Metabolites doi: 10.3390/metabo16070506

Authors: Cong Wang Yanran Li Huihui Meng Gaocheng Shi Yifan Sun Ke Che Hao Yu

Background: Osteoarthritis (OA) pathogenesis involves inflammatory-metabolic crosstalk driving cartilage destruction, yet the mechanisms of potential therapeutics like curcumin remain poorly defined. Methods: We integrated untargeted metabolomics, transcriptomic analysis of four GEO datasets (GSE12021, GSE55235, GSE55457, GSE82107), and three machine learning algorithms (LASSO, Random Forest, XGBoost) to characterize curcumin’s effects on IL-1β-induced human chondrocytes. Results: Metabolomic profiling demonstrated that IL-1β caused significant depletion of TCA cycle intermediates compared to blank controls, including pyruvate (log2FC = −1.34, p < 0.001) and malate (log2FC = −0.54, p < 0.001). High-dose curcumin (10 μM) significantly restored these metabolites towards normal levels (pyruvate log2FC = −0.01 vs. model; malate log2FC = −0.20 vs. model). Three machine learning algorithms converged on a six-gene inflammatory-metabolic signature (NFKBIA, MMP9, LCK, TDO2, HADHA, VEGFA), all showing excellent discriminative performance for OA (individual AUCs > 0.75). qRT-PCR validation confirmed that high-dose curcumin significantly downregulated pro-inflammatory genes compared to IL-1β treatment alone: JUN (log2FC = −0.68, p < 0.001), IL6 (log2FC = −1.13, p < 0.001), PTGS2 (log2FC = −0.94, p < 0.001), CCL20 (log2FC = −1.51, p < 0.001), and MMP9 (log2FC = −0.42, p < 0.001). Conversely, curcumin significantly upregulated the NF-κB inhibitor NFKBIA (log2FC = 0.40, p < 0.001), whose expression was initially suppressed by IL-1β (−log2FC = 0.76 vs. blank, p < 0.001). Conclusions: This systems-level analysis suggests curcumin modulates metabolic-inflammatory networks in OA chondrocytes, with NFKBIA as a candidate mediator, offering a mechanistic framework for drug-like molecule development despite curcumin’s own translational limitations.

Metabolites doi: 10.3390/metabo16070505

Authors: Marcin Sadowski Emilia Zawieja Agata Muzsik-Kazimierska Ewa Bulczak Agata Chmurzynska

Background: The main aim of this study was to assess the effects of short-term N-acetylcysteine (NAC) supplementation on concentrations of homocysteine (Hcy) and reduced glutathione (rGSH), blood lipid profile and liver enzyme activities in endurance-trained adults, and to determine whether these effects are modified by methylenetetrahydrofolate reductase (MTHFR) C677T and glutathione S-transferase Pi 1 (GSTP1) A313G. Methods: A total of 56 males and 21 females completed a randomized, double-blind, placebo-controlled crossover trial. Participants received 1200 mg of NAC or a placebo for seven days in a crossover design. Serum Hcy and plasma rGSH concentrations were assessed using dedicated biochemical assays, while blood lipid profile and liver enzyme activities were measured using the biochemical analyzer Konelab 20i. Genotyping was conducted using TaqMan probes. A series of within-subject/between-subject repeated-measures analysis of variance (ANOVA) within a general linear model framework were performed to compare Hcy, rGSH, blood lipid profile and liver enzymes activities before and after the intervention. Results: Hcy concentrations significantly decreased following NAC supplementation (18.58 ± 5.45 µmol/L vs. 16.51 ± 4.97 µmol/L; p = 0.009), although subgroup analysis indicated that the decrease was significant only among females (15.40 ± 4.96 µmol/L vs. 13.60 ± 3.68 µmol/L; p = 0.002) without any significant effect among males. We did not observe any significant changes in rGSH, lipid profile, or liver enzyme activities. There was no interaction between NAC supplementation, MTHFR and GSTP1 genotypes and the changes noted in the parameters we analyzed. Conclusions: In conclusion, short-term NAC supplementation may reduce circulating Hcy concentrations in endurance-trained adults, particularly in females. No consistent effects were observed for rGSH, lipid profile, or liver enzyme activities.

Metabolites doi: 10.3390/metabo16070504

Authors: Rolivhuwa Carol Mudau Lufuno Ethel Nemadodzi

Background: In the coming decades, the agricultural system will increasingly rely on organic amendments to sustain crop production, maintain soil health and ensure long-term food security. While inorganic fertilizers remain widely used for vegetable production due to their rapid nutrient availability, their prolonged application has been shown to degrade soil quality, disrupt microbial communities and limit the nutritional quality of harvested produce. Consequently, there is a growing need to explore organic alternatives such as biochar and poultry manure that can enhance both crop productivity and functional quality. Objective: This study aimed to determine the influence of different application rates of biochar (5/T1, 10/T2, and 20/T3 t/ha), poultry manure (10/T1, 20/T2, 30/T3 t/ha), and NPK (2:3:4) as control on the metabolomic profile of tomato fruit. Methods: The metabolomic profile was determined using 1H-nuclear magnetic resonance (NMR). Results: Common metabolites across biochar rates included allantoin, asparagine and betaine, while rate-specific released metabolites such as inosine (T1), epicatechin (T2) and kynurenine (T3) were also identified. Similarly, poultry manure showed an array of metabolites at the highest application rate, with metabolites such as cellobiose, creatinine and maltose, while histamine (T1) and ADP (T3) were also detected as distinct metabolites.

Metabolites doi: 10.3390/metabo16070503

Authors: Miyu Isogai Norihiro Imai Tadashi Ogawa Yumi Hayashi

Background/Objectives: Vitamin D deficiency (VDD) is a major global health concern. Although maternal VDD during pregnancy may influence metabolic health in offspring, previous studies have focused predominantly on male offspring, leaving its effects in females insufficiently characterized. This study aimed to comprehensively assess hepatic metabolic profiles in female offspring exposed to maternal VDD during gestation. Methods: Pregnant 129/Sv mice were fed either a control diet or a vitamin D-deficient diet throughout pregnancy. After weaning, female offspring were maintained on a normal diet and analyzed at 12 weeks of age following a 16 h fast. Hepatic metabolomic profiling was conducted using GC–MS/MS, followed by multivariate analysis. To evaluate the potential contribution of fasting, publicly available liver RNA-seq data from ad libitum-fed and 16 h-fasted mice (GSE130127) were also analyzed. Results: No overt metabolic abnormalities were detected between the groups. However, principal component analysis revealed differences in hepatic metabolic profiles between the Control and VDD groups. Levels of 4-aminobutyric acid and proline were significantly elevated in the VDD group. Pathway analysis revealed significant alterations in arginine and proline metabolism and purine metabolism, along with changes in pathways associated with amino acid and energy metabolism. Comparison with fasting-associated liver RNA-seq data revealed minimal overlap, although the potential influence of fasting cannot be completely excluded. Conclusions: Maternal VDD during pregnancy was associated with altered hepatic metabolic profiles in female offspring despite the absence of overt metabolic abnormalities. These findings suggest that maternal VDD may influence hepatic metabolism in female offspring and indicate that the potential long-term effects of maternal VDD on offspring metabolism warrant further investigation.

Metabolites doi: 10.3390/metabo16070502

Authors: Morena Munzone Giorgia Maria Marmo Alessandro Polizzi Elena Jovanova Angela Angjelova Saturnino Marco Lupi Gaetano Isola

Periodontitis is a chronic inflammatory disease increasingly recognized as a manifestation of complex microbial dysbiosis extending beyond the oral cavity. Recent advances in spatial metagenomics provide unprecedented resolution to investigate microbial community structure, function, and localization within periodontal niches and along the oral–gut axis. This review aims to explore how spatially resolved metagenomic approaches refine our understanding of the ecological and functional shifts in bacterial populations associated with periodontitis and their systemic implications. By integrating spatial mapping with shotgun metagenomics, we highlight distinct microenvironmental signatures within periodontal pockets, characterized by anaerobic pathobionts, metabolic reprogramming, and localized inflammatory gradients. Furthermore, we examine evidence supporting bidirectional interactions between oral and gut microbiota, suggesting that oral-derived taxa may contribute to gut dysbiosis through translocation and ecological disruption. From a basic science perspective, spatial metagenomics reveals niche-specific microbial functions and interspecies interactions that are not captured by bulk sequencing. Clinically, these insights open avenues for precision diagnostics and targeted therapeutics, including microbiome modulation strategies tailored to spatial microbial organization. Overall, this work underscores the importance of spatial context in metagenomic analyses and advances the conceptual framework linking periodontal disease to systemic microbial dysbiosis.

Metabolites doi: 10.3390/metabo16070501

Authors: Natália Ellen Delmicon Nathália dos Reis Franco Giovanna Cavanha Corsi Roberta Mi Kyong Kim Cho Helen Cristina Vidal Marcelo Macedo Rogero

Nutritional genomics has expanded our understanding of how dietary exposures interact with genetic and epigenetic mechanisms involved in metabolic dysfunction. In this context, metabolic dysfunction associated with excessive visceral adiposity arises from a multifaceted interaction between systemic inflammation, insulin resistance, and inter-individual biological susceptibility. Obesity, particularly when driven by diets rich in saturated fatty acids, disrupts intestinal homeostasis, thereby triggering metabolic endotoxemia and contributing to low-grade systemic inflammation and adipose tissue dysfunction. Advances following the Human Genome Project have broadened our understanding of the molecular mechanisms of metabolic diseases, highlighting the role of genetic variability and epigenetic regulation in obesity-related insulin resistance. In nutritional science, the integration of genomics and proteomics has further elucidated how dietary exposures interact with the biological pathways involved in this dysfunction. From a nutrigenomic perspective, this narrative review aims to discuss how genetic variability and diet-related molecular mechanisms contribute to obesity-related metabolic dysfunction, with emphasis on single-nucleotide polymorphisms in key genes, including FTO, MC4R, PPAR, APOA, and FADS, involved in the regulation of energy homeostasis and insulin secretion. Additionally, we analyze studies on epigenetic mechanisms, including DNA methylation and the action of microRNAs, which act as post-transcriptional regulators sensitive to nutritional and inflammatory stimuli. We also address how dietary patterns, such as the Mediterranean Diet, as well as nutrients and bioactive compounds, can influence epigenetic regulation. We conclude that integrating multiomics data may improve our understanding of the molecular mechanisms underlying metabolic dysfunction and may support the future development of personalized nutritional strategies and molecular biomarkers for obesity and cardiometabolic diseases.

Metabolites doi: 10.3390/metabo16070500

Authors: Raúl Ibarra-Salce José Luis Eduardo Doval-Caballero Daniel Uribe-Cortés Genesis Dinora Eugenio-Ponce Mariela Ibarra-Salce Omar Jaime-Leal Manuel Ramón García-Sáenz

Background/Objectives: Type 2 diabetes is increasingly recognized as a systemic disorder driven not only by chronic hyperglycemia and insulin resistance, but also by dysregulated interorgan communication. Extracellular vesicles (EVs), including exosomes and microvesicles, have emerged as biologically active carriers of proteins, lipids, and microRNAs capable of modulating gene expression in recipient cells. This narrative review integrates clinical, experimental, and translational evidence on EV-associated microRNAs as candidate biomarkers and potential mediators of diabetic complications, with emphasis on diabetic neuropathy, diabetic kidney disease, diabetic retinopathy, and metabolic dysfunction-associated steatotic liver disease (MASLD). Methods: This review was aligned with the SANRA framework and focused on biological plausibility, evidence from tissue and biofluids, biomarker potential, therapeutic implications, and barriers to clinical translation. Studies were additionally interpreted according to biological matrix, EV-carrier specificity, analytical platform, study design, and level of functional validation. Results: Across complications, EV-associated microRNAs appear to participate in shared pathogenic processes, including oxidative stress, inflammation, endothelial dysfunction, fibrosis, angiogenesis, neurodegeneration, and metabolic memory. In diabetic neuropathy, microRNAs such as miR-146a, miR-155, miR-21-5p, and miR-148a-3p have been linked to neuroinflammation, Schwann-cell dysfunction, axonal injury, and neuropathic pain. In diabetic kidney disease, miR-21, miR-29, miR-30, and miR-126 are implicated in podocyte injury, tubulointerstitial fibrosis, albuminuria, and microvascular dysfunction. In diabetic retinopathy, microRNAs including miR-146a, miR-155, miR-21, miR-126, and miR-200b contribute to neurovascular injury, inflammation, barrier disruption, and angiogenesis. In MASLD associated with diabetes, hepatocyte-derived EVs carrying microRNAs such as miR-1 and miR-126a-3p may link hepatic lipotoxicity to endothelial inflammatory and β-cell dysfunction. Conclusions: Although EV-associated microRNAs offer promising opportunities for biomarker discovery, risk stratification, and targeted therapies, clinical translation remains limited by heterogeneity in EV isolation, microRNA quantification, biological matrices, and outcome definitions. Distinguishing EV-associated miRNAs from total circulating extracellular miRNAs remains essential for biological interpretation. Standardized, longitudinal, and externally validated studies are required before these signals can be implemented as actionable tools in precision diabetes care.

Metabolites doi: 10.3390/metabo16070499

Authors: Amedeo Lonardo Ralf Weiskirchen

Hepatocellular carcinoma (HCC), the most common histological type of primary liver cancer (PLC), remains one of the most consequential malignancies arising in chronic liver disease, in part because its incidence and mortality rates remain closely aligned [...]

Metabolites doi: 10.3390/metabo16070498

Authors: Triin Paabo Eliis Grigor Egon Taalberg Natalja Luppova Eliise-Rosalinda Raudmäe Piret Mihkelson Alan Altraja Ain Kaare Rando Porosk Kalle Kilk

Background/Objectives: Discrimination between iron deficiency anemia (IDA) and anemia of inflammation (AI), the major causes of anemia, remains a challenge and novel biomarkers are needed. This prospective study characterizes metabolomic changes in patients with anemia, compares IDA and AI, and evaluates the ability of metabolomic profiling to categorize otherwise unclassifiable anemia (UA) cases. Methods: In the single-center cross-sectional study, patients with anemia were classified as IDA, AI, or their combination (IDA + AI) according to traditional iron biomarkers. Targeted metabolomic analysis was conducted with tandem mass spectrometry using the MxP® Quant 500 kit, with 617 individual metabolites and 227 calculated parameters in the final analysis. Results: The final cohort included 70 patients with anemia and 27 controls. The concentrations of six metabolites and six calculated parameters were significantly different in patients with anemia compared to controls. Anemia was associated with decreased concentrations of several polyunsaturated fatty acid (PUFA)-containing triglycerides (n = 3) and phosphatidylcholines (n = 2), as well as with increased asparagine/aspartate and docosahexaenoic acid/eicosapentaenoic acid ratio. Multivariate analysis using only metabolomic data differentiated between IDA and AI with a general classification accuracy of 88%. Unclassifiable anemia samples were reclassified mostly as IDA (n = 11) or IDA + AI (n = 6), with one sample reclassified as AI. Conclusions: Metabolomic markers of PUFAs differ between patients with anemia and controls, indicating possible alterations in lipid metabolism. Our preliminary findings suggest that metabolomic data may be capable of distinguishing between IDA and AI. However, owing to several limitations of the current study, the potential utility of metabolome-based approaches should be confirmed in independent validation studies.

Metabolites doi: 10.3390/metabo16070497

Authors: Maya Nassif Wendy M. Miller Kathryn M. Ziegler Nadia Ashrafi Romana Mimi Ashrafi Abdullah Khalid Sumeyya Akyol Jay Idler Milda Milčiūtė Vilija Lomeikaitė Austėja Jankevičiūtė Matthew D. Sims Michael E. Maddens Ali Yilmaz Stewart F. Graham

Background/Objectives: Metabolomics has emerged as a tool to gain insight into the body’s biological responses to therapeutic interventions. Bariatric surgery remains the most effective treatment for severe obesity and associated comorbidities, leading to significant weight and metabolic improvements. Using a multi-platform, multi-compartment metabolomics approach, this study systematically characterizes longitudinal changes in fecal and serum metabolomes of 45 patients following sleeve gastrectomy (SG). Participants were stratified by weight loss outcomes to identify metabolic signatures associated with differential responses, which may serve as predictors of weight loss and provide mechanistic insights in developing targeted therapeutic strategies. Methods: Metabolomic and lipidomic responses to SG were analyzed using multivariable linear mixed-effects models based on data collected pre-operatively and at 3 and 12 months post-operatively. Results: The percentage total weight loss for the highest versus lowest weight loss tertiles (T3 vs. T1) at twelve months was 35.81 + 5.4% and 19.49 + 2.62%, p < 0.001, respectively. Substantial alterations in fecal metabolites and lipid species were observed among T3 after twelve months, including aspartate, tyrosine, carnitine, glycine, PC.ae.C36.4, PC.aa.C38.0, PC.ae.C44.4, PC.ae.C40.2, and PC.aa.C40:5. Specifically, changes in serum lipid species including SM.OH.C22:1, PC.ae.C32:1, PC.aa.C34:4, PC.aa.C36:6, PC.ae.C34:3, PC.ae.C34:1, and PC.ae.C32:2, support serum lipidomics as a minimally invasive marker of gut remodeling and adaptation following SG. Sex-stratified analysis revealed unique fecal and serum metabolic changes, highlighting the significance of personalized metabolic monitoring and obesity treatment. Conclusions: Our findings identify metabolic alterations associated with response variability following SG and highlight the potential utility of machine learning to predict weight-loss trajectories and inform personalized interventions.

Metabolites doi: 10.3390/metabo16070496

Authors: Bartłomiej Łukaszuk Adrian Chabowski Andrzej Ziemba Barbara Choromańska Piotr Myśliwiec Katarzyna Supruniuk Agnieszka Mikłosz

Background: Lipoproteins are molecules composed of phospholipids and apolipoproteins that transport triacylglycerol and cholesterol in blood and are implicated in the development of many diseases. Methods: In this study, we fill a knowledge gap by precisely characterizing the apolipoprotein profile (with Bio-Plex Human Apolipoprotein Assay) in three metabolically separate groups of individuals (lean individuals and obese individuals without and with metabolic syndrome) and at four distinct time points (0, 3, 6, and 12 months post bariatric surgery). Results: Obese patients had a higher baseline ApoB/ApoA1 ratio, which returned to the reference level over the follow-up period. The above is of clinical importance, as the ratio is a predictor of adverse cardiovascular events common in obese subjects. Interestingly, plasma concentrations of most of the investigated apolipoproteins appeared to be relatively stable at the onset of the experiment, with changes observed later in time. We detected significant drops in the levels of ApoC3, ApoD, and ApoH that occurred as early as three months post intervention. On the other hand, the levels of ApoA2, ApoE, and ApoJ increased with time. Of the above, ApoE is known to be involved in the removal of TAGs and cholesterol from the blood. Conversely, ApoJ appears to be one of the determinants of the tissues’ responsiveness to insulin. Thus, it may be an indicator of the reduced insulin resistance observed a few months after the surgery. Conclusions: Overall, the investigated proteins have a documented role in the development and progression of vascular pathologies. Hence, our results may be interpreted as a sign of improved cardiovascular fitness of our patients.

Metabolites doi: 10.3390/metabo16070495

Authors: Mark Cannon John Peldyak Eleanor Campbell

Background/Objectives: Cholesterol homeostasis is often framed as a dietary problem, but circulating low-density lipoprotein (LDL) biology is governed largely by endogenous sterol handling, with the liver acting as the principal integrative organ for cholesterol synthesis, LDL receptor-mediated clearance, very-low-density lipoprotein (VLDL) export, bile acid production, and biliary sterol disposal. This narrative review evaluates the hepatic basis of cholesterol regulation, statin pharmacology, gut microbial sterol metabolism, chronic hepatic inflammation, and a proposed oral–gut–liver–artery axis in atherogenesis. The aim of this narrative review is to clarify which elements of the proposed axis are established, which are supported but incomplete, and which remain hypothesis-generating. Methods: Mechanistic, translational, clinical, and review literature were synthesized to separate established mechanisms from emerging and speculative links. PubMed/MEDLINE, Scopus, and Google Scholar were searched from January 2000 through May 2026. Primary search terms included: cholesterol homeostasis, LDL receptor, SREBP2, statin pleiotropic effects, statin-associated muscle symptoms, gut microbiota cholesterol, bile salt hydrolase, MASLD, Porphyromonas gingivalis liver, phosphorylated dihydroceramides, serine dipeptide lipids Bacteroidetes, ceramide atherosclerosis, and oral–gut–liver–artery axis. Results: LDL/apoB causality and hepatic statin mechanism are well-established. Gut microbiota can alter cholesterol absorption, coprostanol formation, bile acid pools, and portal signaling, but these effects are context-dependent. Hepatic free cholesterol loading and lysosomal sterol stress are strongly implicated in the biology of metabolic dysfunction-associated steatotic liver disease (MASLD). Periodontal pathogens, especially Porphyromonas gingivalis, may contribute to liver and vascular inflammation through bacteremia, oral–gut translocation, innate immune activation, and bioactive bacterial sphingolipids. Phosphorylated dihydroceramides (PDHCs) and Bacteroidetes-derived serine dipeptide lipids have been detected in human arterial specimens and shown to enter host ceramide pools, providing a direct lipid metabolic pathway linking microbial community composition to vascular disease. Viridans streptococci and the Streptococcus anginosus group are inflammatory cofactors rather than proven causes of hepatic cholesterol overproduction. Conclusions: The strongest model involves microbial amplification of hepatic cholesterol dysmetabolism, endothelial activation, foam-cell formation, and plaque vulnerability acting on a host-derived LDL/apoB scaffold. This model is testable and should complement guideline-based LDL-lowering therapy.

