Metabolites

16 pages, 2627 KB

Open AccessArticle

Age and Follicle-Stimulating Hormone as Variables Independently Associated with Serum Anti-Müllerian Hormone in Women Attending a Tertiary Gynaecology Clinic: A Retrospective Cross-Sectional Study Using Censoring-Aware Modelling

by Mete Hakan Karalök, Bağnu Dündar, Ayhan Parmaksız, Tugba Elgün, Sevgi Koçyiğit Sevinç and Asiye Gök Yurttaş

Metabolites 2026, 16(9), 610; https://doi.org/10.3390/metabo16090610 - 26 Aug 2026

Abstract

Objective: Anti-Müllerian hormone (AMH) is the most widely used biochemical marker of ovarian reserve, but its associations with other reproductive hormones are usually examined one hormone at a time and without accounting for values reported at the assay floor. This study examined [...] Read more.

Objective: Anti-Müllerian hormone (AMH) is the most widely used biochemical marker of ovarian reserve, but its associations with other reproductive hormones are usually examined one hormone at a time and without accounting for values reported at the assay floor. This study examined the associations between serum AMH and age, follicle-stimulating hormone (FSH), luteinising hormone (LH), estradiol, progesterone and prolactin in women attending a tertiary gynaecology clinic. Materials and Methods: In this retrospective, cross-sectional, single-centre study, the records of women who underwent serum AMH testing together with a reproductive hormone panel between 1 January 2020 and 31 December 2025 were reviewed. Women with polycystic ovary syndrome, primary ovarian insufficiency, pregnancy or previous ovarian surgery were excluded. Bivariate associations were assessed with Pearson and Spearman correlation coefficients on raw and Box–Cox-transformed variables. Because 12.82% (n = 15) of AMH results were left-censored at the analytical reporting floor of 0.02 ng/mL, a multivariable Tobit model with the censoring limit specified on the Box–Cox-transformed scale (λ = 0.309, threshold = −2.270) was fitted, with predictors selected a priori on clinical grounds. Sensitivity analyses examined the influence of high AMH values, an alternative transformation of AMH, and flexible modelling of age. Results: The analysis included 117 women aged 18–45 years. Mean AMH was 2.22 ± 2.24 ng/mL [median 1.61 ng/mL (Q1–Q3, 0.36–3.20)]. In bivariate correlation analysis, AMH showed statistically significant inverse associations with age (r = −0.376, p < 0.001) and FSH (r = −0.445, p < 0.001), whereas LH, estradiol, progesterone, and prolactin showed no statistically significant correlations with AMH (all p > 0.10). In the multivariable Tobit model, only age (β = −0.068; 95% CI [−0.117, −0.018]; p = 0.007) and transformed FSH (β = −3.582; 95% CI [−4.846, −2.317]; p < 0.001) remained independently associated with transformed AMH. LH, estradiol, progesterone, and prolactin were not independently associated with AMH in the multivariable model (all p > 0.05). The standardised association was greater for transformed FSH (β* = −0.559) than for age (β* = −0.234). The associations of age and FSH were consistent in direction and magnitude across all sensitivity analyses. Conclusions: In this selected clinical sample, age and FSH were the only variables independently associated with serum AMH after mutual adjustment. LH, estradiol, progesterone, and prolactin showed no statistically significant associations with AMH in either the unadjusted bivariate analyses or the multivariable model. The absence of independent associations for these hormones should be interpreted cautiously because hormone sampling was not standardised to menstrual cycle day, which may have introduced measurement variability. These findings describe associations within the study population and do not establish causal relationships, reference intervals, or a basis for modifying testing strategies. The analysis also highlights the importance of accounting for left-censoring when modelling AMH data containing a substantial proportion of results at the assay reporting floor. Full article

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

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19 pages, 1056 KB

Open AccessArticle

Plasma as Proxy for Tissue Metabolism When Extending Lifespan in Mice

by Sara Greenfield, C. Titus Brown and Oliver Fiehn

Metabolites 2026, 16(9), 609; https://doi.org/10.3390/metabo16090609 - 25 Aug 2026

Abstract

Objective: Despite most often used in research and medicine, it is unclear how well blood metabolite levels can reflect metabolic changes in tissues. Methods: We used untargeted metabolomic data from plasma, liver, gastrocnemius muscle, kidney, inguinal fat, and gonadal fat tissues from mice [...] Read more.

Objective: Despite most often used in research and medicine, it is unclear how well blood metabolite levels can reflect metabolic changes in tissues. Methods: We used untargeted metabolomic data from plasma, liver, gastrocnemius muscle, kidney, inguinal fat, and gonadal fat tissues from mice treated with lifespan-extending interventions: caloric restriction, rapamycin, canagliflozin, 17-α estradiol, and acarbose. Results: For each tissue, about 37% of the identified metabolites were also found in plasma and used for comparative analyses. We found that plasma metabolites do not primarily reflect the metabolome of a single tissue type. Caloric restriction caused the highest proportion of significantly altered metabolites detected in both organs and blood. Unsaturated triacylglycerols, diacylglycerols, amino acid-derivatives, and sphingomyelins had the most concordant overlaps between four tissues and plasma, followed by carbohydrates with three tissue/plasma intersections. Concordant plasma/tissue changes were found more pronounced in male mice than in female mice. Surprisingly, many compounds that responded similarly to lifespan-extending treatments in tissues and in plasma originated from dietary compounds, specifically, ergothioneine, DHA-containing fats, and diacylglycerides. Ergothioneine, previously associated with healthy aging in humans, showed concordant treatment responses in blood and all tissues except gonadal fat. DHA-containing fats showed consistent regulation between blood and inguinal and gonadal adipose tissue. The kidneys showed coherent trends with blood metabolite levels for LPC 15:0, LPC 17:0, and pinitol. Under treatments with strong life-extending effects, 1,5-anhydro-glucitol blood levels were co-regulated with both liver and kidney levels. Conclusions: Overall, plasma can only serve as limited proxy for tissue metabolism. Yet, several potential blood biomarkers were discovered as concordant in plasma and tissues in lifespan-extending interventions. Full article

(This article belongs to the Section Advances in Metabolomics)

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21 pages, 910 KB

Open AccessReview

MetALD Molecular Signatures: What We Know, What We Lack, and How to Move Forward Through Integrated Multi-Omics

by Miriam Longo, Marica Meroni, Erika Paolini and Paola Dongiovanni

Metabolites 2026, 16(9), 608; https://doi.org/10.3390/metabo16090608 - 25 Aug 2026

Abstract

With the advent of the new definition, fatty liver disorders have been reframed into metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-related liver disease (ALD), and the mixed phenotype referred to as MetALD (MASLD and increased alcohol intake). This change reflects the real-world clinical [...] Read more.

