaling pathways. Results: Our synthesis reveals that local lipid dysregulation in obesity and T2DM involves altered fatty acid transporter dynamics, mitochondrial overload, fibro-adipogenic remodeling, and compartment-specific adipose tissue dysfunction. Crosstalk via myokines, adipokines, osteokines, bioactive lipids, and exosomal miRNAs integrates metabolic responses across these tissues, amplifying insulin resistance and lipotoxic stress. Emerging evidence highlights the underappreciated roles of fascia and marrow adipocytes in regional lipid handling. Conclusions: Collectively, these insights underscore the pivotal role of inter-tissue crosstalk among skeletal muscle, adipose tissue, bone, and fascia in orchestrating lipid-induced insulin resistance, and highlight the need for integrative strategies that target this multicompartmental network to mitigate metabolic dysfunction in obesity and T2DM. Full article

(This article belongs to the Special Issue Lipid Metabolism Disorders in Obesity)

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17 pages, 2407 KB

Open AccessArticle

Urine Metabolomics of Gout Reveals the Dynamic Reprogramming and Non-Invasive Biomarkers of Disease Progression

by Guizhen Zhu, Yuan Luo, Nan Su, Xiangyi Zheng, Zhusong Mei, Qiao Ye, Jie Peng, Peiyu An, Yangqian Song, Weina Luo, Hongxia Li, Guangyun Wang and Haitao Zhang

Metabolites 2025, 15(9), 580; https://doi.org/10.3390/metabo15090580 - 29 Aug 2025

Background/Objectives: Gout, a complex metabolic disorder of increasing global incidence, remains incompletely understood in its pathogenesis. Current diagnostic approaches exhibit significant limitations, including insufficient specificity and the requirement for invasive joint aspiration, highlighting the need for non-invasive, sensitive biomarkers for early detection. Methods: [...] Read more.

Background/Objectives: Gout, a complex metabolic disorder of increasing global incidence, remains incompletely understood in its pathogenesis. Current diagnostic approaches exhibit significant limitations, including insufficient specificity and the requirement for invasive joint aspiration, highlighting the need for non-invasive, sensitive biomarkers for early detection. Methods: Urine metabolites were extracted from 28 healthy controls, 13 asymptomatic hyperuricemia (HUA) patients, and 29 acute gouty arthritis (AGA) patients. The extracted metabolites were analyzed by UHPLC-MS/MS for untargeted metabolomics. Differential metabolites were screened by partial least squares discriminant analysis (PLS-DA) and volcano plot analysis. Pathway analysis determined the core disorder pathway of gout progression. Results: A total of 278 differential metabolites associated with gout progression were identified. The most pronounced metabolic alterations were observed between the AGA and control groups, indicative of substantial metabolic reprogramming during disease transition. Metabolic pathway analysis revealed four significantly dysregulated pathways: histidine metabolism, nicotinate and nicotinamide metabolism, phenylalanine metabolism, and tyrosine metabolism. Receiver operating characteristic (ROC) curve analysis revealed that three urine markers with high diagnostic efficacy—oxoamide, 3-methylindole, and palmitic acid—exhibited progressive alterations across the disease continuum. Conclusions: This metabolomics study identified core regulatory metabolites and newly discovered metabolic pathways underlying gout pathogenesis, along with novel urinary biomarkers capable of predicting HUA-to-AGA progression. The aberrant levels of key metabolites in the disordered pathway implicate neuroimmune dysregulation, energy metabolism disruption, and oxidative stress in gout pathogenesis. These findings provide new foundations and strategies for the daily monitoring and prevention of gout. Full article

(This article belongs to the Special Issue Metabolomics in Clinical Research: Advancing Precision Medicine Through the Analysis of Biological Samples)

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19 pages, 2480 KB

Open AccessArticle

Application of Organic Nanofibers to Boost Specialized Metabolite Production and Antioxidant Potential in Stevia rebaudiana In Vitro Cultures

by Maria Geneva, Antoaneta Trendafilova, Kamelia Miladinova-Georgieva, Mariana Sichanova, Daniela Tsekova, Viktoria Ivanova, Elisaveta Kirova and Maria Petrova

Metabolites 2025, 15(9), 579; https://doi.org/10.3390/metabo15090579 - 29 Aug 2025

Background: Potential advantages for improving plant growth, stress tolerance, and valuable metabolites generation are provided by the implementation of nanotechnology into plant biotechnology. A recently discovered technique with significant promise for agricultural practices is the use of biopolymer-based nanomaterials, like peptidomimetics, as insecticides, [...] Read more.