Metabolites doi: 10.3390/metabo16070494

Authors: Anliang Huang Yunshu Zhang Baoning Wu Tingting Bai Xiaoyang Yuan Dong Shang Shurong Ma Rihong Huang Peiyuan Yin

Background: Clinical lipidomics can capture disease-associated molecular alterations at high resolution, yet translating complex lipid species data into interpretable biological insight remains challenging. Existing workflows often emphasize statistical discrimination while underutilizing the structural information embedded in lipid species. To address this gap, we developed LipiDecipher, a structure-oriented analytical framework designed to summarize lipidomic alterations into interpretable structural patterns and to provide database-supported biological contextualization. Methods: LipiDecipher integrates differential lipid analysis, structure-resolved summarization, multivariate discrimination, and knowledge-based lipid-to-protein/pathway contextualization. We applied this framework to a retrospective serum lipidomics dataset comprising healthy controls and patients with acute myocardial infarction or post-PCI recurrent myocardial infarction. To improve transparency and robustness, the revised analysis includes sex-disaggregated reporting, covariate-adjusted sensitivity analyses for sex and age, and internal separation stability assessment of category-specific LDA projections through resampling-based feature stability analysis, repeated cross-validation, and permutation testing. Results: The framework identified distinct lipid alterations across study groups, including changes in phosphatidylinositols, ceramides, and triglyceride remodeling patterns. These alterations became more interpretable when summarized at the structural level, including lipid class composition, acyl-chain length, and degree of unsaturation. Internal discrimination analyses suggested separability between groups, while repeated resampling highlighted a subset of recurrently selected lipid features. Knowledge-based mapping prioritized lipid-associated biological contexts related to glycerophospholipid metabolism, sphingolipid metabolism, membrane remodeling, inflammatory signaling, and energy-related processes. Importantly, these protein- and pathway-level outputs are presented as database-supported hypotheses rather than direct evidence of target engagement or pathway activation in the studied cohort. Conclusions: LipiDecipher provides a structure-oriented and interpretation-focused framework for clinical lipidomics. In a retrospective acute myocardial infarction cohort, it enabled the prioritization of candidate lipid signatures and biologically plausible hypotheses from complex lipidomic data. These findings support its use as a hypothesis-generating analytical tool, while external validation and experimental follow-up remain necessary before mechanistic or clinical claims can be established.

Metabolites doi: 10.3390/metabo16070493

Authors: Qi Lu Hongqun Zhao Kureshi RuKeye Yao Geng Jincheng Du Liyang Chen Qiuhui Zhu Congfang Xi Jianbin Li

Background/Objectives: Drought stress is a primary constraint on maize productivity, yet the role of rhizosphere microbial communities in modulating cultivar-specific drought resilience remains poorly understood. This study aimed to investigate the physiological and microbiome-mediated responses underlying differences in drought tolerance between contrasting cultivars to better understand drought tolerance mechanisms. Methods: Two maize cultivars with contrasting drought tolerance—NK718 (tolerant) and Zhongdan 808 (sensitive)—were subjected to drought stress at the V12 stage. We assessed yield components, oxidative stress indicators (Malondialdehyde (MDA)), and antioxidant enzyme activities (Superoxide Dismutase (SOD), Peroxidase (POD), Catalase (CAT)). Metagenomic sequencing was employed to analyze structural and functional shifts in the rhizosphere microbiota. Results: Drought significantly suppressed yield and physiological performance in both cultivars. However, the sensitive cultivar suffered more pronounced yield losses and severe oxidative stress, indicated by elevated Malondialdehyde (MDA) and decreased antioxidant enzyme activities. Conversely, the tolerant cultivar maintained superior physiological homeostasis. Metagenomic sequencing revealed drought-induced microbial shifts, including decreased Proteobacteria and Ascomycota, alongside increased Actinobacteriota and Mucoromycota. Notably, the drought-tolerant cultivar exhibited enhanced microbial community stability and more complex co-occurrence networks. Furthermore, it enriched specific functional pathways, such as phenylpropanoid biosynthesis, which positively correlated with yield stability and antioxidant capacity. Conclusions: Maize drought tolerance is underpinned by the coordinated regulation of plant physiological adaptation and the structural and functional stabilization of the rhizosphere microbiome. These findings offer a theoretical framework for developing breeding strategies that leverage root-microbe interactions to optimize maize yields under water-limited conditions.

Metabolites doi: 10.3390/metabo16070492

Authors: Yange Yu Dandan Dai Guixiao La Xiangyang Li Xiaoyang Guo Yi Wen Tiegang Yang

Background/Objectives: Dioscorea opposita Thunb. is widely cultivated as a nutritious crop; however, the dynamic effects of different rotation years on its agronomic traits, photosynthetic performance, and tuber metabolome remains poorly understood. This study aimed to systematically investigate the effects of varying rotation years on these parameters. Methods: Six field treatments were established: Y0 (0-year rotation, continuous cropping), Y1 (1-year), Y2 (2-year), Y3 (3-year), Y4 (4-year), and CK (fallow land with ≥8 years of rotation). Tuber metabolomic profiling was performed using UPLC-MS/MS. Results: Rotation years <4 showed no differences in tuber length or yield, with tuber length ranging from 35.42 to 47.18 cm and yield from 103.31 to 133.77 g. Shorter rotations (<4 years) exhibited significantly reduced chlorophyll content, as well as diminished photosynthetic parameters (Pn, Gs, and Tr). Metabolomic analysis identified 93 metabolites, of which 30 were differential, with 11 showing enrichment in Y4. Notably, procyanidin B1, kaempferol, dihydroquercetin, pyridoxine, and L-cystine exhibited higher levels in Y0. Sinapic acid, tyramine, glutamine, dibutyl phthalate, and fructose reached peak levels in fallow land (CK). All pairwise comparisons except Y4 vs. CK were enriched in the flavonoid and flavone biosynthesis pathway, with flavonoids representing the predominant class of differential metabolites. Cluster analysis showed that metabolites in clusters 1 and 7 peaked at Y4, while those in clusters 3, 4, 5, and 6 reached minimum levels at Y4. Conclusions: Rotation years of less than 4 years led to restricted growth, reduced yield, impaired chlorophyll synthesis, and altered metabolic profiles. A four-year rotation is identified as a critical turning point in metabolite accumulation, providing valuable guidance for sustainable D. opposita cultivation.

Metabolites doi: 10.3390/metabo16070491

Authors: Mariana Luna Bruno Rodrigues Andréa Ramalho

Background: Vitamin D deficiency is highly prevalent in individuals with severe obesity and may worsen after malabsorptive bariatric procedures. Adolescence represents a critical period of skeletal and metabolic maturation and may influence mineral–hormonal adaptation after Roux-en-Y gastric bypass (RYGB). Objective: To investigate whether developmental stage influences longitudinal mineral–hormonal adaptation after RYGB in adolescents and adults with severe obesity. Methods: This prospective observational cohort study included 120 participants undergoing RYGB: 60 adolescents (15–19 years) and 60 adults (20–49 years) with a history of severe obesity. Assessments were performed preoperatively and at 6 and 12 months postoperatively. Serum 25-hydroxyvitamin D, ionized calcium, phosphorus, and parathyroid hormone (PTH) were measured. Group comparisons were performed using non-parametric tests within a translational life-course framework. Results: Vitamin D inadequacy (<30 ng/mL) was highly prevalent at baseline in both groups (78.3% vs. 85.0%). Despite substantial weight loss in both cohorts, adolescents exhibited higher frequencies of hypocalcaemia and hypophosphataemia (p < 0.001), progressive elevation of PTH levels, and a higher prevalence of secondary hyperparathyroidism at 12 months. Adults showed a comparatively less pronounced endocrine–mineral response but also experienced persistent increases in PTH throughout follow-up. Vitamin D inadequacy remained highly prevalent in both groups despite standardized supplementation. Conclusions: Postoperative mineral–hormonal adaptation after RYGB differs according to developmental stage. Adolescents exhibited greater endocrine–mineral vulnerability during a critical period of skeletal maturation, suggesting that biological stage may influence postoperative adaptation beyond anthropometric response alone. These findings support developmental stage-specific monitoring and individualized postoperative management after metabolic surgery.

Metabolites doi: 10.3390/metabo16070490

Authors: Mirela Frandes Adriana Gherbon Anca Tudor Oana Albai Mihaela Maria Vlad Călin Muntean

Background: Metabolic dysfunction is a complex process arising from coordinated interactions among insulin resistance, dyslipidemia, hepatic dysfunction, obesity, low-grade inflammation, and endocrine alterations. The triglyceride–glucose (TyG) index is a simple, reproducible surrogate of insulin resistance, but most studies have evaluated it through isolated association-based analyses. We characterized the endocrine–metabolic architecture associated with TyG in patients with thyroid dysfunction using a systems-phenotyping approach. Methods: In this retrospective, single-center, cross-sectional study of 387 adults evaluated for thyroid dysfunction, unsupervised phenotypes were derived by principal component analysis (PCA), K-means, Gaussian mixture models (GMM), and hierarchical (Ward) clustering using fully measured primary metabolic variables (fasting glucose, triglycerides, HDL- and LDL-cholesterol, body mass index, alanine, and aspartate aminotransferase). TyG was then examined as a descriptor of the identified architecture. Model-based latent profile analysis (BIC, entropy) and a censoring-aware, rank-based Gaussian graphical model (GGM) of partial correlations were additionally estimated. Results: Three overlapping, clinically interpretable phenotypic partitions of an underlying metabolic continuum were identified: a metabolically preserved phenotype (MP), an intermediate hepatic-dominant phenotype (IHD), and a severe insulin-resistance-dominant phenotype (SIRD), characterized by obesity, atherogenic dyslipidemia, and hyperuricemia. TyG values increased monotonically across the three partitions (medians 8.24, 8.74, and 8.87 in MP, IHD, and SIRD, respectively; p < 0.001), providing an accessible single-number summary of the metabolic gradient. Cluster separation was modest (silhouette = 0.17), consistent with a continuum, but the three-profile solution was supported by latent profile analysis (ΔBIC = −96.7; relative entropy = 0.75) and was reproduced across frameworks (adjusted Rand index of 0.75 with GMM and 0.46 with Ward). In the censoring-aware GGM, metabolic and thyroid variables formed two near-orthogonal blocks (maximum absolute metabolic–thyroid partial correlation: 0.16; median: 0.05). Conclusions: The systems phenotyping approach identified three clinically interpretable phenotypic partitions (MP, IHD, SIRD) along a metabolic continuum in patients evaluated for thyroid dysfunction. TyG values increased monotonically across partitions (medians 8.24, 8.74, 8.87) and provided a pragmatic single-number summary of the principal metabolic axis. The IHD phenotype indicates that hepatic dysregulation can emerge as a distinct early stage rather than solely a late consequence of insulin resistance. Metabolic and thyroid axes were near-orthogonal, positioning thyroid autoimmunity as a parallel modulatory layer. These findings support TyG as an accessible descriptor for multidimensional endocrine–metabolic risk stratification.

Metabolites doi: 10.3390/metabo16070489

Authors: Jin Jin Yang Cheng

Background/Objectives: Metabolic-dysfunction-associated steatotic liver disease (MASLD) and metabolic-dysfunction-associated steatohepatitis (MASH) arise in the setting of obesity, insulin resistance, type 2 diabetes, and metabolic syndrome. This review examines how mitochondrial dysfunction participates in the transition from lipid accumulation to hepatocyte injury, inflammation, and fibrosis, and how evidence from human, animal, and in vitro studies should be interpreted. Methods: We provide a narrative synthesis of mechanistic, translational, and clinical studies on hepatic mitochondrial metabolism, fatty acid oxidation, oxidative phosphorylation, redox stress, organelle crosstalk, mitophagy, mitochondrial biogenesis and proteostasis, mitochondrial danger signals, the gut-liver-mitochondria axis, and mitochondria-related therapeutic strategies. Results: In early metabolic overload, mitochondrial oxidation may increase as an adaptive response. With persistent substrate pressure, this adaptation can become inefficient, with impaired fatty acid disposal, less efficient oxidative phosphorylation, reactive oxygen species production, redox imbalance, defective mitochondrial quality control, altered mitochondrial biogenesis, mitochondrial unfolded protein response (UPRmt)-related proteostatic stress and mtDNA instability. Mitochondrial DNA and RNA released from damaged organelles may also activate cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING), inflammasome, and RNA-sensing pathways, linking hepatocyte stress to macrophage activation, stellate cell activation, extracellular matrix deposition, and fibrosis. Conclusions: The current evidence supports mitochondria as a stage-dependent amplifier of metabolic liver injury rather than a uniform initiating event. Clinically, the strongest evidence remains with upstream metabolic unloading and liver-directed metabolic therapy, whereas direct mitochondrial restoration and quality-control targeting remain promising but less mature.

Metabolites doi: 10.3390/metabo16070488

Authors: Alihan Tigli Yakup Baykus Rulin Deniz Guzide Ece Akinci Nazli Sener Yasemin Ercan Degirmenci Oguzhan Karakoc Muhammet Bora Uzuner Sefer Ustebay Sermin Kilic Engin Korkmazer Murat Erdemir Suleyman Aydin

Background: This study aimed to evaluate the phenotype-specific profiles of serum Isthmin-1 (ISM-1), Trimethylamine N-Oxide (TMAO) and Nitric Oxide (NO) levels in women diagnosed with Polyendocrine Metabolic Ovarian Syndrome (PMOS, formerly known as Polycystic Ovary Syndrome—PCOS) according to the Rotterdam criteria. Methods: This cross-sectional study enrolled 90 reproductive-aged women, divided equally into five groups (n = 18 per group) with similar baseline metabolic parameters: healthy controls and PMOS Phenotypes A, B, C, and D. To minimize confounding effects, individuals with recent use of specific medications were excluded, and 24 h dietary recalls were obtained. Fasting blood samples were collected during the early follicular phase. Serum ISM-1, TMAO, and NO levels were quantified via ELISA, and insulin resistance was determined using the HOMA-IR index. Data were adjusted for potential confounders, including age, BMI, and smoking status, using multivariate linear regression models. Results: No statistically significant differences were observed between the groups in key parameters such as BMI and HOMA-IR. Serum ISM-1 levels did not show a significant difference between the groups (p = 0.501). In contrast, NO levels were found to be significantly lower in all PMOS phenotypes compared to the control group (p < 0.001), and this reduction remained independent in regression models. TMAO levels, however, exhibited a phenotype-specific distribution; in the non-hyperandrogenic Phenotype D, they were found to be significantly lower than in the control group and hyperandrogenic phenotypes A and B. In the multivariate regression analysis, it was confirmed that Phenotype D was independently associated with low TMAO levels (B = −0.131, p = 0.027). Conclusions: Although PMOS patients share a similar profile of obesity and insulin resistance, they exhibit marked biochemical heterogeneity. Whilst the reduction in NO levels may indicate a generalised vascular change affecting all phenotypes, the observation of low TMAO levels specifically in the non-hyperandrogenic Phenotype D highlights a distinct biochemical signature associated with this subgroup, observed in the absence of hyperandrogenism. Our findings support the notion that adopting phenotype-specific, individualised approaches in the management of PMOS may be beneficial.

Metabolites doi: 10.3390/metabo16070487

Authors: Ruoyu Li Guofeng Li Shilin Chen Xuejie Lv Dan Wang Jianjun Xiang Yu Jiang Dong Tan Chuancheng Wu

Background: Gastric cancer remains a leading cause of cancer-related deaths worldwide. Although significant progress has been made in clinical diagnosis and treatment, the molecular mechanisms underlying gastric cancer have not yet been fully elucidated. To address this, this study employs a multi-omics approach to systematically analyze the molecular characteristics of gastric cancer. Methods: This case–control study enrolled 218 GC patients and 218 healthy controls, and adopted a multi-omics strategy combining inductively coupled plasma mass spectrometry (ICP-MS), element-related genome-wide association study (eGWAS), and untargeted metabolomics to explore the element-gene-metabolite regulatory axis in GC. Results: A total of nine plasma differential elements associated with gastric cancer were identified, with a combined diagnostic accuracy of 0.918. Specifically, elements such as Fe, Co, and Li showed significant correlations with 63 genes involved in key signaling pathways, including MAPK, SMAD, and Wnt. Genome-wide association studies (GWAS) revealed that gastric cancer-related genes were significantly enriched in cancer-associated pathways and signaling cascades such as Rap1. Metabolomic analysis further demonstrated that 20 elements in the gastric cancer cohort correlated with 94 metabolites, predominantly enriched in pyrimidine and glutathione metabolism pathways. Conclusions: These nine plasma differential elements showed high combined diagnostic efficacy and were associated with genes and metabolites enriched in cancer-related signaling, metabolic reprogramming, and DNA damage response pathways. Together, these findings suggest potential multi-level associations among plasma elemental alterations, genetic variation, and metabolic dysregulation in GC, providing candidate circulating biomarkers and mechanistic clues for future investigation.

Metabolites doi: 10.3390/metabo16070486

Authors: Mengli Zhang Min Ou Xuancheng Wang Song Kou Xianghua Xia Wenyan Fan Senhua Lu Yu Chen Xiaonan Yang

Background/Objectives: This study is the first to investigate the potential mechanism of star anise extract (SAE) in protecting against cold stress-aggravated acute lung injury (CSALI) in rats. Methods: A rat CSALI model was induced via combined lipopolysaccharide challenge and cold stress exposure. The preventive effects of SAE were evaluated using cytotoxicity assays, quantification of biochemical indices and inflammatory factors, and histopathological examination. Ultra-performance liquid chromatography coupled with high-resolution mass spectrometry (UPLC–HRMS)-based serum metabolomics was employed to systematically profile CSALI-associated metabolic alterations and decipher the potential mechanism underlying the preventive effects of SAE. Results: SAE alleviated pathological progression of CSALI, suppressed inflammatory cell migration, markedly reduced pulmonary inflammatory cell infiltration, and ameliorated lung tissue injury in CSALI rats. SAE also improved abnormal liver function indicators and lowered the levels of pro-inflammatory factors in both serum and bronchoalveolar lavage fluid (BALF). Serum metabolomics analysis identified and annotated 24 disease-altered differential metabolites and evaluated the protective effects of SAE on them. These metabolites were significantly enriched in two key metabolic pathways related to the pathogenesis of CSALI, including arachidonic acid metabolism and glycerophospholipid metabolism. Furthermore, based on metabolite changes, phospholipase A2 was hypothesized as a potential key regulatory factor that may cooperate with arachidonic metabolism to suppress the inflammatory cascade. Conclusions: These findings demonstrated that SAE exerted prominent anti-inflammatory activity and effectively protected against lung injury in CSALI rats.