With the advent of the new definition, fatty liver disorders have been reframed into metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-related liver disease (ALD), and the mixed phenotype referred to as MetALD (MASLD and increased alcohol intake). This change reflects the real-world clinical practice, where metabolic dysfunction and alcohol frequently coexist and synergize to increase risks of steatohepatitis, fibrosis, and hepatocellular carcinoma (HCC). While conventional non-invasive tests (NITs) remain the backbone of risk stratification, lipidomics and metabolomics can capture biological information on disease mechanisms and may improve early detection and prognosis. Here, we summarize the current evidence on circulating and tissue lipidomic and metabolomic signatures across MASLD, ALD and MetALD, discuss how the new definitions affect clinical risk assessment, and highlight recent studies which partially distinguish molecular fingerprints for mixed etiology disease. Full article

(This article belongs to the Special Issue Metabolomics and MASLD: Pathways, Biomarkers, and Clinical Insights)

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18 pages, 14321 KB

Open AccessArticle

Targeted Metabolomic Profiling of Emotional and Reflex Tears: A Paired Exploratory Study

by Jiahua Liu, Xiqiao Gao, Hao Liang and Jiahao Ye

Metabolites 2026, 16(9), 607; https://doi.org/10.3390/metabo16090607 - 25 Aug 2026

Abstract

Objectives: Emotional tears are generated in a distinct neurophysiological context from reflex tears, but their metabolic composition remains poorly understood. Methods: This exploratory paired targeted-metabolomics study compared emotional and reflex tears collected from 22 healthy volunteers using a 600-multiple-reaction-monitoring platform. Among 412 detected [...] Read more.

Objectives: Emotional tears are generated in a distinct neurophysiological context from reflex tears, but their metabolic composition remains poorly understood. Methods: This exploratory paired targeted-metabolomics study compared emotional and reflex tears collected from 22 healthy volunteers using a 600-multiple-reaction-monitoring platform. Among 412 detected metabolites, 344 were retained after data preprocessing. Paired statistical analysis prioritized 23 candidate metabolites based on the combined criteria of unadjusted p-value, fold change, and consistency of within-subject change. Results: Seven candidates were lower, and 16 were higher in emotional tears. Salicylic acid was retained in the descriptive candidate set but excluded from the primary machine-learning analysis because a contribution from the reflex-tear induction procedure could not be ruled out. Among the remaining 22 candidates, 4-hydroxy-3-methylbenzoic acid, vanillic acid, cytidine-5′-monophosphate, and hydroxyphenyllactic acid were consistently ranked among the leading features. A fixed four-metabolite combination achieved an area under the receiver operating characteristic curve of 0.864 (95% CI, 0.756–0.957) under ordinary leave-one-subject-out cross-validation. When candidate screening, feature selection, and model fitting were repeated within each training fold, the best nested pipeline achieved an area under the curve of 0.725 (95% CI, 0.603–0.843). Pathway mapping further linked the candidate metabolites to histidine, tyrosine, fatty-acid, ether-lipid, and ubiquinone-related metabolism. Conclusions: These findings demonstrate measurable within-subject metabolic differences between emotional and reflex tears and identify a focused set of candidate metabolites for future validation. Because no individual metabolite remained significant after false discovery rate correction and no independent validation cohort was available, the candidate signals and discrimination models should be confirmed in larger, independently collected cohorts. Full article

(This article belongs to the Topic Advances in Analysis Methods for Metabolomics and Lipidomics)

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19 pages, 10933 KB

Open AccessArticle

Metabolomic Profiling of Medicinal Plant-Based Soft Porridge and Evaluation of Cytotoxicity

by Phato Avheani Matsheketsheke, Nakisani Babra Moyo and Bono Nethathe

Metabolites 2026, 16(9), 606; https://doi.org/10.3390/metabo16090606 - 25 Aug 2026

Abstract

Background/Objectives: Traditional medicinal plants play a crucial role in infants’ healthcare in underdeveloped countries and communities where access to modern medicine is limited. In Limpopo, the Vhavenda tribe has a custom of feeding babies as young as a day old with tshiunza, [...] Read more.

Background/Objectives: Traditional medicinal plants play a crucial role in infants’ healthcare in underdeveloped countries and communities where access to modern medicine is limited. In Limpopo, the Vhavenda tribe has a custom of feeding babies as young as a day old with tshiunza, a very light and warm, soft porridge prepared in medicinal plant extracts, believed to help treat various ailments and boost the immune and digestive systems. However, reports of negative side effects, including vomiting, haematuria, renal inflammation and hospitalisations, highlight safety concerns of these traditional practices. This study aimed to profile the chemical composition of soft porridge samples prepared in aqueous extracts of medicinal plants reported to be commonly used in infants’ food in the Venda region of Limpopo; Annona senegalensis (roots), Piliostigma thonningii (leaves), Carissa edulis (roots) and Bauhinia galpinii (leaves). Methods: Ultrahigh-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-qTOF-MS) was used for metabolic profiling, followed by putative compound identification using feature-based molecular networking and a compound fragmentation predictor tool, SIRIUS. To evaluate the toxicity of these plants, a cytotoxicity assay was conducted using plant extracts on African monkey kidney cells. Results: Different classes of polyphenols, including flavonoids (flavan-3-ols and flavonols) and hydroxycinnamoyl amides, were among the dominant compounds putatively identified in the methanolic extracts of soft porridge prepared from the four plant extracts. A. senegalensis aqueous extracts were inactive (IC₅₀ > 500 µg/mL, 55.57% viability at 500 µg/mL), while P. thonningii was non-cytotoxic (105–132% viability within the tested concentration range). Conclusions: Although no toxic compounds were identified and no cytotoxic potential was observed in the tested plant extracts, this does not translate to the safe use of medicinal plants in infants’ food. Therefore, future studies should conduct pharmacological and toxicological evaluations to better understand the potential risks of these plant extracts to infant health. Full article