Background: Potential advantages for improving plant growth, stress tolerance, and valuable metabolites generation are provided by the implementation of nanotechnology into plant biotechnology. A recently discovered technique with significant promise for agricultural practices is the use of biopolymer-based nanomaterials, like peptidomimetics, as insecticides, growth regulators, and nutrient carriers. This study explores the impact of biopolymer-based organic nanofibers—specifically peptidomimetics formed through the self-assembly of L-valine and nicotinic acid (NA) (denoted as M6) on Stevia rebaudiana in vitro propagation and specialized metabolite production. The central hypothesis was that such nanofibers, particularly when used as hormone carriers, can beneficially influence plant morphology, physiology, and biochemistry, thereby promoting the synthesis of antioxidant compounds with therapeutic potential. Methods: The nanofibers were tested either alone (M6) or as carriers of the plant hormone indole-3-acetic acid (IAA) (M6+IAA), supplemented to the cultivation MS medium at variable concentrations (0, 1, 10, and 50 mg L⁻¹). Results: The results revealed that treatment with 10 mg L⁻¹ M6 significantly enhanced shoot growth parameters, including the highest fresh weight (0.249 g), mean shoot height (9.538 cm), shoot number (1.95), and micropropagation rate. Plants treated with M6 alone outperformed those treated with M6+IAA in terms of shoot growth, total soluble sugars, and steviol glycoside content. Conversely, M6+IAA treatment more effectively promoted root initiation, the increased accumulation of mono- and dicaffeoylquinic acids, and boosted antioxidant enzyme activity. Conclusions: These findings highlight the potential of organic nanofibers, both with and without hormone loading, as novel tools for optimizing micropropagation and metabolite enhancement in Stevia rebaudiana. Full article

(This article belongs to the Special Issue Bioactive Metabolites from Natural Sources (2nd Edition))

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12 pages, 1649 KB

Open AccessArticle

Untargeted GC-MS Metabolic Profiling of Anaerobic Gut Fungi Reveals Putative Terpenoids and Strain-Specific Metabolites

by Lazarina V. Butkovich, Candice L. Swift, Chaevien S. Clendinen, Heather M. Olson, Samuel O. Purvine, Oliver B. Vining and Michelle A. O’Malley

Metabolites 2025, 15(9), 578; https://doi.org/10.3390/metabo15090578 - 29 Aug 2025

Background/Objectives: Anaerobic gut fungi (Neocallimastigomycota) are biotechnologically relevant, lignocellulose-degrading microbes with under-explored biosynthetic potential for secondary metabolites. Untargeted metabolomic profiling with gas chromatography–mass spectrometry (GC-MS) was applied to two gut fungal strains, Anaeromyces robustus and Caecomyces churrovis, to establish a foundational [...] Read more.

Background/Objectives: Anaerobic gut fungi (Neocallimastigomycota) are biotechnologically relevant, lignocellulose-degrading microbes with under-explored biosynthetic potential for secondary metabolites. Untargeted metabolomic profiling with gas chromatography–mass spectrometry (GC-MS) was applied to two gut fungal strains, Anaeromyces robustus and Caecomyces churrovis, to establish a foundational metabolomic dataset to identify metabolites and provide insights into gut fungal metabolic capabilities. Methods: Gut fungi were cultured anaerobically in rumen-fluid-based media with a soluble substrate (cellobiose), and metabolites were extracted using the Metabolite, Protein, and Lipid Extraction (MPLEx) method, enabling metabolomic and proteomic analysis from the same cell samples. Samples were derivatized and analyzed via GC-MS, followed by compound identification by spectral matching to reference databases, molecular networking, and statistical analyses. Results: Distinct metabolites were identified between A. robustus and C. churrovis, including 2,3-dihydroxyisovaleric acid produced by A. robustus and maltotriitol, maltotriose, and melibiose produced by C. churrovis. C. churrovis may polymerize maltotriose to form an extracellular polysaccharide, like pullulan. GC-MS profiling potentially captured sufficiently volatile products of proteomically detected, putative non-ribosomal peptide synthetases and polyketide synthases of A. robustus and C. churrovis. The triterpene squalene and triterpenoid tetrahymanol were putatively identified in A. robustus and C. churrovis. Their conserved, predicted biosynthetic genes—squalene synthase and squalene tetrahymanol cyclase—were identified in A. robustus, C. churrovis, and other anaerobic gut fungal genera. Conclusions: This study provides a foundational, untargeted metabolomic dataset to unmask gut fungal metabolic pathways and biosynthetic potential and to prioritize future efforts for compound isolation and identification. Full article

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

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24 pages, 4693 KB

Open AccessArticle

Essence of Chicken Supplementation Alters Brain and Blood Metabolite Signatures in Sleep-Deprived Mice

by Yu Long, Zhaorong Wang, Xinyang Hu, Sisi Wang, Liujie Zheng, Zhengwei Fu and Yinhua Ni

Metabolites 2025, 15(9), 577; https://doi.org/10.3390/metabo15090577 - 29 Aug 2025

Background: Essence of chicken (EC) has been found to improve brain function, increase short-term working memory, and reduce fatigue. However, the specific bioactives after EC consumption remain unknown, and the effect of EC on sleep deprivation (SD) is also elusive. The aim [...] Read more.