Metabolites doi: 10.3390/metabo16070485

Authors: Filip Bieg Agnieszka Galanty Patricia Arancibia-Ávila Shela Gorinstein Paweł Paśko

Background/Objectives: Interest in alternative, non-animal sources of vitamin D has increased due to the global prevalence of its deficiency and the growing demand for plant-based dietary options. Mushrooms and algae have emerged as potential sustainable sources of vitamin D2 and, in selected cases, vitamin D3 following ultraviolet (UV) exposure. However, the comparative bioavailability and clinical effectiveness of vitamin D2 relative to vitamin D3 remain controversial. This review aims to evaluate the content of vitamin D2 in mushrooms and algae, the impact of UV irradiation on its synthesis, and the effectiveness of vitamin D2 supplementation compared with vitamin D3 in humans. Methods: PubMed, ScienceDirect, and Google Scholar were searched (1996–2026). Only human intervention studies were included when assessing clinical efficacy. Data on natural sources and pharmaceutical formulations were analyzed. Results: UV irradiation markedly increases vitamin D2 content in mushrooms, as compared to cultivated products. Algal vitamin D content varies, depending on species and UV exposure, with no robust clinical trials confirming improvement of serum 25(OH)D after algal supplementation. Across multiple randomized controlled trials, vitamin D2 consistently increased circulating 25(OH)D2 but frequently reduced 25(OH)D3 and demonstrated lower efficacy in raising total 25(OH)D compared with vitamin D3, as confirmed by a recent meta-analysis. Conclusions: Although UV-enhanced mushrooms represent a quantifiable dietary source of vitamin D2, clinical evidence consistently indicates lower efficacy of vitamin D2 compared with vitamin D3. Algae cannot currently be considered a validated source of vitamin D for improving human vitamin D status. Further mechanistic and long-term clinical studies are required.

Metabolites doi: 10.3390/metabo16070484

Authors: Valentina Annamaria Genchi Angelo Cignarelli Andrea Sansone Dimitri Yannas Leonardo Dalla Valentina Daniele Renda Livraghi Giorgia Spaggiari Daniele Santi

The authors would like to make the following correction to their published paper [...]

Metabolites doi: 10.3390/metabo16070483

Authors: Mario Muñoz-López Gonzalo Quesada-Fernández Edgar Simón Sancho-Haro Xabier Ramírez de la piscina-Viúdez Eneko Baz-Valle José Francisco López-Gil José Francisco Tornero-Aguilera

Background: Biomarkers are increasingly used in sport science and sports medicine to monitor training load, recovery, metabolic stress, nutritional status, and potential clinical risk in athletes. However, their interpretation is often limited by overreliance on isolated values, population reference ranges, and simplified thresholds. This narrative review aims to provide a contextual and metabolically informed framework for interpreting routine and emerging biomarkers in athletes. Methods: A critical narrative synthesis was conducted across key physiological domains relevant to athlete monitoring, including exercise intensity, metabolic flexibility, muscle damage, protein catabolism, hydration, hematological and iron status, micronutrient and bone–muscle health, inflammation, endocrine stress, sport-specific interpretation, and emerging metabolomics. The review integrated routine laboratory markers with pathway-level metabolomic interpretation and practical decision-making principles. Results: Routine markers such as lactate, creatine kinase, urea/blood urea nitrogen (BUN), creatinine, electrolytes, ferritin, C-reactive protein, cortisol, testosterone, and vitamin D are useful only when interpreted in relation to individual baseline, sampling conditions, recent workload, nutrition, hydration, sleep, illness, sex-specific physiology, and performance. Metabolomics expands interpretation by identifying pathway-level signatures involving glycolysis, β-oxidation, amino acid turnover, purine degradation, ketone bodies, acylcarnitines, bile acids, oxylipins, kynurenine metabolites, and exercise-induced signaling molecules such as lactate, β-aminoisobutyric acid (BAIBA), and N-lactoyl-phenylalanine (Lac-Phe). However, omics-derived markers require careful standardization and validation before routine applied use. Conclusions: Biomarkers should refine, not replace, clinical reasoning and athlete monitoring. A BASE framework (Baseline, Analytical standardization, Sport-specific context, and Evidence of functional change) may support more precise and proportionate interpretation of both routine blood tests and emerging metabolomic tools in athletes.

Metabolites doi: 10.3390/metabo16070482

Authors: Horia Silviu Branea Ciprian Ilie Rosca Daniel Florin Lighezan Violeta Ariana Nicoras Adrian Sebastian Zus Romina Georgiana Bita Daniel-Dumitru Nisulescu

Background: Atrial fibrillation (AF) is a major substrate for ischemic stroke, but cerebrovascular risk is heterogeneous and influenced by AF phenotype, comorbidities, anticoagulant exposure, renal function, and metabolic risk. The triglyceride–glucose index (TyG index) is a simple surrogate marker of insulin resistance calculated from fasting triglycerides and fasting plasma glucose. Whether the TyG index is associated with ischemic stroke burden and recurrent cerebrovascular events in patients with different AF phenotypes remains insufficiently characterized. Objective: This study aimed to evaluate the association between the TyG index and ischemic stroke burden in patients with paroxysmal and permanent AF, with particular focus on recurrent ischemic stroke. Methods: We performed a retrospective observational analysis of patients with AF divided according to AF phenotype: paroxysmal AF and permanent AF. Clinical, biological, therapeutic, and cerebrovascular variables were extracted from an existing real-world clinical database. The TyG index was calculated as ln [fasting triglycerides (mg/dL) × fasting plasma glucose (mg/dL)/2]. Triglycerides and fasting plasma glucose were measured during hospitalization; therefore, the analysis was framed as a retrospective cross-sectional association with recorded ischemic stroke burden, not as a prospective prediction study. The main outcome was any ischemic stroke. Secondary outcomes included recurrent ischemic stroke, defined as ≥2 recorded ischemic stroke events, and stroke burden categorized as no stroke, single stroke, or recurrent stroke. Continuous variables were reported as mean ± standard deviation and compared using independent samples t-tests or one-way analysis of variance, as appropriate. Results: After patient-level de-duplication, 1031 unique patients with AF were identified: 310 with paroxysmal AF and 721 with permanent AF. The strict TyG-eligible analytical cohort included 941 patients: 295 with paroxysmal AF and 646 with permanent AF. Permanent AF was associated with a higher ischemic stroke burden than paroxysmal AF. Any ischemic stroke was recorded in 325/646 patients with permanent AF compared with 79/295 patients with paroxysmal AF (50.3% vs. 26.8%, p < 0.001). Recurrent ischemic stroke was also more frequent in permanent AF (7.7% vs. 4.1%, p = 0.035). Among stroke-positive patients, the proportion with recurrent stroke was similar between permanent and paroxysmal AF (15.4% vs. 15.2%, p = 0.966). The TyG index was significantly higher in paroxysmal AF than in permanent AF (8.93 ± 0.69 vs. 8.73 ± 0.61, p < 0.001), but it did not differ significantly across stroke burden categories. In logistic regression, the TyG index was not associated with any ischemic stroke or recurrent ischemic stroke in unadjusted, age/sex-adjusted, AF phenotype-adjusted, or clinically adjusted models. Conclusions: In this real-world retrospective cohort, permanent AF was associated with a substantially higher ischemic stroke burden than paroxysmal AF. However, the TyG index was not independently associated with ischemic stroke occurrence or recurrence. Although patients with paroxysmal AF had a more adverse lipid metabolic profile and higher TyG index values, this did not translate into a higher TyG-related cerebrovascular burden. These findings suggest that the TyG index alone has limited utility as a marker of ischemic stroke burden in heterogeneous AF cohorts and that its prognostic value may depend on cardiometabolic phenotype, adiposity distribution, AF substrate, anticoagulant exposure, and the clinical context in which it is applied.

Metabolites doi: 10.3390/metabo16070481

Authors: Yun-Seong Lee Sooah Kim

Background/Objectives: Hydrochloric acid (HCl)/ethanol-induced gastric mucosal injury is closely associated with oxidative stress and inflammatory responses. Probiotics are promising therapeutic agents for gastrointestinal disorders. Therefore, this study evaluated the preventive effects of Cheonggukjang-derived Bacillus strains on HCl/ethanol-induced gastric mucosal injury in a rat model (n = 5 per group), with emphasis on inflammatory mechanisms. Methods: Eight-week-old male Sprague–Dawley rats were orally administered Bacillus amyloliquefaciens C393 1.0 × 109 CFU (B393), Bacillus subtilis C439 1.0 × 109 CFU (B439), or B. subtilis C512 1.0 × 109 CFU (C512). Gastric injury was induced by oral administration of HCl/ethanol (150 mM HCl in 60% ethanol). Results: HCl/ethanol exposure significantly increased symptom scores, gastric mucosal lesion area, and histopathological damage. Pretreatment with B393 and B439 significantly attenuated these alterations. Moreover, HCl/ethanol administration increased gastric secretion volume and decreased gastric pH, both of which were significantly normalized by B393 and B439. Serum levels of pro-inflammatory cytokines, including tumor necrosis factor-α and interleukin-6, were significantly elevated following HCl/ethanol exposure but were markedly reduced by B393 and B439. Immunohistochemical analysis demonstrated that nuclear factor-kappa B activation in gastric tissues was significantly suppressed in these groups. Conclusions: These findings indicate that Cheonggukjang-derived Bacillus strains exert strain-specific gastroprotective effects possibly by suppressing NF-κB-mediated inflammatory signaling.

Metabolites doi: 10.3390/metabo16070480

Authors: Gessica Di Carlo Maria Lucia Tommolini Alberto Frisco Giorgia Spalluto Dominic Foley Mirco Zucchelli Maria Concetta Cufaro Ilaria Cicalini Ines Bucci Luca Federici Vincenzo De Laurenzi Damiana Pieragostino Claudia Rossi

Lysosomal Storage Diseases (LSDs) include roughly 70 inherited metabolic disorders, most of which are expressed in an autosomal recessive pattern. These conditions arise from mutations in genes encoding lysosomal enzymes, leading to intracellular buildup of substrates and subsequent lysosomal dysfunction. LSDs can be broadly classified based on the nature of the stored substrate, encompassing Sphingolipidoses, Mucopolysaccharidoses, Lysosomal Glycogen Storage Disease, Oligosaccharidoses, Mucolipidoses, and Lysosomal Proteinoses. Although individually rare, LSDs collectively affect approximately 1 in 5000 live births. They usually manifest in childhood, but adult-onset types are also detected. Clinical manifestations are heterogeneous and may involve the central nervous system, skeletal system, skin, heart, muscles, kidneys, and other organs. Several therapeutic strategies are available for LSDs, including Enzyme Replacement Therapy to restore deficient enzymes, Hematopoietic Stem Cell Transplantation to provide functional donor-derived cells, Substrate Reduction Therapy and pharmacological chaperones to modulate substrate turnover or enhance enzyme stability, alongside symptomatic and supportive treatments. Ongoing research is also exploring gene therapy-based strategies. Current diagnostic criteria remain insufficient for reliable presymptomatic diagnosis, highlighting the need for more sensitive and specific approaches. In this context, untargeted metabolomics is a powerful strategy to investigate pathogenic pathways, identify novel diagnostic and prognostic biomarkers, and uncover potential therapeutic targets. Accordingly, this review provides an overview of LSDs, focusing on untargeted metabolomics studies and their contribution to the discovery of novel biomarkers and previously unrecognised pathogenic mechanisms relevant to diagnostic and therapeutic innovation.

Metabolites doi: 10.3390/metabo16070479

Authors: Siqian Xiao Dan Gao Tielin Wang Binbin Yan Feng Xiong Chongning Lv Chuanzhi Kang

Background: Light intensity and spectral quality are important abiotic factors that induce metabolic reprogramming in medicinal plants, thereby enabling adaptive responses to diverse radiation environments. This systematic review examines how different light conditions influence secondary metabolism, emphasizing that the observed differences can be interpreted as variations in response strategies and regulatory plasticity. Methods: Published transcriptomic and metabolomic studies on light-regulated secondary metabolism in medicinal plants were reviewed, with attention paid to light intensity, spectral quality, photoreceptor signaling, phytohormone interactions, and accumulation of major bioactive compounds. Results: Plants are often described as heliophytic or sciophytic; however, this classification primarily reflects ecological adaptations rather than inherent metabolic differences. Changes in metabolism are commonly associated with accumulation patterns of phenolic acids, terpenoids, alkaloids, and other bioactive compounds and are closely linked to dynamic regulation at the gene expression level. Based on transcriptomic and metabolomic evidence, we summarized signaling networks from photoreceptors, including phytochromes, cryptochromes, phototropins, and UV RESISTANCE LOCUS 8, to the Constitutive photomorphogenic 1–ELONGATED HYPOCOTYL 5 regulatory module and its interactions with JA, SA, and GA pathways. Variations in metabolic outcomes are mainly related to response thresholds, signaling intensity, and resource allocation, rather than exclusive production of specific metabolites. Conclusions: This review provides a framework for understanding light-regulated metabolic plasticity and offers insights into optimizing light environments and improving medicinal plant quality.

Metabolites doi: 10.3390/metabo16070478

Authors: Haifeng Geng Zhibo Zhou Lingfei Meng Mingnan Zhuang Yan Zhao

Caffeine is among the most widely used supplements in sports nutrition, with substantial evidence supporting its efficacy for enhancing athletic performance. However, the relevance of pre-exercise caffeine supplementation extends beyond its ergogenic effects. Exercise itself acts as an acute cardiometabolic stressor, eliciting dynamic responses in blood pressure, heart rate, vascular tone, substrate utilization, and glucose regulation. Caffeine may further modify the magnitude, temporal profile, and recovery kinetics of these responses. This focused narrative review examines the acute cardiometabolic responses associated with pre-exercise caffeine supplementation and its potential regulatory effects. It outlines the underlying biological mechanisms, including adenosine receptor antagonism, hemodynamic and vascular pathways, and metabolic and substrate-utilization pathways, while synthesizing current evidence from the literature. Available evidence indicates that the acute effects of caffeine are highly context dependent. In some exercise settings, caffeine may promote lipolysis and fat oxidation; in others, particularly among susceptible individuals or under specific exercise conditions, it may be associated with greater acute cardiovascular or autonomic load, reflected by higher peripheral vascular resistance and blood pressure, altered vascular reactivity, or delayed post-exercise autonomic recovery. Its effects may vary according to dose, timing, supplement form, exercise modality and intensity, training status, habitual caffeine intake, genotype, sex, and hormonal status. Overall, pre-exercise caffeine should not be regarded solely as a uniformly beneficial ergogenic aid, but rather as a physiological modulator that may reshape the acute cardiometabolic milieu during and after exercise. Future studies should integrate hemodynamic, vascular, metabolic, and individual-variability measures over extended observation periods to support more evidence-based and individualized guidance on the appropriate use of pre-exercise caffeine.

Metabolites doi: 10.3390/metabo16070477

Authors: Markel Rico-González Damiano Formenti Carlos D. Gómez-Carmona Luca Paolo Ardigò

Background/Objectives: The systematic review aims to highlight the effects of school-based physical activity and nutritional supplementation programs in obese children from preschool to high school, based on randomized controlled trials. Methods: The search strategy was designed based on the PICOS framework. Then, a systematic review of relevant articles was conducted across six databases (Cochrane Library, PubMed, ProQuest, SCOPUS, Web of Sciences and SPORTDiscus) to identify articles that included children from preschool to high school who engaged in physical activity at school and received nutritional supplementation. All the included studies were assessed using the RoB-2 checklist. Results: Of the 234 studies reviewed, six met the inclusion criteria for this systematic review (publication years: 2023–2025). The results revealed highly heterogeneous interventions and mixed outcomes, often influenced by factors such as supplement type, dosage and participant gender. This limited and inconsistent body of evidence underscores a significant gap in the literature concerning the combined effects of school-based exercise and nutritional supplementation in obese youth. Conclusions: Limited evidence suggests mixed results with multi-micronutrient supplementation showing some benefits in boys from resource-limited settings, while several interventions demonstrated no effects. Energy-dense supplementation proved counterproductive. Gender-stratified approaches are recommended, but cautious implementation is warranted given methodological limitations and inconsistent findings.

Metabolites doi: 10.3390/metabo16070476

Authors: Tao Zhang Junchao Liu Huiyi Wen Jianqun Liu

Background/Objectives: Tripterygium glycosides (TG) are used to treat inflammatory and autoimmune diseases, but their clinical application is limited by toxicity and the lack of process-responsive quality markers. This study examined whether roasting and dealkalization remodel the TG metabolite profile and alter the post-dose serum profile of circulating prototype constituents. Methods: Self-prepared TG, roasted TG (RTG), roasted–dealkalized TG (RDTG), and five marketed products were profiled by ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS/MS). Seven representative compounds were quantified by validated high-performance liquid chromatography (HPLC). Rat serum after oral administration was analyzed to compare circulating prototype constituents. Results: We characterized 243 constituents in material samples and 63 circulating prototype constituents in serum. Roasting primarily reshapes the profiles of diterpenoids and triterpenoids. Celastrol was not detected in the RTG and RDTG material samples, nor in the corresponding single-time-point serum profiles under the current analytical conditions. In contrast, wilforlide A exhibited an increase in material samples. Dealkalization preferentially reduced alkaloid-related constituents, including wilforine in material samples and tripterygiumine T in serum. Conclusions: Integrated material profiling, targeted quantification, and serum prototype analysis identified candidate process-responsive markers for processed TG preparations. Because the serum study was based on relative signal intensities rather than full pharmacokinetics, these markers require further pharmacokinetic and toxicological validation.

Metabolites doi: 10.3390/metabo16070475

Authors: Leilei Zuo Yan Chen Yuxuan Luo Huan Yang Dayi Chen Ying Zhang Xiao Meng Waralee Watcharin

Background/Objectives: Styphnolobium japonicum cv. Jinhuai (SJvJ) represents a medicinal and edible plant whose metabolite composition is strongly shaped by its growing location. Current quality control methods mainly rely on rutin quantification, lacking comprehensive metabolic markers for origin discrimination. Therefore, this study aimed to profile interregional metabolic differences between Guangxi and Sichuan SJvJ flower buds, identify characteristic differential markers, and clarify relevant metabolic pathways, thereby guiding quality control, germplasm evaluation, and functional food development. Methods: Ultra-high performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) was employed to identify metabolites. The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Cancer HSP were applied to screen the key active ingredients of traditional Chinese medicine (TCM-KAIs) and disease-related pharmaceutical ingredients (PDRIs). Specifically, we targeted six highly prevalent human diseases and another five disorders based on therapeutic indications documented in the Chinese Pharmacopoeia. Multivariate analyses, such as principal component analysis, hierarchical clustering analysis, and other statistical methods, were applied to investigate differential metabolites. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database was utilized for pathway enrichment analysis of marker metabolites. Results: In total, 1550 metabolites were identified across 12 categories, predominantly flavonoids. Additionally, 152 TCM-KAIs and 204 PDRIs against 11 diseases were screened. Multivariate analyses indicated that geographical origin was closely associated with observed metabolic variation among the tested samples: Guangxi samples accumulated higher lipids and nucleotides, whereas Sichuan samples showed higher levels of flavonoids and phenolic acids. Vanilloloside, protocatechuic acid-4-O-glucoside, and gallic acid-4-O-glucoside were identified as key inter-group biomarkers. KEGG enrichment analysis revealed enhanced metabolism of nucleotide/pyrimidine in Guangxi, whereas zeatin biosynthesis was upregulated in Sichuan, consistent with discrepancies in regional climatic patterns. Conclusions: This study established a more comprehensive metabolomic dataset for FBSJvJ. It also clarified the correlations between origin and quality and unraveled the underlying mechanisms. These findings facilitate origin authentication, standardized quality control, and rational exploitation of FBSJvJ as raw materials of functional foods.

Metabolites doi: 10.3390/metabo16070474

Authors: Eleni Mavrogonatou Dimitris Kletsas

The authors would like to make the following correction to their published paper [...]

Metabolites doi: 10.3390/metabo16070473

Authors: Makayla A. Guinn Dara N. Orbach Hussain Abdulla

Background/Objectives: Dolphins inhabiting coastlines can be influenced by anthropogenic factors. As biochemical changes accumulate in blubber over weeks to months, blubber metabolites may be informative biomarkers of molecular adaptations to environmental changes. Methods: We investigated the blubber metabolomic signatures of live free-ranging bottlenose dolphins for the first time. This exploratory study analyzed blubber samples from 35 common bottlenose dolphins (Tursiops truncatus) in South Texas waters using untargeted ultra-high-performance liquid chromatography-Orbitrap metabolomics. Results: Blubber samples exhibited distinct temporal and spatial metabolic patterns. Pathway enrichment analyses comparing detected metabolites (n = 2777) revealed that dolphins sampled in the spring had enhanced lipid quality and immune regulation, while dolphins sampled in the summer showed stress-associated metabolic responses. Dolphins inhabiting areas previously reported to experience heavy vessel traffic and contaminant burdens exhibited enriched immune- and inflammation-associated pathways. Dolphins that visually appeared to have poorer body condition exhibited metabolite profiles suggestive of increased protein catabolism. Dolphins in extreme salinity conditions had more abundant membrane maintenance and endocrine pathways. Conclusions: Dolphins from each system exhibited distinct metabolic signatures that may be associated with differing physiological responses, highlighting the potential utility of blubber biomarkers for assessing physiological adaptations in free-ranging marine mammals. Improved understanding of habitat-specific physiological responses offers critical insights into how cumulative impacts may affect the health and adaptive capacity of vulnerable species in dynamic coastal ecosystems.