(This article belongs to the Section Food Metabolomics)

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45 pages, 6630 KB

Open AccessFeature PaperArticle

Metabolomic–Metabolite Profiling: Progressive Insight and Biochemical Pathway in Crude Oil Waste Sludge Co-Composting Bioremediation

by Onyedikachi Ubani and Veronica M. Ngole-Jeme

Metabolites 2026, 16(9), 605; https://doi.org/10.3390/metabo16090605 - 25 Aug 2026

Abstract

Background: Crude oil refinery waste sludge (COWS) ranks among the most compositionally complex and ecotoxicologically hazardous industrial residues. Although bulk total petroleum hydrocarbon (TPH) and summed polycyclic aromatic hydrocarbon (PAH) removal are routinely reported, the metabolite-level biochemical fate of individual petrogenic compounds, spanning [...] Read more.

Background: Crude oil refinery waste sludge (COWS) ranks among the most compositionally complex and ecotoxicologically hazardous industrial residues. Although bulk total petroleum hydrocarbon (TPH) and summed polycyclic aromatic hydrocarbon (PAH) removal are routinely reported, the metabolite-level biochemical fate of individual petrogenic compounds, spanning ring dihydroxylation, catechol cleavage, and entry into central carbon metabolism, remains largely unmapped under co-composting with diverse animal manures. Objectives: This study aimed to construct a metabolite-resolved, microbially anchored biochemical fate map of crude oil sludge during co-composting. Methods: Aerobic microcosms combining crude oil sludge, garden soil, and a wood-chip bulking agent were amended separately with poultry, horse, cow, or swine/pig manure alongside an unamended control and then incubated at 22 °C for 300 days. Analyses integrated untargeted gas chromatography-mass spectrometry (GC-MS) metabolomics, targeted PAH quantification (EPA Methods 3541/8270), 16S rRNA gene amplicon sequencing (Illumina MiSeq, V1–V3, paired-end 300 bp), physicochemical monitoring, and culture-dependent isolation, with National Institute of Standards and Technology (NIST) Mass Spectral library annotation. Results: GC-MS resolved 1169 metabolite features across 17 samples, comprising 538 annotated compounds within 11 chemical classes and 631 unknowns, of which 151 recurred in at least 10 samples. Petrogenic markers (n-alkanes C₁₄–C₃₆, hopanoids, steranes, and alkylated dibenzothiophenes) and ring-cleavage intermediates (2-hydroxyfluorene, 1,4-naphthoquinone, phenanthrene-methanol, benzenediols, butanedioic acid, fatty alcohols C₁₆–C₂₀) elucidated a four-stage degradation cascade consistent with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways map01220 and map00624. PAH mean-removal ranked swine/pig (88.0%) > horse (87.0%) > poultry (80.5%) > cow (79.1%) > control (68.2%). Sequencing recovered 2969 operational taxonomic units (OTUs) enriched in Pseudomonas, Achromobacter, Stutzerimonas, Dietzia, Gordonia, and Mycobacterium, with Pseudomonas dominating high-removal systems; respiration peaked at 18.7 mg CO₂-C g⁻¹ in poultry treatments. Conclusions: This work establishes a metabolite-resolved map linking hydrocarbonoclastic taxa to separate degradation steps. The co-occurrence of oxygenated PAH intermediates with decreasing parent PAH concentrations serves as an indicator of transformation processes and may assist in identifying potential residual-risk signals, thereby supporting remediation evaluation and process optimization. Full article

(This article belongs to the Section Advances in Metabolomics)

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34 pages, 1154 KB

Open AccessArticle

Metabodeconplus—An R Package for Automated Deconvolution and Alignment of 1D NMR Metabolomics Data

by Tobias Schmidt, Maximilian Sombke, Helena U. Zacharias, Peter J. Oefner, Rainer Spang and Wolfram Gronwald

Metabolites 2026, 16(9), 604; https://doi.org/10.3390/metabo16090604 - 24 Aug 2026

Abstract

Background: In one-dimensional NMR spectra of complex biofluids such as urine and plasma, extensive signal overlap obscures individual metabolite signals. Resolving this overlap by deconvolution is only the first step: turning a set of spectra into a table for subsequent statistical analysis also [...] Read more.

Background: In one-dimensional NMR spectra of complex biofluids such as urine and plasma, extensive signal overlap obscures individual metabolite signals. Resolving this overlap by deconvolution is only the first step: turning a set of spectra into a table for subsequent statistical analysis also requires the alignment of signals across samples and their integration into a single feature matrix. Methods: Here, metabodeconplus is presented, an R package that unifies this entire path into a single reproducible end-to-end workflow. From raw one-dimensional spectra, it deconvolutes overlapping signals, aligns resulting signals across samples, and integrates them into a data matrix for built-in sample classification or downstream statistical analysis. Automated parameter optimization removes manual tuning, and a Rust computational backend with parallelization leads to fast runtimes. Results: On the simulated Sim3 spectra, a combined score of correctly identified signals and reconstruction accuracy (maximum 1) rose from 0.712 for the predecessor package to 0.801 for metabodeconplus. For the urinary AKI dataset, metabodeconplus reached a classification accuracy of 73.7 ± 2.20% and an

AUC = 0.827 \pm 0.025

, which is comparable to the binning baseline. An advantage is the potential unambiguous metabolite assignment of the deconvoluted signals. Conclusions: The package is freely available as open source on GitHub and on CRAN. Full article

(This article belongs to the Special Issue Advances in NMR-Based Metabolomics for Biomedical Research)

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28 pages, 2419 KB

Open AccessSystematic Review

The Statin Paradox: Drivers and Consequences of Therapy Discontinuation

by Adrianna Dylik, Mikołaj Musiał, Michał Radke, Dominika Tuzimek, Dominika Rogoża, Bartosz Czekała, Anna Wawrzyniak, Nadzeya Zhuk, Katarzyna Skrypnik and Damian Skrypnik

Metabolites 2026, 16(9), 603; https://doi.org/10.3390/metabo16090603 - 24 Aug 2026

Abstract

Background: Statins are among the most frequently prescribed medications worldwide, with proven benefits in reducing all-cause and cardiovascular mortality, preventing major adverse cardiovascular events (MACEs), and lowering healthcare costs. Despite their well-established safety and effectiveness, discontinuation of statin therapy remains a common problem [...] Read more.