Background: Essence of chicken (EC) has been found to improve brain function, increase short-term working memory, and reduce fatigue. However, the specific bioactives after EC consumption remain unknown, and the effect of EC on sleep deprivation (SD) is also elusive. The aim of the present study is to clarify the metabolic changes induced by EC supplementation in the serum and brain and identify characteristic bioactive metabolites significantly altered after EC consumption. Methods: Firstly, a kinetic analysis of EC consumption was performed to determine the time-sequential change in serum and brain metabolites in mice using gas chromatography coupled with mass spectrometry (GC/MS). Next, the impact of EC on the metabolic signatures in an acute SD mouse model was assessed. Results: Based on the results of the kinetic study, myristoleic acid and L-tyrosine were significantly increased in the serum, whereas gentisic acid was significantly increased in the brain after the administration of EC. In addition, EC administration differentially modulated SD-induced alterations in gene expression across brain regions of acute sleep-deprived mice, ameliorated abnormal neurotransmitters, and increased several specific metabolites in the serum. Conclusions: These results suggest that EC might be an effective nutritional supplement to alleviate SD-induced physiological changes. Full article

(This article belongs to the Section Food Metabolomics)

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17 pages, 908 KB

Open AccessArticle

A Surveillance of Paracetamol and Nonsteroidal Anti-Inflammatory Drug Consumption in Cluj-Napoca, Romania, Using Wastewater-Based Epidemiology

by Mihail Simion Beldean-Galea, Mihaela-Cătălina Herghelegiu, Audrey Combès, Jérôme Vial, Robert Tötös, Maria Concetta Bruzzoniti and Maria-Virginia Coman

Metabolites 2025, 15(9), 576; https://doi.org/10.3390/metabo15090576 - 28 Aug 2025

Paracetamol and nonsteroidal anti-inflammatory drugs are the most popular first-line analgesics, being freely available without any medical prescription. For this reason, it is difficult to estimate their actual consumption among the population. One tool for surveillance of pharmaceutical use is wastewater-based epidemiology, a [...] Read more.

Paracetamol and nonsteroidal anti-inflammatory drugs are the most popular first-line analgesics, being freely available without any medical prescription. For this reason, it is difficult to estimate their actual consumption among the population. One tool for surveillance of pharmaceutical use is wastewater-based epidemiology, a useful approach for monitoring public health by analyzing specific biomarkers in wastewater. Background/Objectives: In this study, the consumption of paracetamol and four nonsteroidal anti-inflammatory drugs (ibuprofen, naproxen, ketoprofen, and diclofenac) was evaluated by analyzing their residues as specific biomarkers in wastewater and the fraction excreted as drug metabolites in urine. Methods: For this purpose, composite wastewater samples were collected from the influent of the wastewater treatment plant in Cluj-Napoca, Romania, in four sampling campaigns (September 2021, February 2022, February 2024, and October 2024), and the target biomarkers were analyzed by liquid chromatography–tandem mass spectrometry. Results: The results of consumption expressed in g/day/1000 inhabitants showed variations for the five studied pharmaceuticals in the following ranges: 6.65–185.57 for paracetamol, 0.32–2.44 for ibuprofen, 0.29–0.82 for naproxen, 0.21–2.65 for ketoprofen, and 0.23–1.11 for diclofenac, depending on the sampling period. This variation can be explained either by the different behaviors regarding the consumption of the pharmaceutical products studied by the population during the sampling periods or by an inappropriate estimate of the number of inhabitants connected to the sewage system. Conclusions: Future studies need to establish a more comprehensive model that considers many other variables that may influence the results obtained through WBE. Full article

(This article belongs to the Special Issue Targeted and Non-Targeted LC- and GC-HRMS Workflows for the Analysis of Emerging Contaminants and the Environmental Exposome)

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18 pages, 1886 KB

Open AccessArticle

Multi-Omics Feature Selection to Identify Biomarkers for Hepatocellular Carcinoma

by Rency S. Varghese, Xinran Zhang, Sarada Giridharan, Muhammad Salman Sajid, Md Mamunur Rashid, Alexander Kroemer and Habtom W. Ressom

Metabolites 2025, 15(9), 575; https://doi.org/10.3390/metabo15090575 - 28 Aug 2025

Introduction: Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, ranks as the third leading cause of mortality globally. Patients diagnosed with HCC exhibit a dismal prognosis mostly due to the emergence of symptoms in the advanced stages of the disease. Moreover, [...] Read more.