Metabolites doi: 10.3390/metabo16070472

Authors: Yingfeng Chen Renqing Zhao Ji Ma Weidong Zheng Jian Gong

Objectives: Obesity disrupts adipose and systemic immune–metabolic homeostasis, yet the molecular mechanisms through which exercise restores abnormal tissue function remain incompletely defined. This study aimed to screen cross-tissue candidate genes associated with exercise-mediated correction of obesity-related transcriptional disorders via multi-tissue transcriptome profiling and bioinformatic gene prioritization. Methods: Transcriptomic datasets of mouse visceral white adipose, subcutaneous white adipose and skeletal muscle were downloaded from the public GEO database, covering normal control, high-fat induced obese and post-exercise intervention groups. R programming was applied to complete differential analysis, GO/KEGG enrichment, PPI network, LASSO and GSEA; independent human adipose datasets from GEO validated candidate genes. Results: Exercise reversed obesity-triggered transcriptional changes in adipose tissues. Exercise-responsive genes concentrated on immune inflammation, lipid and energy metabolism. Key hub genes for tissue remodeling were screened, and depot-specific pathway regulation was verified by GSEA. CCL2 showed consistent expression trends across mouse and human adipose data. Conclusions: This study identifies distinct tissue-specific transcriptional responses to exercise: visceral adipose mainly achieves reversal of obesity-induced inflammatory dysregulation, subcutaneous adipose undergoes combined immune–inflammatory and metabolic reprogramming, while skeletal muscle presents only energy-metabolism adaptive remodeling without obvious reversal of obese gene disorders. Immune–metabolic pathways dominate exercise-induced restoration in adipose tissues. Integrated network screening and cross-species validation identified CCL2 as a conserved candidate associated with exercise-responsive immune–metabolic pathways, providing valuable molecular candidates for further anti-obesity research.

Metabolites doi: 10.3390/metabo16070471

Authors: Arjun Prasad Tiwari Blake R. Rushing Larissa Silva Susan J. Sumner Pinku Mukherjee

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy characterized by limited treatment options and poor prognosis. Gemcitabine is a commonly used chemotherapy; however, gemcitabine resistance in PDAC poses a critical barrier to effective treatment, as the underlying mechanisms are not yet fully understood. Methods: This study employs an exploratory untargeted metabolomics approach to investigate metabolic differences in PDAC cells in the presence and absence of gemcitabine treatment. HPAF-II, MIA PaCa-2, and BxPC-3 cell lines were used as models for gemcitabine-resistant, moderately responsive, and permissive PDAC cells, respectively. Results: MTT assay results revealed that BxPC-3 cells are highly sensitive to gemcitabine treatment, HPAF-II cells are the most resistant, and MIA PaCa-2 cells exhibit moderate sensitivity. Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) of the metabolomics data demonstrated clear differentiation of gemcitabine-treated and untreated (control) cells. When comparing the treated vs. control conditions, 170 metabolites matched to an in-house library of standards were significant (p < 0.05 or fold change ≥ 2 or VIP ≥ 1) differentiators in HPAF-II cells, whereas MIA PaCa-2 and BxPC-3 cells had 178 and 218 differentiating metabolites, respectively. HPAF-II cells treated with gemcitabine had significantly higher levels of N-acetylneuraminic acid and 7-dehydrocholesterol compared with the control group. In contrast, these metabolites were significantly lower or non-significant in BxPC-3 treated cells. Pathway analysis revealed that the steroid biosynthesis pathway was significantly perturbed in HPAF-II cells, whereas amino sugar and nucleotide sugar metabolism was predominantly altered in BxPC-3 cells. Conclusions: Overall, this exploratory study reveals metabolic differences between treated and untreated cells to derive targeted therapeutic strategies that could be used in the future to improve treatment outcomes for PDAC patients.

Metabolites doi: 10.3390/metabo16070470

Authors: Juliana Sanches Trevizol Motoki Okamoto Shohei Yamashita Nanako Kuriki Susanne Brueckner Satoru Shindo Toshihisa Kawai Raissa Estefane Vaz Damião Aline Dionizio Marilia Afonso Rabelo Buzalaf Maiko Suzuki

Background/Objectives: Fluoride (F) is widely used in public water fluoridation to prevent dental caries, and an optimal level of F has been linked to improved glucose metabolism in animal models. Per- and polyfluoroalkyl substances (PFAS), including fluorotelomer alcohols (FTOHs), are persistent environmental contaminants with potential effects on pancreatic function. Methods: This in vitro and in vivo study investigated the effects of 8:2 FTOH and F (NaF) on pancreatic β-cells, focusing on Ca2+ homeostasis, insulin secretion, and the GPR40 pathway. Results: Results showed that 8:2 FTOH alters Ca2+ influx in a dose-dependent, biphasic manner, enhancing it at low doses and inhibiting it at high doses, while F increased Ca2+ signaling at high doses. High-dose 8:2 FTOH also downregulated GPR40 protein in βTC-6 pancreatic cells and modulated pathways related to lipid metabolism, endoplasmic reticulum stress, and insulin regulation in the mouse pancreas by proteomic analyses (in vivo). Conclusions: These findings exploratory indicate that both PFAS and F can impact β-cell function through complex mechanisms, potentially affecting Ca2+ homeostasis. This work highlights the hormesis effect of F and provides novel insights into the pancreatic effects of environmentally relevant PFAS exposures, emphasizing the need for further mechanistic studies at low, human-relevant doses.

Metabolites doi: 10.3390/metabo16070468

Authors: Lara Šamadan Marković Hana Panić Juraj Krznarić Branimir Gjurašin Neven Papić

Background: Metabolic-dysfunction-associated steatotic liver disease (MASLD) is associated with adverse outcomes in sepsis, but risk stratification within MASLD remains insufficiently defined. We investigated whether an admission liver–metabolic phenotype framework combining cardiometabolic burden with liver injury/fibroinflammatory risk markers identifies clinically relevant organ-support vulnerability in community-acquired sepsis. Methods: This secondary analysis of the prospective SepsisFAT cohort (378 adults with community-acquired sepsis) classified patients into four phenotypes by cardiometabolic burden (≥2 of: diabetes, hypertension, dyslipidemia, BMI ≥ 30 kg/m2) and liver-risk positivity (FIB-4 ≥ 2.67, APRI ≥ 1.0, liver stiffness ≥ 10 kPa, or FAST ≥ 0.55). The primary outcome was acute kidney injury (AKI), while continuous renal replacement therapy (CRRT), other organ-support outcomes and in-hospital mortality were secondary endpoints. Results: Phenotype distribution was Low-risk 137 (36.2%), Cardiometabolic-only 84 (22.2%), Liver-dominant 88 (23.3%), and Mixed liver–cardiometabolic 69 (18.3%). AKI and CRRT increased across phenotypes (13.9% to 40.6% and 5.1% to 26.1%, respectively), and in-hospital mortality was highest in the Mixed phenotype (26.1%). After Firth-penalized adjustment for age, sex, and admission SOFA, the Mixed phenotype remained independently associated with AKI (aOR 2.82, 95% CI 1.37–5.90) and CRRT (aOR 3.87, 1.50–10.80), confirmed in non-renal SOFA and admission eGFR-adjusted sensitivity analyses. Cardiometabolic burden alone did not confer excess organ-support risk. The same gradient persisted within the MASLD subgroup. Conclusions: Admission liver–metabolic phenotyping identified a renal-vulnerable sepsis subgroup not captured by binary MASLD classification alone. These findings support prospective, multicenter external validation of liver–metabolic phenotyping as a pragmatic approach to renal risk stratification in community-acquired sepsis.

Metabolites doi: 10.3390/metabo16070469

Authors: Igor Goryanin Leonid Slovianov Irina V. Goryanin Alexander Kel

Background/Objectives: Diagnostic metabolites measured in newborn screening, inherited metabolic disease, lysosomal storage disease, oncometabolite testing and routine clinical biochemistry are direct read-outs of human metabolic state. Their mechanistic interpretation requires linking measured metabolites to enzymes, pathways, regulatory context, disease knowledge and, increasingly, AI-assisted quantitative systems pharmacology (AI-QSP) workflows. We developed EHMN2026®T as a license-aware AI-QSP integration framework that connects the EHMN2026® metabolic backbone with licensed geneXplain knowledge resources while keeping ownership, licensing and redistribution constraints explicit. Methods: EHMN2026®T integrates the SBML-encoded EHMN2026® metabolic backbone with licensed TRANSFAC® 2025.2, TRANSPATH® 2025.2 and HumanPSD™ 2025.2 resources. TRANSFAC® position weight matrices were used for promoter-level analysis of EHMN metabolic genes. The resulting transcription factor (TF)–gene connections were mapped to EHMN genes, TRANSPATH® signalling/molecular-state entries and HumanPSD™ disease/drug context. The framework is positioned as a controlled component of the IQANOVA AI-QSP environment, but only aggregate statistics, non-proprietary EHMN-derived summaries and manuscript-level examples are reported publicly unless separate permission is obtained from the relevant rightsholders. Results: Promoter analysis of 1681 EHMN2026® metabolic genes using 1147 mapped TRANSFAC® matrices identified 291,387 ENSG-level TF–gene regulatory-potential connections involving 398 TFs and 1,107,264 predicted binding sites. The diagnostic panel contained 80 covered genes (63.5%), including complete coverage of oncometabolite enzymes and high coverage of organic acidaemia, steroidogenesis and fatty-acid oxidation categories. Mapping to TRANSPATH® expanded the EHMN genes into 144,529 molecular-state representations and 14,879 gene–pathway or gene–chain pairs. HumanPSD™ was used as a licensed translational context layer; EHMN-specific HumanPSD™ outputs are treated as license-controlled derived outputs and are therefore not redistributed as open detailed tables in this manuscript. Conclusions: EHMN2026®T provides a license-aware AI-QSP integration framework for tracing a diagnostic metabolite from a measured clinical value to candidate enzyme nodes, regulatory potential, signalling/molecular-state context and disease or therapeutic interpretation. PWM-derived TF–gene links are presented as regulatory hypotheses, not proof of active regulation. Public release should be limited to aggregate statistics and non-proprietary EHMN-derived components; detailed TRANSFAC®, TRANSPATH® and HumanPSD™-derived edges, mappings, annotations and SBML outputs remain subject to geneXplain ownership and licensing terms.

Metabolites doi: 10.3390/metabo16070467

Authors: Qiaoliang Huang Yingjun Mu Ruirui Ma Jiayao Zhu Xudong Wang Qingyao Wang Junyao Huang Hui Zuo Jinming Yu

Background: 4-Hydroxyproline, a product of collagen turnover generated through prolyl hydroxylation, has been implicated in metabolic regulation. While previous studies have associated circulating proline with diabetes, the relationship between 4-hydroxyproline and diabetes remains unclear. Methods: We conducted a cross-sectional analysis of 796 adults aged 35–74 years from Changshu, eastern China. Plasma 4-hydroxyproline levels were quantified using ultra-high-performance liquid chromatography–tandem mass spectrometry. Unconditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Results: Higher plasma 4-hydroxyproline levels were associated with increased odds of diabetes after multivariable adjustment (per SD increase: OR = 1.35, 95% CI: 1.10–1.66; p = 0.004). Participants in the highest quartile had higher odds of diabetes than those in the lowest quartile (Q4 vs. Q1: OR = 1.86, 95% CI: 1.01–3.47; p for trend = 0.006). The associations remained materially unchanged after excluding insulin users, individuals with diabetes-related complications, and those using antidiabetic medication. Further adjustment for dietary intake and proline did not materially alter the results. Conclusions: Higher plasma 4-hydroxyproline levels were associated with diabetes. Given the cross-sectional design, causality cannot be inferred, and reverse causation cannot be excluded. Prospective studies are needed to confirm these findings.

Metabolites doi: 10.3390/metabo16070466

Authors: Olivia Jakubowicz-Zalewska Angelika Biełach-Bazyluk Hanna Myśliwiec Mateusz Matwiejuk Iwona Flisiak

Acne vulgaris is a common chronic inflammatory disorder of the pilosebaceous unit that is increasingly recognized as a condition linked to systemic metabolic disturbances. Growing evidence suggests that alterations in lipid metabolism, both in sebum composition and circulating lipid profiles, may play a key role in acne pathogenesis. This narrative review aims to summarize current knowledge on the relationships between lipid metabolism, body composition, diet, and acne. Acne vulgaris should be considered not only a dermatological condition but also a disorder with metabolic components. A deeper understanding of lipid-related mechanisms may support the development of more personalized and metabolically targeted therapeutic strategies.

Metabolites doi: 10.3390/metabo16070465

Authors: Stylianos Kopanos Jasper David Feldkamp Johanna Tyssen Xinjun Li Kristina Sundquist Carolina Pape-Köhler Marcel Binnebösel Annika Hoyer Per Wändell Joachim Feldkamp

Objective: Thyroid hormone treatment is the standard therapy for hypothyroidism, particularly in women. Concerns have been raised that exogenous thyroid hormone use may increase breast cancer risk, but evidence remains inconclusive. This study aimed to systematically review and synthesize observational evidence on the association between thyroid hormone treatment and breast cancer risk in women. Design: We conducted a systematic review and meta-analysis of observational studies. Methods: MEDLINE, EMBASE, and Web of Science were searched from January 1976 to February 2025. Eligible studies assessed breast cancer incidence in adult women receiving thyroid hormone treatment versus non-users. Pooled ORs were calculated. Findings from cohort studies reporting hazard ratios were synthesized qualitatively. Heterogeneity, publication bias, and certainty of evidence were assessed. PROSPERO ID: CRD42022348966. Results: Four case–control studies including 221,254 women receiving thyroid hormone treatment and 4,385,666 controls were included in the prespecified primary OR-based meta-analysis. In the primary random-effects meta-analysis, thyroid hormone treatment showed a possible epidemiological signal with breast cancer risk (OR 1.43, 95% CI: 0.90–2.28; I2 = 94.3%), although the confidence interval crossed unity and heterogeneity was substantial. Formal assessment of publication bias was performed but should be interpreted cautiously given the small number of included studies. The certainty of evidence was rated as low due to heterogeneity, serious inconsistency and imprecision. Conclusions: Thyroid hormone treatment was associated with a possible epidemiological signal for breast cancer in observational studies; however, the primary pooled estimate was not statistically significant and should be interpreted as hypothesis-generating because of substantial heterogeneity and residual confounding. Further well-designed prospective studies are required before causal or clinical inferences can be made.

Metabolites doi: 10.3390/metabo16070464

Authors: Beiyan Chen Xin Chen Jing Li Shuang Gao Xuezhu Wang Jieru Han

Beyond their established role in lipid digestion, bile acids function as key metabolic and immune signaling molecules. This review synthesizes recent advances in bile acid metabolism within the context of gout and hyperuricemia, proposing a gut–liver–joint crosstalk framework. Dysregulated bile acid metabolism—characterized by a reduced total bile acid pool, decreased hydrophobic secondary bile acids, elevated 12α-hydroxy bile acids, and impaired enterohepatic circulation—has been mechanistically linked to both hepatic urate overproduction via the PPAR-α/xanthine oxidase pathway and monosodium urate crystal-induced NLRP3 inflammasome activation, although human causal evidence remains to be established. The nuclear receptor FXR suppresses NLRP3 at the transcriptional level, while the membrane receptor TGR5 acts post-translationally through Cyclic adenosine monophosphate/Protein Kinase A (cAMP/PKA) and Glucagon-like peptide-1 (GLP-1) signaling. Gut microbiota dysbiosis amplifies these abnormalities through a vicious cycle of reduced bile acid signaling, increased intestinal permeability, and systemic endotoxemia. Based on these insights, we summarize five therapeutic strategies: FXR modulators, TGR5 agonists, microbiota-based interventions, natural products, and ursodeoxycholic acid replacement therapy. Future research should prioritize gout-specific preclinical models, clinical trials of TGR5 agonists, standardized microbiota-based therapies, dual-target molecules, and personalized patient stratification based on bile acid profiles.

Metabolites doi: 10.3390/metabo16070463

Authors: Petr G. Lokhov Elena E. Balashova

Aging is a major risk factor for numerous chronic diseases and a leading contributor to global mortality. Slowing the rate of aging would have revolutionary implications for health and longevity. A fundamental barrier to achieving this goal, however, is the difficulty of accurately measuring the effects of rejuvenating interventions. The development of precise gerontometric methods, therefore, is a priority for both science and preventive medicine. In this opinion article, the authors suggest the principles and discuss the implementation of precision gerontometry using recent advances in metabolomics. Although metabolomic approaches have limited accuracy in determining biological age, the described approach, which averages multiple metabolites from a large metabolomic signature of aging, circumvents this limitation. It allows for measurement of biological age change with an accuracy of approximately one month. Such precision gerontometry enables accelerated testing of candidate anti-aging interventions, helping to eliminate ineffective ones, speed the development of effective ones, and ultimately extend the duration of healthy human life, with profound social and humanitarian benefits.

Metabolites doi: 10.3390/metabo16070462

Authors: Vladimir Grubelnik Marko Marhl

Background/Objectives: Gamma-aminobutyric acid (GABA) is increasingly recognized as an important modulator of pancreatic beta-cell function, but the mechanisms by which it regulates intracellular Ca2+ oscillations and coordinated beta-cell activity remain insufficiently understood. The aim of this study was to investigate how GABA influences the amplitude, frequency, phase adjustment, entrainment, and synchronization of beta-cell Ca2+ oscillations. Methods: We developed a reduced ATP–Ca2+ oscillation model, based on established beta-cell oscillatory frameworks, and coupled it to the GABA-shunt subsystem derived from our previously established Dual Anaplerotic Model. The model incorporates explicit dynamics of cytosolic Ca2+, endoplasmic reticulum Ca2+, ATP, and a regulatory variable controlling Ca2+ influx, while the interstitial GABA signal is represented as a delayed feedback signal acting on cellular excitability. Single-cell and two-cell simulations were performed to analyze GABA-dependent oscillatory regulation and intercellular coupling. Results: The model reproduced key experimental observations under both control and GABA-deficient conditions, including reduced Ca2+-oscillation amplitude and a prolonged oscillation period when GABA production was suppressed. Mechanistically, GABA affected single-cell oscillations through two complementary pathways: metabolically, by modulating ATP production through PEP-related and TCA-related contributions linked to the GABA shunt, and as an interstitial/paracrine signal, by adjusting the phase of Ca2+ influx through fast and delayed inhibitory feedback. In the reduced two-cell model, delayed interstitial GABA signaling could phase-lock non-identical oscillators over finite ranges of parameter mismatch. When included as an additional weak effective term, electrical coupling broadened these ranges, consistent with a complementary interaction between GABA-mediated phase adjustment and established electrical coupling. Conclusions: GABA acts as a dual regulator of beta-cell dynamics, linking intracellular metabolism to Ca2+-oscillation patterning and promoting coordinated activity through intercellular phase adjustment. The model provides a mechanistic framework connecting GABA metabolism, ATP dynamics, Ca2+ signaling, and beta-cell synchronization in pancreatic islets.

Metabolites doi: 10.3390/metabo16070461

Authors: Wendy Leslie González-Alfonso Gustavo Ignacio Vázquez-Cervantes Itamar Flores María E. Gonsebatt Gonzalo Pérez de la Cruz Saúl Gómez Manzo Aleli Salazar Benjamín Pineda Verónica Pérez de la Cruz

Sulfur-containing amino acids (SCAA) and their metabolites constitute an integrated metabolic network essential for central nervous system (CNS) function. In mammals, sulfur metabolism links one-carbon metabolism, the methionine cycle and the transsulfuration pathway, thereby connecting nutrient availability with redox regulation, methylation reactions, neurotransmitter synthesis and cellular adaptation to stress. Among these metabolites, methionine, cysteine, glutathione, taurine, homocysteine and hydrogen sulfide play key roles in neuronal physiology, mitochondrial homeostasis, synaptic plasticity and antioxidant defense. Alterations in SCAA metabolism have been increasingly associated with neurological and neurodevelopment disorders, which share common features such as oxidative stress, mitochondrial dysfunction, altered glutamatergic signaling, impaired methylation capacity and neuroinflammation. These pathological mechanisms are also observed following exposure to toxic metals, suggesting the existence of convergent pathways between environmental neurotoxicity and neurological diseases. Several studies showed that chronic exposure to arsenic, mercury, cadmium, lead, and other toxic metals disrupts sulfur amino acid homeostasis by affecting methionine remethylation, transsulfuration activity, glutathione synthesis and reactive sulfur species production. Due to sulfur-containing metabolites possessing antioxidant and metal-binding properties, these pathways are also involved in adaptive detoxification response. However, sustained disruption of sulfur metabolism may compromise neuronal resilience and increase vulnerability to neurological dysfunction. This narrative review integrates current evidence on the physiological roles of SCAA in the CNS, and examines how toxic metals disrupt sulfur metabolic pathways. By combining findings from experimental studies, human data and exploratory transcriptomic analyses, we propose that disruption of SCAA homeostasis represents a mechanistic link between environmental metal exposure and increased vulnerability to neurological disease.