Background: Statins are among the most frequently prescribed medications worldwide, with proven benefits in reducing all-cause and cardiovascular mortality, preventing major adverse cardiovascular events (MACEs), and lowering healthcare costs. Despite their well-established safety and effectiveness, discontinuation of statin therapy remains a common problem in both primary and secondary prevention. Methods: A systematic literature review was conducted in accordance with PRISMA guidelines and registered in the PROSPERO database (CRD420261295172). Original studies published since 1 January 2014 were identified through searches of PubMed (MEDLINE) and Google Scholar using predefined keywords. Methodological quality and risk of bias of the included observational studies were evaluated using the Newcastle-–Ottawa Scale (NOS) and Joanna Briggs Institute (JBI) Critical Appraisal Tools. Results: Synthesized data from 29 included studies indicate that up to half of patients discontinue statin therapy within the first year (discontinuation rates ranging from 27.1% to 47.0% in primary prevention and 18.5% to 32.4% in secondary prevention), with rates increasing over time. Major factors contributing to non-adherence include fear of side effects, particularly statin-associated muscle symptoms (SAMSs), misinformation, limited patient–physician communication, socioeconomic barriers, and polypharmacy. Discontinuation is associated with significantly higher all-cause and cardiovascular mortality (Hazard Ratios ranging from 1.30 to 4.65), higher rates of cardiovascular and cerebrovascular events, worsening metabolic outcomes, reduced quality of life, and greater healthcare expenditures. Conclusions: Improving adherence requires better patient education, addressing misconceptions, strengthening patient–physician relationships, and optimising treatment regimens. A multidisciplinary approach is needed to prevent unjustified discontinuation and improve long-term clinical outcomes. Full article

(This article belongs to the Section Pharmacology and Drug Metabolism)

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20 pages, 736 KB

Open AccessReview

Pharmacomicrobiomics: From Host–Microbiome–Drug Interactions to Clinical Translation in Precision Medicine

by Guilherme Araújo, Sara Domingues, Gabriela Jorge da Silva and Tiago Lima

Metabolites 2026, 16(9), 602; https://doi.org/10.3390/metabo16090602 - 23 Aug 2026

Abstract

Marked interindividual variability in drug response remains a major challenge in clinical pharmacology and cannot be fully explained by host genetics alone. Increasing evidence indicates that the gut microbiota constitutes an additional determinant of drug efficacy and toxicity through bidirectional interactions with pharmacological [...] Read more.

Marked interindividual variability in drug response remains a major challenge in clinical pharmacology and cannot be fully explained by host genetics alone. Increasing evidence indicates that the gut microbiota constitutes an additional determinant of drug efficacy and toxicity through bidirectional interactions with pharmacological therapies. This recognition has led to the emergence of pharmacomicrobiomics, a field that investigates how microbial communities influence drug disposition and response, and how drugs, in turn, alter the microbiome. Microbiome-mediated effects on drug efficacy and toxicity have been described across several therapeutic areas, including oncology, multiple sclerosis, and type 2 diabetes mellitus. Although these findings are promising, most mechanistic evidence derives from preclinical and animal studies, with relatively limited validation in controlled clinical trials. Strategies to modulate the gut microbiota, including prebiotics, probiotics, and faecal microbiota transplantation, have shown preliminary promise in optimising drug efficacy and reducing adverse effects, although methodological heterogeneity and incomplete mechanistic understanding limit their current clinical application. The identification of robust microbiome-derived biomarkers and the integration of multi-omics approaches, particularly metabolomics, are expected to accelerate the translation of pharmacomicrobiomics into precision medicine. This review summarises current evidence regarding microbiome–drug interactions, the mechanisms underlying microbiome-mediated modulation of pharmacokinetics and pharmacodynamics, emerging therapeutic strategies, and the challenges that remain before pharmacomicrobiomics can be implemented in clinical practice. Full article

(This article belongs to the Special Issue The Role of Metabolites and the Gut Microbiota in Development, Homeostasis, and Diseases)

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18 pages, 12547 KB

Open AccessArticle

Integrating Network Pharmacology and Metabolomics to Decipher the Mechanisms Underlying the Therapeutic Effects of Wuzhi Dripping Pills Against MASLD

by Huijun Wang, Miaoyuan Zhang, Kangkang Gao, Yaping Zhou, Aoxing Xiao, Jinyi Liu and Xiangjun Qiu

Metabolites 2026, 16(9), 601; https://doi.org/10.3390/metabo16090601 - 22 Aug 2026

Abstract

Background: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is a progressive condition predisposing to cirrhosis and hepatocellular carcinoma, with prevalence rising globally. Yet effective therapies remain limited. Wuzhi Dripping Pills (WZDP), derived from Schisandra sphenanthera, possess hepatoprotective and anti-inflammatory properties, though their [...] Read more.

Background: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is a progressive condition predisposing to cirrhosis and hepatocellular carcinoma, with prevalence rising globally. Yet effective therapies remain limited. Wuzhi Dripping Pills (WZDP), derived from Schisandra sphenanthera, possess hepatoprotective and anti-inflammatory properties, though their efficacy against MASLD remains unexplored. Methods: Network pharmacology predicted active ingredients and targets, followed by KEGG enrichment analysis. A high-fat diet MASLD rat model was established to evaluate WZDP effects on weight, liver index, and serum markers. Serum metabolomic profiling via UPLC-MS/MS, combined with multivariate statistics and KEGG annotation, identified perturbed pathways. Results: Twelve bioactive compounds and 434 WZDP targets were retrieved, of which 74 intersected with 838 MASLD-associated genes. Enrichment implicated AGE-RAGE, insulin resistance, and HIF-1 signaling. In vivo, WZDP significantly improved anthropometric and biochemical parameters. Metabolomic analysis distinctly separated WZDP-treated from model groups, highlighting phospholipase D signaling as a key differential pathway. Conclusions: This integrative approach confirms that WZDP confers therapeutic benefits in MASLD through coordinated regulation of neuroactive ligand–receptor interaction, bile acid biosynthesis, phospholipase D signaling, and arginine–proline metabolism. Our findings furnish a molecular and metabolic rationale for further mechanistic studies and drug discovery efforts. Full article