Introduction: Hepatocellular carcinoma (HCC), the most prevalent form of liver cancer, ranks as the third leading cause of mortality globally. Patients diagnosed with HCC exhibit a dismal prognosis mostly due to the emergence of symptoms in the advanced stages of the disease. Moreover, conventional biomarkers demonstrate insufficient efficacy in the early detection of HCC, hence highlighting the need for the identification of novel and more effective biomarkers. Methods: In this paper, we investigate methods for integration of multi-omics data we generated by both untargeted and targeted mass spectrometric analysis of serum samples from HCC cases and patients with liver cirrhosis. Specifically, the performances of several feature selection methods are evaluated on their abilities to identify a panel of multi-omics features that distinguish HCC cases from cirrhotic controls. Results: The integrative analysis identified key molecules associated with liver including such as leucine and isoleucine as well as SERPINA1, which is involved in LXR/RXR Activation and Acute Response signaling. A new method that uses recursive feature selection in conjunction with a transformer-based deep learning model as an estimator led to more promising results compared to other deep learning methods that perform disease classification and feature selection sequentially. Conclusions: The findings in this study reinforce the importance of adapting or extending deep learning models to support robust feature selection, especially for integration of multi-omics data with limited sample size to avoid the risk of overfitting and the need for evaluation of the multi-omics features discovered in this study via blood samples from a larger and independent cohort to identify robust biomarkers for HCC. Full article

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

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15 pages, 838 KB

Open AccessArticle

Predictive Utility and Metabolomic Signatures of TG/HDL-C Ratio for Metabolic Syndrome Without Cardiovascular Disease and/or Diabetes in Qatari Adults

by Noora Kano, Najeha Anwardeen, Khaled Naja, Asma A. Elashi, Ahmed Malki and Mohamed A. Elrayess

Metabolites 2025, 15(9), 574; https://doi.org/10.3390/metabo15090574 - 28 Aug 2025

Background: Metabolic syndrome (MetS) is a major risk factor for cardiovascular disease (CVD) and type 2 diabetes mellitus (T2DM), especially in Middle Eastern populations with a high metabolic burden. This study aimed to evaluate the predictive utility of different lipid ratios, including triglyceride-to-high-density [...] Read more.

Background: Metabolic syndrome (MetS) is a major risk factor for cardiovascular disease (CVD) and type 2 diabetes mellitus (T2DM), especially in Middle Eastern populations with a high metabolic burden. This study aimed to evaluate the predictive utility of different lipid ratios, including triglyceride-to-high-density lipoprotein cholesterol (TG/HDL-C), total cholesterol (TC)/HDL-C, low-density lipoprotein (LDL-C)/HDL-C, and non-HDL-C/HDL-C, for identifying MetS. In addition, we aimed to characterise the underlying metabolic dysregulation using the most predictive lipid ratio by comparing metabolomic profiles between high-risk (T3) and low-risk (T1) groups. Method: We conducted a cross-sectional study using data from 2179 Qatari adults without CVD and/or T2DM. The predictive value of each lipid ratio for MetS was compared. Untargeted metabolomics was performed to profile metabolic changes between T3 and T1. Results: After adjustment for age, sex, and BMI, TG/HDL-C showed the highest discriminative ability for MetS (AUC = 0.896, 95% CI: 0.88–0.91; OR = 4.36, 95% CI: 3.63–5.28, p < 0.0001). In pairwise AUC comparisons, TG/HDL-C outperformed LDL-C/HDL-C (p = 2.6 × 10⁻⁴, after correction for multiple comparisons), with no significant differences versus other ratios. The high-risk group exhibited raised levels of phosphatidylethanolamines, phosphatidylinositols, and diacylglycerols, and lower levels of sphingomyelins and plasmalogens. These lipid classes have been suggested to be implicated in insulin resistance and metabolic dysfunction. Elevated monoacylglycerols were identified in high-TG/HDL-C groups, representing a previously underreported pattern. Conclusions: The TG/HDL-C ratio showed a better association with MetS compared with other lipid ratios and was linked to distinct metabolomic signatures. These findings suggest potential value for early risk evaluation, but longitudinal and mechanistic studies are needed to confirm clinical applicability. Full article

(This article belongs to the Special Issue Current Research in Metabolic Syndrome and Cardiometabolic Disorders)

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