Metabolites doi: 10.3390/metabo16070460

Authors: Bogdan Mihai Pascu Irina Bojoga Anca Bălănescu Paul Cristian Bălănescu Ioan Gherghina

Background and Objectives: GLP-1 receptor agonists (GLP-1 RAs) are effective weight-loss therapies, but data on body composition changes in pediatric obesity remain scarce. The primary objective was to evaluate the effects of GLP-1 RAs on body composition in children with obesity. Materials and Methods: We conducted a retrospective study of children with obesity evaluated at the National Institute for Mother and Child Health “Alessandrescu-Rusescu”, Bucharest, Romania, who initiated weekly injectable GLP-1 RA therapy (semaglutide) between January and December 2025. Patients were assessed at baseline and after a median follow-up of 5 months. Eight of ten participants with complete paired data were included in the final analysis; two were excluded because one was a non-responder with weight gain and suspected non-compliance, while one responder could not maintain the standing position for bioimpedance measurement. Bioimpedance analysis and anthropometry were performed at both visits. Paired data were analyzed using Wilcoxon signed-rank tests. Results: Eight children (4 boys, 4 girls; mean age 14.9 ± 1.8 years) completed the study. Significant Body Mass Index (BMI) Z-score improvements were observed (CDC: −0.14, p = 0.012; WHO: −0.37, p = 0.012), with a median weight reduction of 4.75 kg (p = 0.036). While absolute muscle mass showed non-significant change (−1.3 kg, p = 0.362), predicted muscle mass percentage increased significantly (+1.9%, p = 0.012), suggesting selective fat loss. Fat-free mass percentage increased (+2.0%, p = 0.012) with reciprocal fat mass reduction (absolute: −3.85 kg, p = 0.017; percentage: −2.0%, p = 0.012). Fat-free mass index remained stable (−0.67 kg/m2, p = 0.161). No serious adverse events occurred. Sensitivity analysis (n = 10) confirmed the robustness of the results, with improvements in BMI Z-scores remaining significant. Conclusions: In this preliminary pilot study, GLP-1 RA therapy in children with obesity was associated with significant improvements in BMI Z-scores and favorable shifts in body composition, consistent with selective fat loss and relative preservation of lean mass. These exploratory findings are hypothesis-generating and support the conduct of larger prospective controlled studies with body composition as a primary endpoint.

Metabolites doi: 10.3390/metabo16070459

Authors: Mohamed A. Fareid Gamal M. El-Sherbiny Nancy M. Elafandy Nagat E. Eltoum Mohamed S. Othman Ahmad S. El-Hawary Amr M. Shehabeldine Fatma A. Hamada Amira Salah El-Din Youssef

Background: Rosmarinus officinalis L. is a medicinally important aromatic plant rich in bioactive secondary metabolites with diverse therapeutic properties. This study aimed to characterize the phytochemical profile of R. officinalis leaf extracts, isolate carnosic acid as a major bioactive diterpene, and evaluate its biological activities. Methods: Leaf extracts were prepared using solvents of increasing polarity and analyzed by phytochemical screening and UHPLC/QTOF-MS. Carnosic acid was isolated by thin-layer chromatography and assessed for antibacterial, antibiofilm, antioxidant, anti-inflammatory, antidiabetic, and antiproliferative activities using in vitro assays. Expression of apoptosis-related genes was also investigated. Results: Methanolic and ethanolic extracts exhibited the highest abundance of phenolic compounds and secondary metabolites, whereas the hexane extract showed lower phytochemical content. UHPLC/QTOF-MS identified seven major metabolites, including phenolic acids, flavonoids, and abietane-type diterpenes. Purified carnosic acid demonstrated potent antibacterial activity (MIC: 10–23 μg/mL) and inhibited biofilm formation by up to 90%. Strong antioxidant activity was observed, with DPPH and ABTS radical-scavenging IC50 values of 125 and 130 μg/mL, respectively. The compound also exhibited notable anti-inflammatory activity and markedly inhibited α-amylase and α-glucosidase activities. Furthermore, carnosic acid exhibited dose-dependent antiproliferative activity against MCF-7, HepG2, and MCF-10A cells, reducing cell viability to 10.8%, 16.9%, and 70.4 ± 1.8%, respectively, at 250 μg/mL, with corresponding IC50 values of 28.3, 37.8, and >250 μg/mL, respectively. Gene expression analysis revealed upregulation of BAX and downregulation of BCL2, indicating activation of mitochondrial-mediated apoptosis. Conclusions:R. officinalis leaves represent a valuable source of multifunctional phytochemicals, particularly carnosic acid. Its broad-spectrum biological activities and apoptosis-inducing potential support its promising application in pharmaceutical, nutraceutical, and biomedical fields.

Metabolites doi: 10.3390/metabo16070458

Authors: Chantal E. Holtkamp Dawid Warmus Klaudia Bonowicz Maciej Gagat Kinga Linowiecka Agnieszka Wolnicka-Glubisz Russel J. Reiter Markus Böhm Andrzej T. Slominski Kerstin Steinbrink Konrad Kleszczyński

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Metabolites doi: 10.3390/metabo16070457

Authors: Haitao Hu Yuwa Cao Mei Tian Hongrui Li Zhaokun Liu Thant Mon Paing Huilin Ma Siyu Feng Ruiting Zhang Dangdang Wang Lamei Wang Yangchun Cao

Background/Objectives: This study evaluated the effects of a compound probiotic fermented feed (CPFF) containing Lactobacillus plantarum, Bacillus subtilis, yeast, and Aspergillus niger on rumen in vitro fermentation, in situ feed degradation, and growth performance in beef cattle. Methods: We established a control group (CON) and experimental groups with 2%, 4%, and 8% CPFF supplementation for in vitro fermentation. Results: The results indicated that the NH3-N concentration in the 4% CPFF group was significantly higher than in the other groups (p < 0.001). Similarly, microbial crude protein (MCP) production was significantly greater in the 4% CPFF group compared to the CON group (p = 0.016). The molar proportions of acetate, butyrate, isobutyrate, and valerate were significantly higher in the 2% and 4% CPFF groups than in the control group (p < 0.001), while propionate levels were significantly lower (p < 0.001). After 48 h, gas production was highest in the 4% CPFF group. Based on improvements in gas production, MCP synthesis, and fermentation intensity, the 4% inclusion level was determined to be optimal for further studies. We conducted an in situ degradation trial using 4% CPFF. Results showed that at 12 h, the neutral detergent fiber (NDF) degradation rate in the 4% CPFF group was significantly higher than in the CON group at 4, 8, 12, and 48 h (p < 0.05). At 48 h, the acid detergent fiber (ADF) degradation rate in the 4% CPFF group was also significantly higher than in the CON group (p < 0.001), and this group exhibited a significant increase in crude protein (CP) degradation (p = 0.030). We analyzed rumen fluid samples from both the CON and 4% CPFF groups after in vitro fermentation using 16S rRNA sequencing and untargeted metabolomics. Microbial community analysis revealed significantly increased abundances of functional bacterial groups such as Rikenellaceae_RC9_gut_group, Christensenellaceae_R-7_group, and UCG-002 in the 4% CPFF group (p < 0.05). Differential metabolites were primarily involved in pathways related to tryptophan metabolism, and tyrosine metabolism signaling. A feeding trial was conducted by adding 4% CPFF to the diet of Angus growing cattle. The results indicated that average daily gain (ADG) (p = 0.004) and average daily feed intake (ADFI) (p = 0.001) were significantly higher in the CPFF group than in the CON group. Conclusions: In conclusion, our results demonstrate that CPFF enhances rumen fermentation activity, optimizes the microbiota and metabolic profiles of rumen fluid, and improves the average daily gain of beef cattle. This research provides a valuable theoretical basis for applying CPFF in beef cattle breeding.

Metabolites doi: 10.3390/metabo16070456

Authors: Mingxia Han Xiaoyu Liu Yi Guo Qingyu Xu Lin Wei Jinjin Wei Muhammad Zahoor Khan Changfa Wang Zhenwei Zhang

Anti-nutritional factors (ANFs) in terrestrial plant feeds constrain efficient herbivore production, an issue intensified by rising feed costs and growing demand for animal products. Unlike previous reviews that focus on single ANFs or feed types, this review provides an integrated, cross-species framework linking ANF chemistry, rumen microbial interactions, and mitigation strategies. It examines major ANF classes—tannins, phytates, saponins, oxalates, protease inhibitors, lectins, glucosinolates, and gossypol—and their distribution and biochemical modes of action. Mechanistic pathways are grouped into digestive effects (reduced palatability and enzyme inhibition), microbial effects (altered rumen microbiota and fermentation), metabolic effects (impaired absorption), and mineral interactions (nutrient complexation and chelation). Species-specific responses are evaluated, emphasizing the partial detoxification capacity of the rumen microbiome and the dose-dependent nature of ANF effects. Mitigation strategies—physical, chemical, microbial, enzymatic, probiotic, and genetic—are critically assessed for efficacy, scalability, and sustainability. Emerging metabolomic and metagenomic evidence shows that certain ANFs confer functional benefits at controlled doses; for example, tannins improve nitrogen retention, saponins reduce methane, and phytic acid scavenges free radicals. This synthesis supports strategic management rather than complete elimination, informing safe and sustainable use of terrestrial feeds under evolving food-security and environmental challenges.

Metabolites doi: 10.3390/metabo16070455

Authors: Yu Xie Ziying Chen Zhen Chen Yiming Yang

Background/Objectives: Lipid metabolism plays a critical role in tumor progression and immunotherapy efficacy in oral squamous cell carcinoma (OSCC). However, clinically applicable lipid metabolism-based models for predicting prognosis and immunotherapy response remain limited. This study aimed to develop and validate such a model in OSCC. Methods: Using transcriptomic data of OSCC from the TCGA database and a set of lipid metabolism-related genes (LMRGs), we constructed an LMRG-based risk score model via LASSO regression to predict patient survival. This model was subsequently validated using the independent GEO dataset GSE41613. Results: Patients in the high-risk group exhibited significantly poorer overall survival than those in the low-risk group (training cohort: p < 0.0001; validation cohort: p = 0.0086). We also developed a nomogram incorporating the risk score and clinical characteristics, and the risk score was identified as an independent prognostic factor for OSCC patients. Furthermore, the risk score was significantly associated with the tumor immune microenvironment; samples with a lower risk score showed elevated CD8+ T cell infiltration and a better response to immunotherapy. Additionally, the high-risk group exhibited an increased tumor mutation burden and resistance to most chemotherapeutic agents. Notably, several drugs (e.g., obatoclax mesylate) showed significant efficacy in the high-risk group, representing promising therapeutic candidates. Conclusions: This study reveals that the LMRG signature could serve as a valuable tool for prognosis assessment, risk stratification, and therapy guidance in OSCC.

Metabolites doi: 10.3390/metabo16070454

Authors: Seong-Uk Baek Jin-Ha Yoon

Objectives: Occupational physical activity (OPA) and leisure-time physical activity (LTPA) have contrasting health effects, a phenomenon known as the “physical activity paradox.” We explored the domain-specific associations between physical activity and non-alcoholic fatty liver disease (NAFLD). Methods: This cross-sectional study included 20,584 Korean workers (10,846 women). Physical activity was assessed using the Global Physical Activity Questionnaire, and NAFLD was assessed using the hepatic steatosis index and the presence of metabolic dysfunction. Logistic regression models were employed to explore the association between each domain of physical activity and NAFLD. The associations are presented as odds ratios (ORs) and 95% confidence intervals (CIs). Results: The prevalence of NAFLD was 30.6% in men and 18.1% in women. For male workers, ≥300 min/week of OPA was positively associated with NAFLD (OR: 1.41; 95% CI: 1.15–1.72), while ≥300 min/week of LTPA was negatively associated with NAFLD (OR: 0.79; 95% CI: 0.67–0.93). In female workers, LTPA was negatively associated with NAFLD from a lower level (OR: 0.63; 95% CI: 0.52–0.78 for 1–149 min/week; OR: 0.71; 95% CI: 0.56–0.89 for 150–299 min/week; OR: 0.58; 95% CI: 0.43–0.78 for ≥300 min/week of LTPA), while OPA had no clear association with NAFLD. Conclusions: OPA and LTPA were differentially associated with NAFLD in workers. Domain- and sex-specific effects of physical activity should be considered for the prevention and management of NAFLD.

Metabolites doi: 10.3390/metabo16070453

Authors: Joan A. Ramos-Olvera J. Martín Torres-Valencia Mario I. Ortiz Eduardo Fernández-Martínez Carlos A. Gómez-Aldapa Víctor Manuel Muñoz-Pérez Raquel Cariño-Cortés

Background/Objectives: The obesogenic environment is a key factor in the rising prevalence of metabolic syndrome (MetS), a major global public health challenge. Mangiferin (Mgf) is a C-glycosylated xanthone, and its preventive and therapeutic potential stems from its multisystemic pharmacological profile. This review integrates findings on Mgf in the management of metabolic syndrome, aiming to identify gaps and propose prospective studies to enable the scaling up of Mgf for clinical applications. Methods: To this end, a literature search was conducted, the level of evidence was identified, and the available scientific information on Mgf in metabolic syndrome was synthesized from PubMed, Scopus, and Web of Science from 2016 to 2025. Results: Mgf improves overall metabolic dysfunction by activating the AMPK pathway, reduces inflammation by activating Nrf2, suppressing NF-κB, and decreasing pro-inflammatory mediators (COX-2, IL-6, NLRP3), modulates CB1 and PPAR receptors and other markers associated with obesity (adiponectin, leptin, resistin), as well as autophagy processes. However, most of the evidence comes from in silico, in vitro, and preclinical studies, with few clinical observations. Conclusions: This underscores the need to integrate studies on the correlation between the bioavailability of Mgf and norathyriol with the regulation of the microbiota, as well as their effects on metabolomic and epigenetic mechanisms in MetS.

Metabolites doi: 10.3390/metabo16070452

Authors: Ruimin Chi Xiaoxia Hao Jiamin Lin Jiawei Liu Bingjin Liu Tao Xu

Objective: This study aims to explore the effects of exercise on gut microbiota and short-chain fatty acid (SCFA) metabolism, as well as its relationships with joint degeneration. Methods: To explore the impact of exercise on obesity-associated osteoarthritis (OA), rats were fed a high-fat/high-sucrose (HFS) diet with or without exercise. Histological staining and micro-computed tomography (micro-CT) were used to assess the effects of exercise on articular cartilage and subchondral bone. 16S rRNA sequencing and Gas Chromatography–Mass Spectrometry (GC-MS) were performed to analyze alteration in fecal gut microbiota and serum SCFAs. Results: Exercise prevented articular cartilage degeneration and subchondral bone loss in the HFS diet with exercise (HE) group compared to the HFS-diet control sedentary (HS) group. Gut microbiota analysis revealed that exercise reduced the relative abundances of families Lachnospiraceae, Ruminococcaceae, genera Ruminococcus, Colidextribacter, Caproiciproducens, and the unidentified genus of Lachnospiraceae, while increased the relative abundance of genus Akkermansia. Metabolomic analysis indicated exercise prevented AA reduction in the HE group. In addition, the level of AA was negatively correlated with OA severity and with the abundances of families Lachnospiraceae and Ruminococcaceae, genus Colidextribacter and the unidentified genus of Lachnospiraceae. Conclusions: Exercise effectively preserves the integrity of the cartilage–subchondral bone unit. The observed modifications in gut microbiota and AA levels following exercise intervention may be associated with the protective mechanisms against obesity-associated OA.

Metabolites doi: 10.3390/metabo16070451

Authors: Yaqi Chang Bin Jia Yaran Si Zexin Zhang Jiachen Liu Yue Gao Junhao Wang Yanhui Wang Juan J. Loor Bingbing Zhang Wei Yang

Background/Objectives: Exposure to high and sustained levels of non-esterified fatty acids (NEFA) in the peripartal period is the main cause of fatty liver disease in dairy cows. Rumen-protected choline is often fed as part of the nutritional management of peripartal cows, with in vivo and in vitro data indicating positive effects of this nutrient on alleviating liver lipid accumulation. Although hepatic molecular mechanisms associated with choline supply have been studied using a target gene, protein, or metabolite approach, application of high-throughput technologies could vastly enhance fundamental knowledge on the functional role of choline. The main objective was to challenge isolated hepatocytes with a mixture of NEFA and determine proteome- and metabolome-wide effects in response to choline supply. Methods: Three healthy female calves (1 d old, 30–45 kg) were sacrificed to harvest hepatocytes. During a 12 h incubation, isolated hepatocytes were challenged without NEFA (control), 1.2 mM NEFA (c9-18:1, 18:2, 16:0, 18:0, and c9-16:1 at 43.5%, 4.9%, 31.9%, 14.4%, and 5.3% of total NEFA, respectively), or NEFA for 6 h followed by 10 μM choline chloride for another 6 h (NEFA + Chol). iTRAQ labeling-based protein profiling and GC/MS-based metabolomics profiling were used to determine changes in proteins and metabolites. Differentially abundant proteins for each group comparison were determined at a threshold of 1.4-fold change. Differences in metabolite profiles were assessed via pairwise comparisons. A subset of differentially abundant proteins was validated via qRT-PCR and Western blotting. Results: Compared with the control, there were 90 proteins and 22 metabolites in the NEFA group, and 83 proteins and 29 metabolites in the NEFA + Chol. Compared with NEFA, there were 49 proteins and 17 metabolites in the NEFA + Chol group. Greater abundance of hexokinase-1 (HK1), fructose-bisphosphate aldolase (ALDOA), mitochondrial pyruvate carrier 1 (MPC1), and increased concentrations of lactate with high NEFA treatment alone suggested greater glycolytic and TCA cycle activity. Accumulation of triacylglycerol in the NEFA group was associated with lipotoxicity and markers of inflammation, such as greater abundance of prostaglandin reductase 1 (PTGR1), serious cell autophagy processes, such as greater abundance of cell division cycle 42 (CDC42), and NFκB-related proteins. Choline supplementation reduced TAG partly due to greater VLDL secretion driven by greater abundance of diacylglycerol acyltransferase (DGAT1), perilipin 3 (PLIN3), and apolipoprotein C-III (APOC3). In addition, a greater abundance of carnitine O-palmitoyltransferase 1b (CPT1B) with choline suggested enhanced mitochondrial β-oxidation. Activation of the CDC42/JNK pathway and ROS/NFκB axis-related proteins, along with depressed PI3K/AKT/RAC-related proteins, indicated enhanced mitochondrial autophagy in response to NEFA. Conclusions: Overall, data confirmed published effects of choline on TAG accumulation, VLDL secretion, and fatty acid oxidation, while highlighting negative effects of NEFA on the respiratory electron transport chain, autophagy, and inflammatory processes.

Metabolites doi: 10.3390/metabo16070449

Authors: Alissa M. Cutrone Thomas Agius Sofia Baptista Eleonore Baughan Korkut Uygun Alban Longchamp Heidi Yeh

Background/Objectives: Early allograft dysfunction (EAD) is a common complication after liver transplantation and is associated with inferior graft survival. While normothermic machine perfusion (NMP) has reduced EAD incidence, the prediction of early graft performance prior to implantation remains elusive. We aimed to correlate the peri-transplant energetic and metabolic profile of liver grafts with post-transplant outcome in a cohort that included grafts preserved with NMP. Methods: Sequential biopsies were taken from 20 transplanted livers (10 immediate graft function [IGF] and 10 EAD), preserved by either static cold storage or NMP. Samples were collected immediately prior to implantation and 30 min after hepatic arterial reperfusion. Untargeted liquid chromatography-mass spectrometry was performed, and energy charge was calculated as (ATP + 1/2 ADP)/(ATP + ADP + AMP). Univariate and receiver operating characteristic analysis identified metabolites correlated with EAD and assessed predictive accuracy. Results: Hepatic concentrations of adenine nucleotides and calculated energy charge did not differ between outcome groups either before implantation or after reperfusion. In contrast, trans-urocanate was significantly enriched in IGF livers across both time points, and additional histidine catabolism pathway metabolites were preferentially increased in IGF grafts. Trans-urocanate demonstrated discriminatory performance for EAD with 80% sensitivity and 80% specificity, confirmed as the single strongest predictive feature among >1600 detected metabolites. Conclusions: These data identify histidine catabolism as a novel metabolic pathway associated with early graft function and a potential indicator of allograft resilience to ischemia-reperfusion injury. Integration of histidine pathway metabolites into perfusion-era viability assessment may serve as a discriminative biomarker of EAD and support future metabolite-guided graft optimization strategies.