(This article belongs to the Special Issue Metabolomics and MASLD: Pathways, Biomarkers, and Clinical Insights)

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30 pages, 8877 KB

Open AccessReview

Machine Learning–Integrated Metabolomics for Precision Pharmacotherapy: Advances, Challenges, and Clinical Translation

by Pan Li, Jing Mao, Xianglin Hu, Yujiao Hu, Xiaoke Zhang, Qian Zheng, Xiaoying Hou, Yuchen Liu and Min Huang

Metabolites 2026, 16(8), 600; https://doi.org/10.3390/metabo16080600 - 21 Aug 2026

Abstract

Machine learning (ML) integrated with metabolomics has emerged as a promising strategy to advance precision pharmacotherapy, enabling data-driven prediction of drug response. This review provides an overview of commonly applied ML methodologies in metabolomics-based pharmacological studies, including supervised models (Random Forest, Extreme Gradient [...] Read more.

Machine learning (ML) integrated with metabolomics has emerged as a promising strategy to advance precision pharmacotherapy, enabling data-driven prediction of drug response. This review provides an overview of commonly applied ML methodologies in metabolomics-based pharmacological studies, including supervised models (Random Forest, Extreme Gradient Boosting, Support Vector Machine, Logistic Regression, K-Nearest Neighbors), unsupervised models (K-Means Clustering, Principal Component Analysis), and deep learning approaches. We summarize recent progress in the application of metabolomics-driven ML to personalized medication, with a focus on drug dosage optimization, therapeutic efficacy prediction, and adverse drug reaction assessment. Despite these advances, significant challenges remain, including limited explainability, insufficient prospective clinical validation, lack of standardization and reproducibility, and data dimensionality and quality issues. Addressing these issues will be essential for the clinical translation of ML-metabolomics integration. Looking ahead, continued methodological innovation, large-scale multi-center prospective validation, and integration with other omics platforms will be key to unlocking the full potential of metabolomics combined with ML in precision healthcare. Full article

(This article belongs to the Section Pharmacology and Drug Metabolism)

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17 pages, 11978 KB

Open AccessArticle

Mammalian Arachidonic Acid 15-Lipoxygenases: Fed-Batch Fermentation, Enzyme Purification and Functional Characterization

by Vladislav Aksenov, Angelina V. Kurchatova, Alexey Golovanov, Veronika Ulasenko, Olga Zubkova, Alexander Zhuravlev, Ekaterina Makishvili, Nikolay E. Kushlinskii, Hartmut Kuhn and Igor Ivanov

Metabolites 2026, 16(8), 599; https://doi.org/10.3390/metabo16080599 - 21 Aug 2026

Abstract

Background: Mammalian arachidonic acid lipoxygenases (ALOXs) are non-heme iron-containing enzymes that oxygenate polyunsaturated fatty acids (PUFAs) with at least two isolated double bonds to hydroperoxy derivatives. The patho-physiological roles of these enzymes in inflammatory, hyperproliferative, and neurological diseases have made them promising targets [...] Read more.

Background: Mammalian arachidonic acid lipoxygenases (ALOXs) are non-heme iron-containing enzymes that oxygenate polyunsaturated fatty acids (PUFAs) with at least two isolated double bonds to hydroperoxy derivatives. The patho-physiological roles of these enzymes in inflammatory, hyperproliferative, and neurological diseases have made them promising targets for pharmacological interventions. Unfortunately, the expression levels of ALOX isoforms in mammalian cells are very low, which makes functional characterization of native enzymes and the development of isoform-specific inhibitors challenging. Methods: Here, we developed a unifying experimental protocol for fed-batch fermentation of mammalian ALOX isoforms in a bioreactor, followed by purification of the recombinant proteins and their functional characterization. Results: Our methodological protocol allowed the preparation of mg amounts of catalytically active human ALOX15, mouse Alox15 and human ALOX15B. The purified proteins are suitable for high-throughput inhibitor screening assays but can also be used as antigens for the preparation of isoform-specific antibodies and for direct structural analyses. Antibodies cross-reacting with human ALOX15 and ALOX15B have been detected in the blood of patients suffering from colorectal cancer. Conclusions: Our functional ALOX data stresses the catalytic differences between mouse and human ALOX15 orthologs, and these catalytic peculiarities need to be considered when the results of mechanistic studies obtained in mouse models of human diseases are transferred to the human situation. Full article

(This article belongs to the Special Issue Novel Insights into Lipid Metabolism in Health and Diseases)

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18 pages, 6228 KB

Open AccessArticle

Volatile Profiling and Transcriptomic Analysis of Peel and Flesh in Wampee (Clausena lansium (Lour.) Skeels)

by Ruibing Xu, Qingshan Li, Gengrui Zhu, Yi Chen and Gaoyang Zhang

Metabolites 2026, 16(8), 598; https://doi.org/10.3390/metabo16080598 - 21 Aug 2026

Abstract

Background: Wampee (Clausena lansium (Lour.) Skeels) is an understudied Rutaceae crop native to southern China, whose fruit features a complex aroma profile with simultaneous sour, sweet, bitter and astringent notes. Although bioactive compounds including flavonoids, alkaloids and volatile oils in wampee [...] Read more.

Background: Wampee (Clausena lansium (Lour.) Skeels) is an understudied Rutaceae crop native to southern China, whose fruit features a complex aroma profile with simultaneous sour, sweet, bitter and astringent notes. Although bioactive compounds including flavonoids, alkaloids and volatile oils in wampee fruit have been partially characterized, the tissue-specific metabolic and transcriptional basis underlying its distinctive aroma formation remains largely unclear. Methods: We performed an integrated volatile metabolomic and transcriptomic analysis on the pericarp (peel) and flesh of wampee fruit across three cultivars (Shanyellowpi, Heijingang, Bingtangxin). Volatile metabolites were profiled via headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS), and transcriptome profiles were generated by RNA-Seq. Multi-omics integration was conducted using Procrustes analysis, gene–metabolite correlation network construction and weighted gene co-expression network analysis (WGCNA). Results: A total of 288 volatile metabolites were identified, representing the most comprehensive volatile inventory for C. lansium reported to date. Principal component analysis and partial least squares discriminant analysis revealed distinct volatile profiles between pericarp and flesh; terpenoids were the dominant chemical class, accounting for 71.56–91.48% of total volatiles in pericarp and 61.88–67.22% in flesh. Notably, organoheterocyclic compounds were significantly enriched in Shanyellowpi flesh (40.45%), forming a cultivar-specific metabolic signature absent in the other two cultivars. Transcriptomic analysis showed that phenylpropanoid biosynthesis was the most significantly enriched pathway among differentially expressed genes, followed by monoterpene biosynthesis and sesquiterpenoid biosynthesis. Procrustes analysis demonstrated a strong global concordance between the two omics layers (M² = 0.535, p < 0.001). Gene–metabolite correlation networks identified terpene synthase (TPS) genes (HP075360, HP217350) and oxidoreductase genes (SOD1, GST, 10HGO) as candidate co-regulators of terpenoid biosynthesis. WGCNA further prioritized TPS genes, cytochrome P450 genes and MYB transcription factor genes as key regulators driving volatile metabolic divergence between tissues. Conclusion: This study provides a comprehensive volatile and transcriptomic atlas of wampee fruit, and identifies tissue-specific and cultivar-specific metabolic signatures as well as their candidate regulatory genes. These findings advance our understanding of quality differentiation in Rutaceae fruits and lay a foundation for molecular breeding and flavor improvement of wampee. Full article

(This article belongs to the Topic Metabolomics in Plants)

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38 pages, 11369 KB

Open AccessReview

Nicotinamide Mononucleotide Adenylyltransferase 1 and NAD⁺ Homeostasis in Neuroprotection and Aging

by You Sun, Bowei Li and Zhengjiang Qian

Metabolites 2026, 16(8), 597; https://doi.org/10.3390/metabo16080597 - 21 Aug 2026

Abstract

Nicotinamide adenine dinucleotide (NAD⁺) is a fundamental metabolic cofactor and signaling molecule that supports redox reactions, DNA repair, chromatin regulation, stress adaptation, inflammation, and neuronal maintenance. Age-associated NAD⁺ decline has been implicated in brain aging and neurodegenerative disorders, but the [...] Read more.

Nicotinamide adenine dinucleotide (NAD⁺) is a fundamental metabolic cofactor and signaling molecule that supports redox reactions, DNA repair, chromatin regulation, stress adaptation, inflammation, and neuronal maintenance. Age-associated NAD⁺ decline has been implicated in brain aging and neurodegenerative disorders, but the causal node and limiting compartment differ across tissues and disease states. Nicotinamide mononucleotide adenylyltransferase 1 (NMNAT-1) catalyzes the final step in NAD⁺ biosynthesis and represents the major nuclear isoform of the mammalian NMNAT family. Direct human genetic evidence establishes NMNAT-1 as a causal gene in inherited retinal degeneration, whereas evidence linking endogenous NMNAT-1 to broader brain aging or sporadic neurodegeneration is mainly convergent preclinical, preliminary, or indirect. Beyond NAD⁺ synthesis, biochemical and Drosophila studies suggest possible chaperone-like and proteostasis-supporting functions, but a separable NAD⁺-independent function of endogenous mammalian NMNAT-1 has not yet been established in vivo. Here, we review the molecular structure, localization, and regulation of NMNAT-1, emphasizing calibrated distinctions among catalytic nuclear NAD⁺ supply, engineered axonal protection, pathway-adjacent NAD⁺ interventions, and putative non-catalytic protection. We further discuss how NMNAT-1 dysfunction may contribute to aging-associated genomic instability, neuroinflammation, synaptic impairment, retinal degeneration, selected neurodegenerative models, and glioma biology. Finally, we evaluate therapeutic strategies targeting NMNAT-1 and NAD⁺ pathways, noting that no human trial has yet established efficacy for an NMNAT-1-directed neurological therapy. A compartment-aware and evidence-stratified view is therefore essential for translating NMNAT-1 biology into interventions for age-related neural disease. Full article

(This article belongs to the Special Issue Reactive Oxygen Species and Metabolic Dysregulation: From Bench to Bedside)

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12 pages, 693 KB

Open AccessArticle

Ciliary Neurotrophic Factor in Skeletal Muscle of Older Adults and the Effects of Weight Loss and Aerobic Training

by Alice S. Ryan, Guoyan Li, Colleen Lynch, Sausan M. Jaber and Galya Bigman

Metabolites 2026, 16(8), 596; https://doi.org/10.3390/metabo16080596 - 21 Aug 2026

Abstract

Background/Objectives: Ciliary neurotrophic factor (CNTF), a pleiotropic cytokine with central and peripheral actions, has been implicated in obesity, insulin resistance, and aging, yet its role in skeletal muscle and cardiometabolic health remains unclear. This study examined skeletal muscle CNTF mRNA expression in relation [...] Read more.

Background/Objectives: Ciliary neurotrophic factor (CNTF), a pleiotropic cytokine with central and peripheral actions, has been implicated in obesity, insulin resistance, and aging, yet its role in skeletal muscle and cardiometabolic health remains unclear. This study examined skeletal muscle CNTF mRNA expression in relation to adiposity and glucose tolerance in older adults and assessed the effects of six-month weight loss (WL) and aerobic exercise training (AEX) interventions on its expression. Methods: Sixty-seven adults (age, 60.75 ± 7.58) underwent a vastus lateralis muscle biopsy, VO₂max testing, dual-energy X-ray absorptiometry (DXA) scan, a resting metabolic rate (RMR) and substrate oxidation assessment, and a 3-h oral glucose tolerance test with glucose and insulin area under the curve (AUC) calculation. A subset completed 6 months of either a WL program (n = 21) or a supervised 3 times per week AEX intervention (n = 20). Results: At baseline, skeletal muscle CNTF expression was inversely associated with RMR, fat oxidation, 3-h glucose AUC, and insulin AUC, but not with BMI, percent body fat, or VO₂max. WL reduced body weight, fat mass, glucose AUC, insulin AUC, and basal muscle CNTF expression, whereas AEX increased VO₂max and reduced fat mass without altering body weight, glucose AUC, insulin AUC, or basal CNTF. Insulin-stimulated CNTF expression increased after both WL and AEX, and the intervention-induced change in glucose disposal (M) was positively associated with the change in insulin-stimulated CNTF. Conclusions: In older adults, skeletal muscle CNTF is associated with glucose intolerance but is not associated with body composition or aerobic fitness. Improvements in insulin sensitivity are associated with increases in muscle CNTF during hyperinsulinemia. Further work is needed to determine the mechanism for muscle CNTF change during hyperinsulinemia after weight loss and exercise training, and its role in glucose metabolism and obesity in older adults. Full article