Metabolites doi: 10.3390/metabo16070450

Authors: Hüseyin Aykut Nermin Mutlu Bilgiç Duygu Demirtaş Süleyman Sayar Kamil Özdil

Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD) highlights the central role of metabolic dysregulation in hepatic steatosis. Patients with inflammatory bowel disease (IBD) are increasingly recognized to have an adverse cardiometabolic risk profile; however, data regarding MASLD prevalence and associated factors in this population remain limited, particularly in regions with a high metabolic burden such as Türkiye. This study aimed to determine the prevalence of MASLD in patients with IBD and to identify the metabolic and disease-related factors associated with its development. Methods: In this retrospective cross-sectional study, adult patients with IBD followed at a tertiary referral center in Türkiye were included. Hepatic steatosis was assessed using routine abdominal imaging, and MASLD was defined according to the 2023 Delphi Consensus criteria. Clinical, demographic, and metabolic variables were analyzed. Multivariable logistic regression analysis was performed to identify factors independently associated with MASLD. Results: A total of 194 IBD patients who had abdominal imaging available within the previous 6 months were included, of whom 61.3% had MASLD. MASLD was more prevalent in patients with UC than in those with CD (70.7% vs. 55.5%, p = 0.036). However, UC diagnosis was not independently associated with MASLD after multivariable adjustment. Patients with MASLD were older and had higher body mass index and less favorable metabolic profiles. In multivariable analysis, age (OR 1.055, 95% CI 1.022–1.089; p < 0.001), body mass index (OR 1.199, 95% CI 1.092–1.316; p < 0.001), and triglyceride levels (OR 1.012, 95% CI 1.004–1.020; p = 0.005) were independently associated with MASLD. In contrast, disease-related factors, including disease activity, biologic therapy, and prior surgery, were not independently associated with MASLD. Conclusions: MASLD prevalence was high among selected IBD patients with available abdominal imaging and appears to be more strongly associated with metabolic risk factors than with disease-specific characteristics. In populations with a high background cardiometabolic burden, MASLD in IBD may largely reflect the underlying regional metabolic milieu. These findings support the integration of metabolic risk assessment and proactive MASLD screening into routine IBD care. Prospective longitudinal studies are needed to clarify the causal relationship between metabolic dysfunction, IBD-related factors, and MASLD progression.

Metabolites doi: 10.3390/metabo16070448

Authors: Oznur Oner Canan Akkus Doga Demircioglu Ilhan Karanlık Cevdet Duran

Background/Aim: Albuminuria is a clinical marker associated with microvascular involvement and an independent predictor of cardiovascular risk. Polycystic ovary syndrome (PCOS) is associated with early metabolic and vascular abnormalities; however, whether albumin excretion differs across PCOS phenotypes remains unclear. This study aimed to evaluate the urinary albumin-to-creatinine ratio (U-ACR) across PCOS phenotypes and to examine its association with metabolic parameters. Materials and Methods: In this cross-sectional study, 180 women aged 18–35 years with PCOS and 51 age-matched healthy controls were included. PCOS phenotypes were classified according to the Rotterdam criteria as Phenotype A (n = 96), Phenotype B (n = 19), Phenotype C (n = 35), and Phenotype D (n = 30). Insulin resistance was assessed using the homeostasis model assessment for insulin resistance (HOMA-IR). Urinary albumin and creatinine levels were measured in morning urine samples, and U-ACR was calculated. Results: Age was comparable across all groups. Body mass index, waist circumference, diastolic blood pressure, and HOMA-IR were significantly higher in Phenotype A compared with controls and other phenotypes, reflecting a more adverse metabolic profile. Serum creatinine levels were similar across all groups. Despite this metabolic profile in Phenotype A, U-ACR was significantly elevated only in Phenotype B compared with controls (p = 0.018), and Phenotype D (p = 0.016). No significant correlations were observed between U-ACR and age, body mass index, or HOMA-IR. When participants were categorized according to U-ACR levels (<30, 30–299.9, and ≥300 mg/g creatinine), no significant differences in category distribution were observed between the total PCOS cohort, phenotype subgroups, and controls. Conclusion: Among PCOS phenotypes, U-ACR elevation was observed exclusively in Phenotype B despite similar renal function markers. This finding, in the presence of a more adverse metabolic profile in Phenotype A, suggests a dissociation between metabolic burden and early microvascular involvement across PCOS phenotypes. These findings suggest a potential phenotype-specific pattern that warrants further investigation.

Metabolites doi: 10.3390/metabo16070447

Authors: Yazeed Alshuweishi Ahmed M. Basudan Zeina S. Alkudmani Mohammad A. Alfhili

Background: Uric acid (UA) exhibits a dual role, with anti-oxidant or pro-oxidant effects determined by its concentration. However, its association with lipid metabolism across different uric acid states remains unclear. This study explored lipid abnormalities across the full uric acid spectrum in a large adult population. Methods: A total of 13,223 adults included in this analysis were classified as hypouricemic, normouricemic, or hyperuricemic based on serum uric acid levels. Lipid profiles, prevalence, associations, risk estimates, and diagnostic accuracy were evaluated using descriptive and multivariate statistical analyses. Results: The prevalence of hyperuricemia was 17.26%, while hypouricemia accounted for 2% of the population. Compared with normouricemia, hyperuricemic subjects exhibited substantially greater levels of LDL, TC, and TG and lower HDL concentrations (all p < 0.0001). Conversely, hypouricemia exhibited elevated HDL and lower LDL, TC, and TG levels, a pattern consistent across sex and age groups. Lipid abnormalities were most frequent among hyperuricemic participants, notably low HDL (45.9%), high LDL (52.8%), high TC (48.2%), and high TG (36.8%). In contrast, hypouricemia was associated with the lowest prevalence and reduced odds of each abnormality. Serum UA correlated significantly with all lipid measures. In multiple regression analysis, UA remained an independent positive predictor of LDL-C (β = 3.45), TC (β = 3.09), and TG (β = 11.33), and a negative predictor of HDL (β = −2.66) after adjusting for age, sex, glycemia status, and renal function. Conclusions: Both UA extremes reflect distinct metabolic states: hyperuricemia showed an adverse lipid profile, whereas hypouricemia was associated with a comparatively more favorable lipid profile, highlighting the association between UA levels and lipid metabolism.

Metabolites doi: 10.3390/metabo16070446

Authors: Zhouwei Li Hongfei Wei Jiahui Wu Qiyuan Yang Jiemei Liang Xiaoxun Wang Li Li

Background/Objectives: This study aims to establish a systematic phytochemical characterization and quality evaluation method to systematically evaluate the influence of multiple factors on the chemical composition of Taxillus chinensis, thereby providing a scientific basis for its development, utilization, and quality control standards. Methods: To ensure a targeted and representative metabolic screening, six representative batches covering the major geographical origins and host plants were selected for initial metabolomic profiling. An integrated analytical approach combining UPLC-MS/MS-based widely targeted metabolomics, HPLC fingerprinting, and multi-component quantitative analysis with multivariate statistical analysis was employed. Results: Significant quality variations were identified across the samples. Metabolomics results indicated that while chemical component types were qualitatively consistent across growth conditions, their contents varied significantly. Unique differential metabolites clustered according to specific geographical origins or host plants. KEGG pathway analysis revealed that geographical origin primarily regulated phenylpropanoid biosynthesis, whereas host differences mainly influenced flavonoid and monoterpenoid biosynthesis. Furthermore, HPLC fingerprinting of 20 batches demonstrated similarities greater than 0.9, with 15 common peaks determined. Based on their high relative abundance, differential significance across samples, and documented pharmacological relevance to the herb’s traditional efficacy, six bioactive components—gallic acid, catechin, epicatechin, hyperoside, isoquercitrin, and quercitrin—were identified and quantified. Notably, samples originating from Wuzhou exhibited the highest total content of these components. Consistent with PCA and HCA results, gallic acid, hyperoside, isoquercitrin, and quercitrin were identified as potential markers driving quality differences. Conclusions: This integrated approach allows for a systematic analytical screening of Taxillus chinensis, clarifying chemical variations caused by environmental and biological factors, and supporting the standardization and comprehensive utilization of this medicinal plant.

Metabolites doi: 10.3390/metabo16070445

Authors: Janvière Mutamuliza Elizabeth Gori Léon Mutesa François-Guillaume Debray

Background: Inborn errors of metabolism (IEMs) represent a diverse group of genetic disorders affecting biochemical pathways. Despite advances in diagnostic technologies, comprehensive understanding of their historical evolution, classification systems, and diagnostic approaches remains fragmented. Objectives: This systematic review and meta-analysis aimed to synthesize evidence on the historical development, classification frameworks, and diagnostic modalities for IEMs, diagnostic accuracy, and prevalence estimates, providing a comprehensive resource for clinicians and researchers. Methods: Following PRISMA 2020 guidelines, we conducted a systematic search of seven electronic databases (PubMed/MEDLINE, Embase, Scopus, Web of Science, Google Scholar, SciSpace and ArXiv) from January 2000 to March 2026. Studies addressing historical perspectives, classification systems, or diagnostic approaches for IEMs were included. Two independent reviewers performed screening, data extraction, and quality assessment. Meta-analyses were conducted using random-effects models for diagnostic accuracy and prevalence estimates. Results: From 1342 identified records, 54 studies met the inclusion criteria, encompassing 8,234,567 individuals across 35 countries. Historical analysis revealed 16 major milestones from Garrod’s 1902 “chemical individuality” concept to the current AI-powered diagnostics. Four major classification systems were identified: pathophysiological (intoxication, energy deficiency, complex molecule disorders), biochemical pathway (amino acid, organic acid, urea cycle, carbohydrate, fatty acid oxidation, mitochondrial, peroxisomal, lysosomal disorders), organelle-based, and the integrated Society for the Study of Inborn Errors of Metabolism (SSIEM) nosology. Meta-analysis demonstrated high diagnostic performance of tandem mass spectrometry (MS/MS) with a pooled sensitivity of 99.1% (95% CI: 98.6–99.5) and specificity of 99.8% (95% CI: 99.7–99.9%). The pooled global prevalence of IEMs was 50.9 per 100,000 live births (95% CI 45.2–56.8). Next-generation sequencing achieved a diagnostic yield of 42.8% (95% CI: 38.2–47.5%) in suspected cases. Emerging AI-powered diagnostic tools demonstrated high discrimination performance with area under the curve (AUC) values exceeding 0.95 for specific IEM, though external validation remains limited. Newborn screening expanded from single-disease to comprehensive panels detecting over 50 disorders. Conclusions: This comprehensive review demonstrates that IEMs have evolved from rare curiosities to systematically diagnosable conditions through technological advances. Integration of metabolomics, genomics, proteomics and artificial intelligence promises further diagnostic improvements. Standardized classification systems and evidence-based diagnostic algorithms are essential for optimal patient care. Future directions include artificial intelligence-enhanced diagnostics, expanded screening, and personalized medicine approaches.

Metabolites doi: 10.3390/metabo16070444

Authors: Norashareena Mohamed Shakrin Norzahidah Khalid Nor Azimah Abdul Azize Yusnita Yakob Abdah Md. Akim Julaina Abdul Jalil

Background/Objectives: Aromatic L-amino acid decarboxylase deficiency (AADC-D; OMIM #608643) is a rare autosomal recessive neurometabolic disorder caused by pathogenic variants in the DDC gene, leading to impaired of monoamine neurotransmitter biosynthesis. AADC, a pyridoxal-5′-phosphate (PLP)-dependent enzyme, catalyzes the conversion of L-dopa and 5-hydroxytryptophan (5-HTP) to dopamine and serotonin, respectively. Early diagnosis remains challenging due to the limited specificity of current biochemical approaches. This study aimed to evaluate plasma AADC enzyme activity using these physiological substrates by High-Performance Liquid Chromatography (HPLC)-based method and assess its potential utility in the biochemical diagnosis of AADC deficiency. Methods: Plasma AADC activity was quantified using physiological substrates (L-dopa and 5-HTP) by HPLC with electrochemical and fluorescence detection. Sanger sequencing of the DDC gene was performed in two suspected patients to identify pathogenic variants. Results: Two genetically confirmed AADC-D patients demonstrated reduced enzyme activity. Using L-dopa as substrate, enzyme activity in patients was 12.4 and 26.1 pmol/min/mL, both below the published reference interval (36–129 pmol/min/mL). Using 5-HTP as substrate, enzyme activity was 1.5 and 5.1 pmol/min/mL; Patient 1 showed activity below the reference interval (2.0–7.1 pmol/min/mL), while Patient 2 demonstrated activity within the lower range of reported values. Reduced enzyme activity was consistent with the clinical features and molecular findings with identification of pathogenic variants in the DDC gene (c.175G>A and c.714+4A>T). Conclusions: Plasma AADC activity measurement demonstrates potential as a functional biochemical biomarker that augments molecular genetic testing in the biochemical evaluation of AADC deficiency. Further studies involving larger patient cohorts are required to further evaluate its diagnostic performance and broader clinical applicability.

Metabolites doi: 10.3390/metabo16070443

Authors: Samantha L. Isenberg Charles A. Pickens Rachel Lee Carla Cuthbert Konstantinos Petritis

Background/Objectives: Mass spectrometry-based newborn screening for small-molecule biomarkers typically employs a rapid first-tier screen that omits chromatographic separations before mass spectrometric analysis, followed, only for a subset of samples and disorders, by a longer, more specific second-tier assay that includes liquid chromatographic separation prior to mass spectrometry. The second-tier screen is used when the primary biomarker lacks sufficient specificity and may result in higher false-positive rates. The throughput and specificity of first-tier newborn screening assays have been relatively stagnant over the past two decades despite significant improvements in mass spectrometry instrumentation. With the continuous expansion of disorders added to the Recommended Uniform Screening Panel in the United States, newborn screening laboratories have a need for higher-throughput assays and improved specificity. Methods: We developed and evaluated two first-tier tandem mass spectrometry approaches using a modern dual-needle, dual-loop LC-MS/MS platform: (1) a 30-s flow injection analysis tandem mass spectrometry (FIA-MS/MS) assay and (2) a rapid first-tier liquid chromatography tandem mass spectrometry (LC-MS/MS) assay using a hydrophilic interaction chromatography (HILIC) guard column (1TH). Analytical performance was assessed using dried blood spot quality control and linearity materials, including evaluations of recovery, precision, linearity, and matrix effects. Results: The 30-s FIA-MS/MS assay quadrupled the throughput of current 2-min FIA-MS/MS assays used routinely in newborn screening laboratories. The throughput improvement was achievable due to increased scan speeds of the mass spectrometer as well as the dual needle/loop design of the autosampler. In addition, these instrumentation improvements made it possible to employ liquid chromatographic separations prior to MS/MS analysis without sacrificing the approximately 2-min sample-to-sample throughput of conventional FIA-MS/MS workflows. The 1TH LC-MS/MS method separated critical isobaric and isomeric biomarkers, reduced matrix effects, improved specificity and quantification accuracy, and demonstrated acceptable recovery, precision, and linearity for newborn screening applications. Conclusions: Recent advances in LC-MS/MS instrumentation can be leveraged to either substantially increase first-tier newborn screening throughput or improve analytical specificity while maintaining current workflow timelines. First-tier LC-MS/MS using a HILIC guard column provides improved specificity that can reduce the need for second-tier testing, thereby improving overall throughput and turnaround time of the newborn screening workflow. These approaches provide flexible solutions for newborn screening laboratories seeking to accommodate expanding screening panels without compromising analytical quality or efficiency.

Metabolites doi: 10.3390/metabo16070442

Authors: Xiaobo Liu Julianna M. Santos Takaki Kiritoshi Guangchen Ji Volker Neugebauer Chwan-Li Shen

Background: Managing neuropathic pain (NP) is particularly challenging in the context of opioid use, and the mechanisms behind chronic pain remain unclear. Objective: This study evaluated the impact of turmeric bioactive compounds on brain regions including frontal cortex (FC), hippocampus (HPC), and hypothalamus (HPT) in the spinal nerve ligation (SNL) in a rat model of NP. Methods: Twenty-four SD rats were assigned to four groups (N = 6 per group), namely sham+vehicle (Sham-V), SNL+vehicle (SNL-V), SNL + 100 mg/kg curcumin (SNL+100CUR), and SNL + 50 mg/kg bisdemethoxycurcumin (SNL+50BDMC), treated daily for four weeks via oral gavage. Gene expression levels related to neuroinflammation, oxidative stress, and mitochondrial homeostasis were measured using qRT-PCR. Protein-level or functional mitochondrial assays were not performed due to limited sample availability. Results: In the FC, SNL decreased the expression level of NRF1 and OPA1, but only OPA1 was increased by BDMC. In the HPC, SNL increased CD11b, NRF2, and MFN1; BDMC decreased CD11b and increased IBA1, NRF1, TFAM, PGC1α and Complex I; and CUR increased NRF1, TFAM, DRP1 and Complex I levels. In the HPT, SNL decreased GFAP and MFN1, with CUR and BDMC further decreasing GFAP but not affecting MFN1. Additionally, CUR and BDMC decreased the expression of several key markers of neuroimmune signaling and mitochondrial homeostasis, including IBA1, CD11b, NFkB, NRF1/2, DRP1, OPA1, PGC1α, TFAM, and PINK1. Conclusions: CUR and BDMC induced region-specific transcriptional remodeling of mitochondrial homeostasis across FC, HPC, and HPT in SNL rats, with somewhat limited effects in the FC, mixed effects in the HPC, and broader downregulation in the HPT.

Metabolites doi: 10.3390/metabo16070441

Authors: Oludotun O. Adelusi David P. Casper John O. Adebayo Ahmed E. Kholif Ibukun M. Ogunade Uchenna Y. Anele

Background/Objectives: Direct-fed microbials (DFMs) are widely used in dairy calves to improve gut health and mitigate neonatal disorders, yet their systemic metabolic effects remain poorly defined. This study evaluated the impact of DFM supplementation on the plasma metabolome of pre-weaned dairy calves using untargeted liquid chromatography–mass spectrometry (LC–MS). Methods: Eighty-six Holstein bull calves (2 to 5 days old) were assigned to one of four treatments in a 2 × 2 factorial randomized complete block design: Lactobacillus plantarum in starter (CLP), a culture mix of Bifidobacterium animalis and Lactobacillus animalis in milk replacer (BBCM), and a combination of both (CMLP), or no supplementation (CON). Blood samples collected on days 0 and 56 were subjected to metabolomic profiling, and metabolites were annotated using Human Metabolome Database and Kyoto Encyclopedia of Genes and Genomes databases. Results: A total of 231 plasma metabolites were detected. Compared with CON, 24 metabolites were differentially abundant in DFM-treated calves (fold change ≥ 1.2 or ≤ 0.83; p ≤ 0.05). Supplemented calves exhibited increased abundances of ketone functional groups, aldehydes and amino acid-related metabolites. Metabolite set enrichment analysis identified 11 significantly enriched pathways. Branched-chain amino acid degradation pathways (valine, leucine, and isoleucine) were enriched in CLP and CMLP calves, whereas carbohydrate metabolism pathways, including pentose and glucuronate interconversions, were enriched in the CLP and BBCM groups. Conclusions: These findings demonstrate that DFM supplementation modulates systemic metabolism in dairy calves, particularly pathways involved in amino acid and carbohydrate utilization, suggesting enhanced metabolic efficiency during early life.