(This article belongs to the Special Issue Effects of Exercise and Lifestyle on Cardiometabolic Health)

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15 pages, 4018 KB

Open AccessArticle

Diagnostic Performance of Serum Xenopsin-Related Peptide-1 in Gestational Diabetes Mellitus: A Prospective Observational Study

by Yasin Karadag, Ozgur Ozdemır, Gulseren İpek Karadag and Erinç Tekin

Metabolites 2026, 16(8), 595; https://doi.org/10.3390/metabo16080595 - 21 Aug 2026

Abstract

Background/Objectives: Gestational diabetes mellitus (GDM) is one of the most common metabolic disorders during pregnancy and is associated with adverse maternal and neonatal outcomes. Xenopsin-Related Peptide-1 (XRP-1) has recently emerged as a potential regulator of glucose metabolism and insulin homeostasis. This study [...] Read more.

Background/Objectives: Gestational diabetes mellitus (GDM) is one of the most common metabolic disorders during pregnancy and is associated with adverse maternal and neonatal outcomes. Xenopsin-Related Peptide-1 (XRP-1) has recently emerged as a potential regulator of glucose metabolism and insulin homeostasis. This study evaluated serum XRP-1 levels and assessed their diagnostic performance in women with GDM. Methods: In this prospective observational study, 120 pregnant women between 24 and 28 weeks of gestation were enrolled, including 60 women with GDM and 60 healthy controls. Serum XRP-1 concentrations were measured using an enzyme-linked immunosorbent assay (ELISA). Clinical, biochemical, and obstetric characteristics were compared between groups. Receiver operating characteristic (ROC) curve analysis and multivariable logistic regression were performed to evaluate the diagnostic performance and independent association of XRP-1 with GDM. Results: Serum XRP-1 levels were significantly higher in women with GDM than in healthy controls (3.45 ± 0.47 vs. 2.87 ± 0.46 ng/mL, p = 0.003). ROC analysis demonstrated moderate discriminatory performance for XRP-1 in identifying GDM (AUC = 0.658, 95% CI: 0.560–0.750), with an optimal cut-off value of 3.12 ng/mL, corresponding to 63.3% sensitivity and 61.7% specificity. Multivariable logistic regression demonstrated that serum XRP-1 remained independently associated with GDM after adjustment for maternal age, pre-pregnancy body mass index, gestational weight gain, and parity (adjusted OR 2.74, 95% CI 1.31–5.73; p = 0.007). HbA1c and C-reactive protein levels were also significantly higher in the GDM group. Conclusions: Serum XRP-1 concentrations were independently associated with GDM and demonstrated moderate diagnostic accuracy. Although XRP-1 cannot replace established diagnostic methods, it may represent a complementary biomarker for identifying gestational dysglycemia. Larger multicenter studies are required to validate its clinical utility. Full article

(This article belongs to the Special Issue Metabolic Changes During Pregnancy: Biomarkers, Metabolomics and Pregnancy Complications)

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19 pages, 1163 KB

Open AccessArticle

The Impact of Psychobiotic Therapy on Anxiety and Depressive Symptoms in Patients with Post-COVID Syndrome—A Randomized, Double-Blind, Placebo-Controlled Trial

by Sylwia Drzymała, Anna Blask-Osipa, Anna Szczepańska-Álvarez, Małgorzata Dobrzyńska, Hanna Markowska, Sławomira Drzymała-Czyż and Jarosław Walkowiak

Metabolites 2026, 16(8), 594; https://doi.org/10.3390/metabo16080594 - 19 Aug 2026

Abstract

Background: Recovering from COVID-19 does not always lead to complete recovery, and many patients report symptoms of anxiety and depression. One potential mechanism behind these disorders is dysbiosis. The aim of this study was to evaluate the impact of psychobiotic therapy on [...] Read more.

Background: Recovering from COVID-19 does not always lead to complete recovery, and many patients report symptoms of anxiety and depression. One potential mechanism behind these disorders is dysbiosis. The aim of this study was to evaluate the impact of psychobiotic therapy on the effectiveness of treating anxiety and depressive symptoms in individuals who had previously experienced COVID-19. Methods: This study was designed as a randomized, double-blind, placebo-controlled trial. A total of 62 participants were randomly allocated to one of two groups: a psychobiotic group (PG; 23 women, 9 men) receiving 3 × 10⁹ CFU Lactobacillus helveticus and Bifidobacterium longum, or a control group (CG; 21 women, 9 men) receiving a placebo, for 6 weeks. Fifty-six participants finalized the study and were included in the analysis (28 per group). The severity of depressive and anxiety symptoms at baseline and after the intervention was assessed using validated self-assessment tools: the Hospital Anxiety and Depression Scale (HADS), the Generalized Anxiety Disorder 7-item scale (GAD-7), the Beck Depression Inventory (BDI), and the Hopkins Symptom Checklist (SCL-90). Additionally, the profile of selected short-chain fatty acids (SCFAs) in the stool was assessed. Results: Following the supplementation period, the PG showed significantly lower median levels of depression and anxiety compared to the CG, corresponding to a 57.2% reduction in anxiety severity (GAD-7) and a 50.9% reduction in depressive symptoms (BDI) (HADS—Depression and Anxiety, and GAD-7: p = 0.0001; BDI: p = 0.0003). Additionally, the prevalence of anxiety and depressive symptoms significantly decreased in the PG compared to the CG based on the HADS-A (p = 0.0044), GAD-7 (p = 0.0219), and BDI (p = 0.0011) scores. Among the measured SCFAs, only the butyric acid concentration in PG increased significantly during supplementation (baseline vs. follow-up—p = 0.0338) and was higher in PG than in CG at the study’s end (p = 0.0248). However, in the PG, changes in the concentrations of all analyzed acids correlated with a reduction in the severity of anxiety symptoms measured using the HADS-A. Conclusions: Psychobiotic supplementation in individuals recovering from COVID-19 who exhibit anxiety and/or depressive symptoms led to mood improvement and a reduction in symptom severity, and it may serve as a supportive treatment. Full article