Metabolites doi: 10.3390/metabo16070440

Authors: Ning Wang Jing Xu Jing Leng Jia-Le Xu Da-Sheng Lu Fan Zhang Dong-Sheng Yu Ke-Lei Qian Gong-Hua Tao Ping Xiao Xin-Yu Hong

Background/Objective: Bisphenol AF (BPAF), a fluorinated analogue of bisphenol A, is an environmental contaminant associated with hepatotoxicity and metabolic disruption. However, the systematic molecular mechanisms linking early transcriptional events to metabolic dysfunction in the liver remain poorly defined. The aim of this study is to elucidate the association between BPAF exposure and hepatic lipid accumulation by integrating transcriptomics, cellular metabolomics, and targeted phenotypic assays. Methods: We performed RNA-sequencing on livers from mice exposed to BPAF (0.1–10 mg/kg/day, 28 days), and performed non-targeted metabolomics on AML12 murine hepatocytes co-cultured with RAW264.7 macrophages in a Transwell system (0–2500 nM BPAF, 48 h). Key metabolic pathways were identified through integrated bioinformatics and validated using enzymatic assays, qRT-PCR, Western blotting, and phenotypic staining (lipid droplets, ROS). Results: Multi-omics integration revealed significant disruption of PPAR signaling and the tricarboxylic acid (TCA) cycle. A striking dose-dependent accumulation of succinate was observed in exposed cells, concomitant with a significant inhibition of succinate dehydrogenase (SDH) activity (52% reduction at 2500 nM, p < 0.001). Transcriptomic data confirmed the downregulation of mitochondrial fatty acid β-oxidation genes. Phenotypic validation indicated that BPAF exposure is associated with oxidative stress, pro-inflammatory cytokine release (TNF-α, IL-6), and pronounced intracellular lipid droplet accumulation in hepatocytes. Conclusions: This study suggests that BPAF exposure is associated with SDH dysfunction, TCA cycle arrest, and lipid dysregulation. Whether BPAF directly inhibits SDH or acts through upstream mitochondrial targets warrants further structural and kinetic investigation.

Metabolites doi: 10.3390/metabo16070439

Authors: Germán Perdomo Irene Cózar-Castellano Sonia M. Najjar

The pleiotropic actions of insulin are mediated by cascades of signaling pathways and are regulated by circulating insulin levels. Under physiologic conditions, insulin levels reflect the balance between pancreatic beta-cell secretion and insulin clearance, which occurs primarily in liver hepatocytes and, to a lesser extent, in kidney proximal tubule cells. Therefore, coordination between insulin secretion and clearance is essential for systemic insulin sensitivity. Whereas insulin secretion is widely investigated, exploring the role of insulin clearance in regulating insulin sensitivity remains limited. This review summarizes the main mechanisms underlying insulin clearance along the liver–kidney axis and discusses how they contribute to metabolic regulation in health and disease.

Metabolites doi: 10.3390/metabo16070438

Authors: Pengpeng Xie Yaoye Pei Luyun Xu Yuanhao Shan Xiamin Cao

Aging is a systemic degenerative process that can lead to functional decline in multiple organs, such as skeletal muscles and the heart, and accelerates the overall aging process through organ-to-organ interactions mediated by metabolites such as short-chain fatty acids (SCFAs). SCFAs serve as a crucial link connecting intestinal health and anti-aging, and their levels and functions undergo significant changes with aging. However, current research lacks understanding of the downstream molecular mechanisms of SCFAs, and intervention methods are mostly limited to simple regulation. This article clarifies the intrinsic relationship between SCFAs and aging from a systemic perspective, analyzes their regulatory mechanisms through key signaling pathways, examines their roles in tissue barrier protection, the improvement of metabolic disorders, and immune regulation, and summarizes their therapeutic potential and diversified intervention strategies in aging-related diseases. The detailed molecular mechanisms by which SCFAs regulate aging are still unclear, and there are no precise intervention plans for different aging stages and organ damage. In the future, we need to utilize techniques such as single-cell sequencing and organ models to explore the regulation of aging cell fates, providing support for the development of metabolite-mediated personalized anti-aging intervention measures.

Metabolites doi: 10.3390/metabo16070437

Authors: Desirée Victoria-Montesinos Inmaculada Llopis-Alonso Ana María García-Muñoz María Teresa Mercader-Ros

Background/Objectives: Automated insulin delivery (AID) systems have improved the management of type 1 diabetes (T1D), but exercise and nutrition remain challenging because they rapidly alter glucose flux, substrate oxidation, hepatic glucose output, insulin requirements, and fuel availability. This narrative review aimed to synthesize current evidence on the interaction between AID systems, physical activity, and nutritional strategies from a metabolism-oriented perspective. Methods: A narrative bibliographic approach was used to integrate evidence from clinical trials, observational studies, technical studies, consensus statements, and reviews involving people with T1D across different life stages, including pediatric, adolescent, adult, and pregnancy-related contexts, when available. The review focused on AID systems, exercise physiology, nutritional strategies, meal announcement, bolus adjustment, dual-hormone systems, metabolic biomarkers, and emerging metabolomic approaches. Results: AID systems generally improve time in range and reduce hypoglycemia across several user groups, although most exercise- and nutrition-specific evidence comes from adult and pediatric/adolescent cohorts rather than pregnancy-specific exercise studies. Exercise-related glucose responses remain highly dependent on user input, exercise modality, insulin on board, meal timing, and metabolic state. Planned exercise announcement, prandial bolus reduction before postprandial activity, and individualized carbohydrate intake remain key strategies. Biomarkers such as lactate, ketone bodies, non-esterified fatty acids, and counter-regulatory hormones may help explain interindividual variability and support future personalization. Conclusions: Nutrition and exercise management in AID users should be interpreted as a dynamic metabolic interface among exogenous insulin, endogenous counter-regulation, substrate availability, and algorithmic control. Emerging approaches, including activity sensors, adaptive algorithms, dual-hormone systems, digital twins, and metabolomics-informed personalization, may improve safety and reduce user burden, but several remain exploratory and require further validation in diverse free-living conditions.

Metabolites doi: 10.3390/metabo16070436

Authors: Kenneth D. R. Setchell Xueheng Zhao Stacey Reed Wujuan Zhang

Background/Objectives: Bile acid synthesis disorders (BASDs) represent a distinct category of progressive familiar cholestatic liver disease. A novel targeted mass spectrometry assay was developed for the accurate measurement of the major urinary atypical bile acids and bile alcohols that are biomarkers for HSD3B7, AKR1D1, CYP7B1 and CYP27A1 deficiencies, the four most common BASDs. Methods: Stable-isotope dilution UPLC tandem mass spectrometry was used for the simultaneous quantification of 12 key atypical bile acid biomarkers in urine from patients with BASD. Typical concentration ranges for these metabolites were established from urine samples from patients with biochemically and/or genetically confirmed BASD and compared with non-cholestatic and cholestatic controls. Results: The separation of major 3β-hydroxy-Δ5-bile acid sulfates, taurine- and glycine-conjugated 3-oxo-Δ4-bile acids, and bile alcohol glucuronides was achieved in a 20 min chromatographic run with intra- and inter-batch imprecisions of <15% for all metabolites. The mean ± SEM urinary concentration of total 3β-sulfated-Δ5-cholenoic acids in patients with HSD3B7 deficiency was 704 ± 204 µmol/L (n = 22), approximately 2000-fold higher than in cholestastic patients (n = 168) or non-cholestatic controls (n = 127). Similarly, the concentration of 5β-cholestane-3α,7α,12α,24,25-pentol-glucuronide, the major bile alcohol, in patients with CYP27A1 deficiency was 95 ± 17 µmol/L (n = 12). For CYP7B1 deficiency, two confirmed cases showed elevated levels (average, 7.5 µmol/L) of the glycine conjugate of 3β-sulfooxy-Δ5-bile acid. In AKR1D1 deficiency, total 3-oxo-Δ4-bile acids in urine were elevated (81 ± 16 µmol/L, n = 48), but concentrations showed overlap with cholestatic and non-cholestatic controls. Conclusions: A novel quantitative tandem mass spectrometry assay is described for the measurement of the major atypical metabolites and biomarkers in urine applicable to the accurate monitoring of treatment responses, and for the first time typical concentration ranges are established for each of these BASDs.

Metabolites doi: 10.3390/metabo16070435

Authors: Kaiwen Deng Ran Liu Ruiping He Li Chen

Background: MS/MS spectral databases provide reference spectra for compound identification in metabolomics studies. Their utility depends on clear links among compound identifiers, chemical structures, and MS/MS evidence, yet these links are often complicated by database-specific identifiers, heterogeneous structural representations, and stereochemical specifications. Methods: Here, we present a two-layer structural key framework for linking compound identifiers and MS/MS evidence through standardized structures. Reported SMILES were standardized and converted into InChIKey-derived stereo keys and connectivity keys using a Python-based RDKit workflow. Results: As illustrated using stereoisomeric cases such as L- and D-proline, the stereo key layer preserves compound identifiers and metadata at the stereo level, whereas the connectivity key layer groups comparable MS/MS evidence at the molecular connectivity level. In a database-scale application, 217,920 HMDB compound entries were organized into 216,783 stereo keys and 196,512 connectivity keys, and 144,591 spectra from the spectrum-centered MoNA database were incorporated into the HMDB-centered framework, increasing MS/MS evidence coverage, particularly at the molecular connectivity level. Conclusions: Together, this framework links compound identifiers, standardized structures, and MS/MS evidence at the stereo and connectivity levels, providing a bidirectionally traceable system for spectral database curation without forcing connectivity-level MS/MS evidence into stereo-specific compound identities.

Metabolites doi: 10.3390/metabo16060434

Authors: Yongchen Li Jingwen Liu Diman Mai Renzhi Tan Chao Wang Zengnan Mo

Background: Acute kidney injury (AKI) remains a condition with limited effective therapeutic options, partly due to challenges in early diagnosis and timely intervention. While lactate accumulation is a hallmark of ischemic and septic AKI, the underlying mechanisms remain unclear. Methods: This study integrated single-cell RNA sequencing data from AKI patients (GEO database) with lactate metabolism-related genes (LMRGs) to identify key therapeutic targets. Results: Collecting duct (CD) cells exhibited the highest LMRG expression. Machine learning algorithms and validation in bilateral ischemia/reperfusion injury (bIRI) and lipopolysaccharide (LPS)-induced AKI mouse models, as well as hypoxia/reoxygenation (H/R)-stimulated renal cells, identified Ldhb as a core gene. Disruption of lactate metabolism via BAY876 (selective GLUT1 inhibitor) or siRNA-mediated Ldhb knockdown significantly attenuated kidney injury, reduced inflammatory cytokines (IL-1β, IL-6, TNF-α), and decreased reactive oxygen species in vitro and in vivo. Conclusions: These findings reveal that lactate metabolism is reprogrammed in AKI, particularly in CD cells, and identify LDHB as a novel potential therapeutic target for this condition, though further mechanistic studies are required to establish causality.

Metabolites doi: 10.3390/metabo16060433

Authors: Jacob Ahlberg Weidenfors Bénilde Bonnefille Stefano Papazian

Background: Confident chemical annotation in nontarget small-molecule mass spectrometry critically depends on the availability of high-quality tandem mass spectral (MS2) reference libraries. While community efforts have driven significant expansion of open-access repositories, technical challenges in assembling standardized, metadata-rich records continue to limit broader participation, underscoring the need for improved computational tools to assist contributors. Methods: To promote the creation and sharing of standardized reference MS2 spectral records, we have developed Librarian, a free, open-access web application designed for rapid and scalable assembly of high-resolution MS2 libraries. Librarian integrates automated retrieval and harmonization of chemical identifiers and metadata from PubChem, compound mixture design for high-resolution mass spectrometry (HRMS) acquisition, and assembly of curated MS2 spectra into repository-ready records compatible with public spectral databases. Results: Through a simple in-browser interface, Librarian offers a flexible end-to-end workflow compatible with popular open-source pre-processing tools to lower technical barriers and facilitate broader community participation in library development. As a demonstration, we used Librarian to create and deposit a spectral library comprising over 1500 new MS2 records into MassBank, which was further applied in retrospective analysis of environmental datasets. Conclusions: Librarian streamlines the creation of standardized, metadata-rich and repository-ready MS2 reference records. Addressing a key bottleneck in community spectral library development and sharing, Librarian supports the continued growth of open-access resources for metabolomics, exposomics, and environmental mass spectrometry. The Librarian web application is publicly accessible via the SciLifeLab Serve platform.

Metabolites doi: 10.3390/metabo16060432

Authors: Yessen Konysbek Ayazhan Turar Vilen B. Molotov-Luchanskiy Olga A. Ponamareva

Background/Objectives: Anemia and iron dysregulation are common in chronic heart failure (CHF), but additional metabolic mechanisms may contribute to these alterations. This study aimed to evaluate purine metabolism and oxidative stress markers in patients with CHF and to explore their potential relationship with anemia. Methods: In this cross-sectional study, 176 patients with CHF and 29 control individuals were included. CHF phenotypes were classified according to left ventricular ejection fraction (HFpEF, HFmrEF, HFrEF). Purine metabolites (guanine, hypoxanthine, adenine, xanthine, and uric acid) were measured using high-performance liquid chromatography, while lipid peroxidation (LPO) and advanced oxidation protein products (AOPPs) were assessed spectrophotometrically. Non-parametric statistical tests with correction for multiple comparisons were applied. Results: Anemia was present in 40.3% of patients with CHF. Serum iron and platelet counts were significantly lower in CHF compared with controls (p = 0.001). Among purine metabolites, adenine levels were higher in CHF (nominal p = 0.009), whereas other metabolites did not differ significantly between groups. LPO levels were lower and AOPP levels were higher in CHF (p = 0.021 and p = 0.008, respectively). No statistically significant associations were observed between hemoglobin levels and purine metabolites. Conclusions: CHF is associated with alterations in iron status and oxidative stress markers, as well as changes in purine metabolism. However, no significant associations between purine metabolites and anemia were identified in this cohort, and these findings should be interpreted cautiously given the exploratory design and sample size limitations.

Metabolites doi: 10.3390/metabo16060431

Authors: Uday Sankar Akash Vankayala Ali Sohail Bivin George Madhu Singh Omar Khayat Malek Kreidieh Alia Hasham Luis Quiel

Heart failure (HF) continues to be a major global health burden, with persistent morbidity and mortality despite guideline-directed and device-based therapies. Evidence suggests the gut–heart axis is a critical and underrecognized contributor to HF progression. Alterations in cardiac output and systemic venous congestion in HF lead to intestinal hypoperfusion, mucosal edema, and loss of barrier integrity, increasing intestinal permeability, gut dysbiosis, and translocation of microbial products. This systemic translocation is associated with chronic low-grade inflammation that activates innate immune pathways that correlate with endothelial dysfunction, oxidative stress, fibroblast activation, and adverse cardiac remodeling. Gut-derived metabolites derived by microbial metabolism modulate cardiovascular health by altering the metabolic profiles. Dysbiosis results in loss of protective short-chain fatty acid (SCFA)-producing bacteria and enriches pro-inflammatory taxa such as trimethylamine N-oxide (TMAO)-producing bacteria. Elevated TMAO is associated with increased mortality and hospitalization in HF, whereas SCFAs enhance barrier integrity and immune tolerance. Secondary bile acids and uremic toxins such as indoxyl sulfate and p-cresyl sulfate further link dysbiosis to fibrosis and vascular stiffness. Circulating markers such as TMAO, lipopolysaccharide-binding protein (LBP), and soluble CD14 carry prognostic value beyond traditional cardiac biomarkers. This review highlights current experimental, translational, and clinical evidence describing gut dysbiosis and its molecular links to HF progression. Targeting the gut–heart axis represents a novel therapeutic approach in HF. Dietary modulation, probiotics/prebiotics, fecal microbiota transplantation, and inhibitors of microbial metabolic pathways show promise. Future research should emphasize microbiota-based interventions in HF management.

Metabolites doi: 10.3390/metabo16060430

Authors: Junzhao Yuan Jiaqi Zhang Jinxing Song Lingling Liu Hang Liu Shuangxing Jin Xiaoli Ren

Background: Hexavalent chromium (Cr(VI)) is a widespread environmental toxic heavy metal with strong oxidative properties; however, its immunotoxicity and metabolic mechanisms in rabbit spleen remain largely unclear. Methods: In this study, New Zealand rabbits were exposed to 0, 12.5, 25, and 50 mg/L Cr(VI) (as potassium dichromate, K2Cr2O7) via drinking water for four weeks to investigate splenic damage and the underlying molecular pathways. Spleen pathological injury was evaluated by hematoxylin and eosin (H&E) staining, and the distribution of T cells, B cells, and macrophages was assessed by immunohistochemistry. Antioxidant enzyme activities and antioxidant substance levels were determined using ELISA, and the relative mRNA expression of immune factor genes, antioxidant-related genes, and ferroptosis-related genes was quantified by quantitative real-time PCR (qRT-PCR). In addition, the distribution of iron in splenic tissue was detected by enhanced Prussian blue staining. Results: Our results demonstrate that high-dose Cr(VI) significantly inhibited body weight gain, induced lymphocyte atrophy, vacuolization, and widening of intercellular spaces in the splenic white pulp. Furthermore, Cr(VI) reduced T and B lymphocyte populations, promoted macrophage infiltration and inflammatory cytokine gene expression in a concentration-dependent manner, impaired total antioxidant capacity, and led to a decrease in glutathione (GSH) levels in the spleen. Additionally, Cr(VI) exposure increased iron accumulation, activated the ACSL4–NOX lipid peroxidation cascade, and downregulated GPX4 expression, ultimately triggering ferroptosis. Conclusions: These findings reveal that Cr(VI) causes splenic immune injury by disrupting oxidative homeostasis and inducing ferroptosis, providing novel insights for evaluating immunotoxicity and identifying metabolic targets under Cr(VI) pollution.

Metabolites doi: 10.3390/metabo16060429

Authors: Mark Towers Emmanuelle Claude Lisa Towers Helen Yates Joanne Ballantyne

Background: Recent technology improvements have enabled desorption electrospray ionisation (DESI) mass spectrometry imaging to achieve down to 5 µm (pixel) image resolution. However, operating at this resolution introduces challenges, particularly regarding increased total analysis time and the need for sufficient instrument sensitivity to detect analytes from very small tissue areas. Methods: High mass and image resolution DESI imaging was performed on rat brain tissue using a Xevo™ MRT benchtop mass spectrometer equipped with a multi-reflecting time-of-flight mass analyser and a DESI XS source. Data acquisition was conducted at speeds of up to 100 Hz. Sensitivity was assessed using a dilution series of five Active Pharmaceutical Ingredients (APIs) spotted onto porcine liver tissue. Signal detection limits were evaluated using extracted ion chromatograms (XICs) with signal-to-noise (S/N) calculations against blank samples. Additionally, enhanced duty cycle (EDC) was applied to evaluate improvements in analyte signal intensity across specific mass ranges in both positive and negative ionisation modes. Results: At acquisition speeds of up to 100 Hz, excellent data quality was achieved, with signal intensity remaining suitable for analytical applications. All five tested APIs were detectable at concentrations of 25 pg/mm2. Three of the five compounds were further detected at concentrations as low as 2.5 pg/mm², with signal-to-noise ratios greater than 5. The application of EDC resulted in a significant increase in analyte signal intensity within the targeted mass ranges, particularly for small molecule endogenous metabolites and lipids, in both ionisation modes. Furthermore, the system demonstrated substantially improved spectral quality, achieving mass resolution up to 100,000 FWHM. This enabled the resolution of previously indistinguishable analytes with significantly improved mass accuracy compared to systems operating at approximately 30,000 FWHM. Conclusions: The Xevo™ MRT mass spectrometer with DESI XS source enables high-resolution DESI imaging at speeds up to 100 Hz without compromising data quality or sensitivity. The system demonstrates excellent detection limits for pharmaceutical compounds and improved performance through enhanced duty cycle operation. Overall, the combination of high spatial resolution, increased mass resolution, and improved spectral quality allows for more accurate analyte differentiation, representing a significant advancement over lower-resolution systems.

Metabolites doi: 10.3390/metabo16060428

Authors: Hunter Dlugas Jing Li Xiang Zhang Seongho Kim

Background/Objectives: In gas chromatography–mass spectrometry (GC-MS) library-based compound identification, spectrum preprocessing and associated tuning parameters critically influence identification performance. These parameters are conventionally optimized using grid search, which requires predefined parameter spaces and becomes computationally inefficient as dimensionality increases, often failing to identify optimal values because of discretization. Differential evolution (DE), a population-based metaheuristic optimization algorithm, provides a flexible alternative through efficient global exploration of the parameter space. This study compared the performance of DE and grid search for optimizing compound identification. Methods: Cosine similarity was applied to the NIST GC-MS library. DE was used to maximize either cross-validated accuracy or mean reciprocal rank (MRR). Results were compared with those from a grid search over five equally spaced parameter values. Identification performance was evaluated using accuracy, MRR, and area under the receiver operating characteristic curve (AUC). Results: When all four parameters were optimized simultaneously, DE achieved slightly higher cross-validated accuracy and MRR than grid search, although the absolute differences were modest. More pronounced differences were observed in specific unidimensional tuning scenarios, particularly for the intensity weight factor. Simultaneous multidimensional parameter optimization yielded better performance than isolated parameter tuning. Conclusions: Grid search may be computationally advantageous when the parameter space is known and limited, whereas DE provides a more flexible approach for unknown or high-dimensional search spaces. Overall, DE achieved comparable identification performance to grid search, with modest improvements observed in some optimization settings. A command line Julia-based tool, MSTune, was developed for spectrum preprocessing parameter optimization and is publicly available on GitHub.