(This article belongs to the Special Issue Nutrition and Dietary Supplementation in the Context of Health, Disease, and Physical Performance)

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15 pages, 578 KB

Open AccessArticle

Combined Effects of Combined Resistance Exercise and Vitamin D Supplementation on Cardiometabolic Profiles and Functional Capacities in Elderly Women with Type 2 Diabetes

by Hyoung-Jun Kim, Deok-Su Yoo and Man-Gyoon Lee

Metabolites 2026, 16(8), 593; https://doi.org/10.3390/metabo16080593 - 19 Aug 2026

Abstract

Background/Objectives: This 12-week randomized controlled trial investigated whether progressive resistance training combined with vitamin D supplementation produces enhanced combined improvements in cardiometabolic profiles and functional capacities compared with monotherapies in elderly Korean women with type 2 diabetes mellitus (T2DM) and vitamin D [...] Read more.

Background/Objectives: This 12-week randomized controlled trial investigated whether progressive resistance training combined with vitamin D supplementation produces enhanced combined improvements in cardiometabolic profiles and functional capacities compared with monotherapies in elderly Korean women with type 2 diabetes mellitus (T2DM) and vitamin D deficiency. Methods: In a 2 × 2 factorial design, 52 women (aged 65–80 years) with T2DM and serum 25(OH)D < 20 ng/mL were assigned to four groups: Exercise + Vitamin D (Ex + VitD, n = 15), Exercise + Placebo (Ex + Placebo, n = 13), Vitamin D only (VitD, n = 11), or Control (n = 13). Exercise groups completed supervised progressive resistance training three times weekly, and vitamin D groups received 2000 IU/day cholecalciferol. Results: The Ex + VitD group achieved significant improvements in HbA1c (−0.13%, p = 0.019), fasting glucose (−0.79 mmol/L, p < 0.001), insulin (−1.96 μU/mL, p = 0.050), and HOMA-IR (−0.77, p = 0.020). Serum 25(OH)D increased substantially (+15.57 ng/mL, p < 0.001). Calcitonin rose exclusively in the Ex + VitD group (+2.57 pg/mL, p < 0.001, d = 3.34), while monotherapies showed no change. Total cholesterol (−23.93 mg/dL), triglycerides (−25.07 mg/dL), and LDL-cholesterol (−10.20 mg/dL) decreased significantly. Both exercise groups showed marked strength gains (chair stand +8.33 to +10.00 repetitions, p < 0.001) and balance improvements (functional reach +2.47 to +4.46 cm, p ≤ 0.033). Conclusions: Twelve weeks of progressive resistance training combined with vitamin D supplementation produced enhanced combined improvements in glycemic control, insulin sensitivity, calcitonin secretion, muscular strength, and lipid metabolism in elderly women with T2DM and vitamin D deficiency, targeting complementary pathways that neither intervention engaged alone. Full article

(This article belongs to the Special Issue The Role of Lifestyle, Physical Activity, and Exercise on Cardiometabolic Health and Diseases)

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21 pages, 15691 KB

Open AccessArticle

Cold-Induced Elevation of 3-Hydroxypropionate Exacerbates Colitis by Remodeling Gut Microbiota and Impairing Mitochondrial Respiration in Intestinal Epithelial Cells

by Yankun Jia, Baodong Gao, Kefei Wu, Mengjie Gao, Qi Lin, Tu Qian, Junjie Ma, Hongyu Zhang, Ping Zhu, Zhinan Chen and Yue Zhai

Metabolites 2026, 16(8), 592; https://doi.org/10.3390/metabo16080592 - 19 Aug 2026

Abstract

Background/Objectives: Inflammatory bowel disease (IBD) is a chronic gastrointestinal disorder influenced by environmental factors including cold stress. While cold exposure exacerbates intestinal inflammation, the specific microbial metabolites linking environmental stress to colitis remain unclear. 3-Hydroxypropionate (3-HPA) is a gut microbial metabolite elevated following [...] Read more.

Background/Objectives: Inflammatory bowel disease (IBD) is a chronic gastrointestinal disorder influenced by environmental factors including cold stress. While cold exposure exacerbates intestinal inflammation, the specific microbial metabolites linking environmental stress to colitis remain unclear. 3-Hydroxypropionate (3-HPA) is a gut microbial metabolite elevated following cold exposure, but its pathogenic role in intestinal inflammation has not been investigated. This study aimed to determine whether 3-HPA contributes to colitis progression and to characterize its effects on gut microbiota and intestinal epithelial function. Methods: We employed a dextran sulfate sodium (DSS)-induced colitis mouse model to assess the impact of cold exposure and exogenous 3-HPA administration. Paired shotgun metagenomic and metabolomic analyses were performed to evaluate gut microbial composition and metabolic outputs. Mechanistic studies using NCM460 intestinal epithelial cells were conducted to examine mitochondrial respiration and tight junction integrity under nutrient-limited conditions. Results: Cold exposure increased fecal 3-HPA levels and aggravated DSS-induced colitis, characterized by enhanced weight loss, histological damage, and immune cell infiltration. Direct 3-HPA supplementation alone was sufficient to worsen colitis severity. Multi-omics profiling revealed that 3-HPA reshaped gut microbiota composition, depleted short-chain fatty acids (SCFAs), and disrupted microbial tryptophan and bile acid metabolism. In vitro, 3-HPA impaired mitochondrial oxidative phosphorylation, reduced ATP production, and compromised tight junction organization in intestinal epithelial cells. Conclusions: These findings identify 3-HPA as a gut microbial metabolite elevated by cold exposure that contributes to colitis progression by disrupting beneficial microbial metabolism while also impairing epithelial mitochondrial function and barrier integrity. Modulating 3-HPA production or its downstream epithelial effects may represent a potential therapeutic approach for IBD exacerbated by environmental stress. Full article

(This article belongs to the Special Issue Microbial Metabolites and Host Health)

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