Metabolites doi: 10.3390/metabo16060427

Authors: Nadine Paßlack Helena Veit Henri Funk Jürgen Zentek Sven Schuchardt

Background/Objectives: Dietary fish oil supplementation has been associated with lower total plasma triacylglycerols in felines. The present study aimed to characterize this effect in more detail, using lipidomic analyses. Methods: Plasma samples of cats (n = 10), receiving a complete basic diet, with and without the addition of 0.5 g and 1.0 g fish oil/kg body weight/day, each for 21 days, in a randomized crossover design, were analyzed by an FIA MS/MS-based targeted metabolomics approach. Results: The results demonstrated that 360 metabolites were affected by the dietary treatments, predominantly belonging to triacylglycerols (n = 124), phosphatidylcholines (n = 68), phosphatidylethanolamines (n = 63), phosphatidylglycerols (n = 33), and phosphatidylinositols (n = 21). Lowering effects of fish oil supplementation on plasma triacylglycerols could be confirmed. However, increased levels of specific triacylglycerols were also observed, especially of those containing eicosapentaenoic or docosahexaenoic acid. The decreased triacylglycerols showed a lower number of carbons and a lower degree of unsaturation than the enhanced triacylglycerols. Such a lipid profile is assumed to be beneficial in human medicine; its relevance for feline health, however, is unclear so far. Conclusions: In conclusion, the lipidomic analyses provided a detailed characterization of the feline plasma lipidome and its modulation by a dietary fish oil supplementation. The clinical relevance of these findings warrants further investigation.

Metabolites doi: 10.3390/metabo16060426

Authors: Yaocheng Luo Peng Zeng Shuoya Huang Zhenzhen Peng Jian Zheng Zumin Shi Manoj Sharma Yong Zhao

Background: Cardiovascular disease and mortality are common outcomes of cardiovascular–kidney–metabolic (CKM) syndrome. The integrated role of metabolic dysfunction and frailty, quantified by the triglyceride–glucose–frailty index (TyG-FI), remains insufficiently explored. This study examined the association between TyG-FI and incident composite outcomes among participants with CKM stages 0–3. Methods: Data were obtained from two large cohort studies conducted in China and the United States. The analysis focused on participants classified as CKM stages 0–3. Cox proportional hazards models were used to estimate the relationship between TyG-FI and incident composite outcomes. Nonlinear associations were explored using spline functions. Additional analyses were performed across different subgroups and under varied assumptions. Model performance over time was also assessed. Results: Significant differences in outcome incidence were observed across TyG-FI levels. Higher quartiles showed a gradual increase in risk and displayed a dose–response pattern, with inflection points at 1.01 and 2.29. Associations were consistent across subgroups, and TyG-FI demonstrated moderate discrimination (AUCs 0.714 and 0.744). Conclusions: In the CHARLS and HRS cohorts, higher TyG-FI scores were independently associated with an increased risk of incident composite outcomes among participants with CKM stages 0–3, with a nonlinear relationship observed. Its discriminatory power was moderate, suggesting that TyG-FI may serve as a supplementary indicator for risk stratification in the early to mid-stages, although its clinical predictive value requires further validation.

Metabolites doi: 10.3390/metabo16060425

Authors: Emre Uzun İbrahim Tekeoğlu Hüseyin Çakıroğlu Özcan Budak Elvan Şahin Kemal Nas Muhammed Zahid Sahin Ayhan Kamanlı

Background/Objectives: Although vitamin K has been implicated in osteoarthritis pathophysiology, the specific effects of vitamin K2 (menaquinone) on cartilage degeneration remain poorly characterized. This study aimed to investigate the effect of oral vitamin K2 supplementation in a monosodium iodoacetate-induced osteoarthritis model. Methods: Twenty-four male Sprague Dawley rats were included in the study and divided into 3 equal groups: sham group, control (osteoarthritis) group, and treatment group. Saline was applied to the right knee of the sham group, and MIA was applied intra-articularly to the right knee of the control and treatment groups to create an osteoarthritis model. Rats in the treatment group were given 8 micrograms (μg)/day of vitamin K2 orally in addition to the standard diet. After 28 days of follow-up, all rats were euthanized. The right knee articular cartilage was examined histologically with Hematoxylin–Eosin and Safranin O and immunohistochemically with type II collagen alpha 1 and Matrix Metalloproteinase-13. Results: Histological evaluation demonstrated significantly lower Mankin scores in the treatment group (4.25 ± 0.83) compared with the control group (11.10 ± 0.83). Immunohistochemical analysis showed more intense type II collagen staining and reduced matrix metalloproteinase-13 staining in the treatment group relative to the control group. Conclusions: Oral vitamin K2 administration was associated with reduced cartilage degeneration and improved matrix preservation at the 28-day endpoint in an induced MIA osteoarthritis rat model.

Metabolites doi: 10.3390/metabo16060424

Authors: Yuanying Zhao Hao Chang Chenxue Hou Bingqing Yang Yue Li

Background: The reversal of liver fibrosis is crucial for improving outcomes in chronic liver disease. The gut–liver axis, mediated by the intestinal microbiota, plays a significant role in this process. However, its dynamic changes and mechanisms during reversal remain unclear. This study aimed to systematically reveal these dynamics and explore the link between gut microbiota and metabolism in a spontaneous reversal model. Methods: Intestinal contents were collected from mouse model groups (fibrosis, 4-week reversal, and 12-week reversal). The use of 16S rRNA gene sequencing was employed to analyze gut microbiota structure, and untargeted metabolomics was used to profile metabolic changes. Differential metabolites and microbial taxa were identified using multivariate statistical analysis, followed by pathway enrichment analysis. Spearman correlation analysis was used to construct metabolite–microbiota association networks across different reversal stages. Results: Metabolomic analysis showed significant alterations in multiple pathways during reversal. Linoleic and α-linolenic acid metabolism had a high impact in later stages. Taurine and biotin metabolism remained active throughout. Branched-chain amino acid degradation was enriched later. Microbiota analysis revealed significant structural shifts via beta-diversity. Bacteroidota decreased while Firmicutes increased in 4 weeks. Butyrate-producing families increased, and Akkermansia was enriched later. Integrated analysis demonstrated significant correlations between specific bacteria and metabolites, indicating a close microbiota–metabolism association during reversal. Conclusions: This integrated multi-omics study delineates the potential dynamic reorganization of the gut microbiota and host metabolism during spontaneous liver fibrosis reversal. These findings provide a theoretical basis for understanding the gut–liver axis mechanism in fibrosis reversal and for developing microbiota-targeted intervention strategies.

Metabolites doi: 10.3390/metabo16060423

Authors: Chang Guo Zizhi Tang

Background: Acetaminophen (APAP) overdose remains a major cause of acute liver injury. Although N-acetylcysteine (NAC) is the clinically established antidote for APAP toxicity, its efficacy is greatest when administered early, and additional therapeutic strategies are still needed for patients with delayed presentation or progressive injury. Because APAP hepatotoxicity involves coupled disturbances in redox control, mitochondrial performance, and cellular metabolism, metabolic enzymes that sustain NADPH availability may critically influence disease severity. Malic enzyme 1 (ME1), a cytosolic NADPH-generating enzyme, has not been functionally defined in this context. Methods: To determine the contribution of ME1 to APAP-induced liver injury (AILI), we used hepatocyte-specific ME1 knockout mice, hepatic overexpression and reconstitution approaches, primary mouse hepatocytes, and an enzymatically inactive ME1 mutant. Liver injury and associated changes in oxidative stress, mitochondrial function, energy metabolism, autophagic flux, and endoplasmic reticulum (ER) stress were evaluated using biochemical, histological, molecular, and ultrastructural analyses, together with pharmacological interventions. Results: Genetic loss of ME1 did not substantially alter early APAP metabolic activation-related indices, including APAP-protein adduct formation, but markedly increased hepatocellular metabolic vulnerability after APAP challenge. This phenotype was characterized by enhanced lipid peroxidation, impaired mitochondrial polarization, reduced ATP availability, defective autophagic flux, and amplified ER stress, leading to more severe liver damage. In contrast, ME1 overexpression or reconstitution promoted a more adaptive metabolic response and limited tissue injury. These effects depended largely on ME1 catalytic activity, as protection was markedly weakened with the mutant enzyme. Pharmacological analyses further supported the involvement of AMPK/mTOR-associated autophagy regulation and ER stress adaptation in the downstream actions of ME1. Malic acid also partially attenuated APAP-induced hepatotoxicity in vivo and in vitro. Conclusions: ME1 functions as an endogenous metabolic factor that influences the outcome of APAP-induced liver injury. Its catalytic activity supports hepatocyte survival primarily by preserving reductive capacity, bioenergetic balance, and adaptive stress responses, rather than by altering APAP metabolic activation.

Metabolites doi: 10.3390/metabo16060422

Authors: María Teófila Vicente-Herrero Pedro J. Tárraga López Carla Busquets-Cortés Lluis Rodas Cañellas Ángel Arturo López González José Ignacio Ramírez-Manent

Background: Cardiometabolic diseases are shaped by complex interactions between biological and social determinants. While socioeconomic inequalities in cardiometabolic risk are well established, less is known about how these inequalities are distributed across multidimensional cardiometabolic phenotypes and whether they differ by sex. Objective: We aimed to examine sex differences in the socioeconomic gradient of cardiometabolic phenotypes using latent class analysis in a working-age population. Methods: A cross-sectional study was conducted in 3108 adults aged 18–65 years undergoing occupational health assessments in the Balearic Islands (Spain). Educational level was used as an indicator of socioeconomic position. Cardiometabolic risk was assessed using obesity, insulin resistance (METS-IR), metabolic dysfunction-associated steatotic liver disease (FLI), atherogenic index of plasma, and metabolic syndrome. Latent class analysis was applied to identify cardiometabolic phenotypes. Multinomial logistic regression models stratified by sex and interaction analyses were used to assess associations between educational level and class membership. Tests for linear trend and predicted probabilities were also estimated. Results: Four cardiometabolic phenotypes were identified: low-risk (40.8%), obesity-dominant (24.1%), dysmetabolic (19.3%), and high-risk multimorbid (15.8%). A clear socioeconomic gradient was observed, with lower educational attainment associated with a higher likelihood of belonging to adverse cardiometabolic profiles. This gradient was stronger among women. For the high-risk multimorbid class, the relative risk ratio comparing low vs. high educational level was 1.82 (95% CI 1.34–2.46) in men and 2.47 (95% CI 1.68–3.64) in women (p for interaction = 0.012). A significant linear trend across educational levels was observed in both sexes (p for trend < 0.001). Predicted probabilities further confirmed a steeper increase in high-risk profiles among women with lower educational attainment. Conclusions: Cardiometabolic risk is structured into distinct phenotypic profiles that are socially patterned. Socioeconomic inequalities are strongly associated with adverse cardiometabolic phenotypes, with a more pronounced gradient among women. These findings highlight the need for gender-sensitive strategies addressing social determinants to reduce cardiometabolic health inequalities.

Metabolites doi: 10.3390/metabo16060421

Authors: Zifan Li Yaqian Li Na Mao Xuemin Gao Hong Xu Wenchen Cai Tian Li

Pulmonary fibrosis, particularly idiopathic pulmonary fibrosis (IPF), is a chronic and progressive interstitial lung disease characterized by alveolar epithelial injury, fibroblast activation, and excessive extracellular matrix deposition, which collectively lead to respiratory failure. Despite the availability of antifibrotic agents, disease-modifying therapies remain limited. Emerging evidence has identified dysregulated sphingolipid metabolism, especially ceramide accumulation, as a key driver of fibrotic pathogenesis. Ceramide is a central bioactive lipid in the sphingolipid pathway that regulates multiple cellular processes, including apoptosis, inflammation, endothelial barrier dysfunction, and fibroblast activation, all of which contribute to pulmonary fibrosis. This review is a narrative review that systematically summarizes the biosynthetic and metabolic pathways of ceramide, with an emphasis on chain length-specific functions and the ceramide to S1P rheostat. We further discuss the mechanistic roles of ceramide in alveolar epithelial cell apoptosis, inflammatory responses, and vascular barrier disruption in fibrotic lung disease. Finally, we highlight emerging therapeutic strategies that target ceramide metabolism, including inhibitors of acid sphingomyelinase (ASMase) and serine palmitoyltransferase (SPT), and propose future directions for clinical translation.

Metabolites doi: 10.3390/metabo16060420

Authors: Silvia Hannah Bilotti Ratto Gomes da Silva Danielle Cristina Honorio França Kênia Maria Resende Silva Emanuelle Carolina Honorio França Viviane Francelina Luz Arce dos Santos Sfredo Tassiane Cristina Morais Eduardo Luzía França Adenilda Cristina Honorio-França

Background/Objectives: Obesity is a major public health problem associated with chronic inflammation and functional alterations in multiple organs and systems. Few studies have examined colostrum from obese mothers, particularly with respect to macrophage function, enzyme and cytokine concentrations, and the role of melatonin in immune modulation. This study aimed to evaluate melatonin levels and their effects on macrophage polarization, cytokine concentrations, nitric oxide synthase [iNOS], and arginase in colostrum from obese mothers. Colostrum samples were collected from eutrophic mothers [BMI: 18.5–24.9 kg/m2] and obese mothers [BMI: ≥30 kg/m2]. Methods: Macrophages were isolated by density gradient and treated with melatonin. The expression of M1 and M2 macrophages and cytokine concentrations were assessed by flow cytometry, while melatonin levels in colostrum supernatants, iNOS, and arginase in cell lysates were determined by ELISA. Results: An endogenous increase in melatonin was also observed in the colostrum of obese mothers. Maternal obesity has been shown to reduce M1 and M2 macrophage expression, increase nitric oxide synthase [NOS] activity, and elevate interleukin-6 [IL-6] and interleukin-17 [IL-17] levels. However, melatonin treatment restored M1 and M2 macrophage levels and reduced inducible nitric oxide synthase [iNOS] and arginase production to levels similar to those observed in mothers of healthy weight. Conclusions: these findings suggest that maternal obesity creates a pro-inflammatory environment in colostrum, characterized by altered macrophage polarization, altered cytokine secretion, and an imbalance in the enzymatic activities of iNOS and arginase within the L-arginine metabolic pathway. Both natural and supplemental melatonin exhibited immunomodulatory, antioxidant, and anti-inflammatory effects, helping to restore immune balance in colostrum. These results emphasize the potential benefits of melatonin as an immunometabolic modulator and its contribution to understanding immunometabolic regulation in obese mothers.

Metabolites doi: 10.3390/metabo16060419

Authors: Hezhang Yun Chang Liu Binghong Gao Peijie Chen

Objectives: This study aimed to identify core genes associated with mitochondria-related transcriptomic signatures and evaluate their potential as computational biomarkers, immune characteristics, regulatory mechanisms, and potential therapeutic relevance. Methods: Obesity-related transcriptome datasets were obtained from the GEO database. Differentially expressed genes (DEGs) were intersected with mitochondria-related genes (MRGs) to identify obesity-related MRGs. Functional enrichment, protein–protein interaction (PPI) analysis, CytoHubba, LASSO and random forest algorithms were used to screen core genes. External validation, ROC analysis, immune infiltration analysis, regulatory network construction, candidate drug prediction, and molecular docking were further performed. Results: A total of 527 DEGs and 15 differentially expressed MRGs were identified. Enrichment analysis suggested that these mitochondria-related genes were mainly associated with disrupted mitochondrial energy metabolism, lipid metabolic remodeling, and altered substrate utilization. ECHDC2, FASN, NAT8L, and AASS were identified as core MRGs; these genes are respectively associated with mitochondrial metabolic regulation, de novo fatty acid synthesis, N-acetylaspartate-related mitochondrial metabolism, and lysine degradation. These genes were significantly downregulated in obesity and showed good diagnostic performance. Immune infiltration analysis revealed alterations in the immune microenvironment, and the core genes were negatively correlated with multiple immune cell types. Molecular docking showed that Genistein had the lowest predicted binding free energy with NAT8L (−8.89 kcal/mol), suggesting relatively favorable binding among the tested ligand–target pairs. Conclusions: ECHDC2, FASN, NAT8L, and AASS may serve as candidate computational biomarkers, among which FASN represents a known lipid metabolism-related gene, supporting the biological plausibility of the workflow.

Metabolites doi: 10.3390/metabo16060418

Authors: Evelyn A. Bates Zachary A. Kipp Wang-Hsin Lee Genesee J. Martinez Sally N. Pauss Philipp E. Scherer Terry D. Hinds

Background/Objectives: Signaling mediators of PPARγ influence pathways involved in adipogenesis, lipid storage, inflammation, energy-related processes, and glucose utilization. Recent research indicates that PPARγ coregulators, recruited or released during ligand binding, govern specific gene pathways. It was recently discovered that Gαq, a heterotrimeric G protein subunit, also signals to PPARγ and may significantly affect adipogenesis and glucose sensitivity. Methods: To explore Gαq’s role in adipocytes, we generated CRISPR-mediated Gαq (Gnaq) knockout (Gnaq KO) and scramble control cells from 3T3-L1 preadipocytes. Results: The absence of Gαq resulted in increased lipid accumulation and elevated serine 273 (but not serine 112) phosphorylation of PPARγ. Gαq deficiency also decreased mitochondrial abundance and respiration in response to PPARγ ligands such as rosiglitazone, pioglitazone, and troglitazone. RNA sequencing comparing differentiated Gnaq KO and control adipocytes identified over 800 differentially expressed genes, including those associated with enhanced lipid metabolism and reduced inflammation. Corresponding PamGene kinome profiling showed increased serine/threonine kinase activity and decreased phosphotyrosine kinase signaling in Gnaq KO adipocytes. Conclusions: These findings support Gαq as a regulator of adipocyte function, linking kinase signaling pathways to PPARγ-mediated transcription. This research provides mechanistic insights into targeting Gαq as a potential treatment for individuals with obesity and metabolic disorders.

Metabolites doi: 10.3390/metabo16060417

Authors: Yunong Xia Silin Su Xianyu Tang Lei Qin Junxing Lu Shitou Xia

Rapeseed is a major source of vegetable oil and contains a wide variety of metabolites. Recent advances, particularly the integration of metabolomics with other omics approaches, have enabled not only comprehensive but also detailed analyses of key metabolites that respond to specific conditions. To date, these recent advances in the metabolomics of Brassica crops have not yet been fully clarified. In this review, we seek to summarize the recent progresses in metabolomics studies of Brassica rapa, B. napus and B. juncea, introduce the key metabolites spanning nucleic acids, amino acids, fatty acids, lipids, organic acids, alkaloids, phenylpropanoids, terpenoids, flavonoids and glucosinolates uncovered by this approach, focusing on those associated with growth and development, and abiotic/biotic stresses, including macronutrient availability, temperature, water stress, salt stress, aluminum and cadmium toxicity, and infection of Sclerotinia sclerotiorum, Leptosphaeria maculans, and Plasmodiophora brassicae. Future perspectives and current challenges in metabolomics integrating with other omics are also discussed, along with its potential for breeding applications, especially in new marker discovery, trait prediction, and even metabolic selection, aimed at developing new rapeseed varieties with stable, high-yielding, and quality traits.

Metabolites doi: 10.3390/metabo16060416

Authors: Albion Dervishi

Background: Autism spectrum disorder (ASD) is associated with immune dysregulation in a subset of individuals, though findings remain heterogeneous and poorly defined, particularly regarding immune subtypes and metabolic context. Methods: We analyzed whole-blood microarray data from GSE18123 (GPL570: ASD n = 46, controls n = 19; GPL6244: ASD n = 68, controls n = 21) using an integrated immunometabolic framework. CD4+ T-cell transcriptional programs were used to assign dominant immune phenotypes (TH1, TH2, TH17, Tfh, FOXP3+ Treg, Tr1-like). Metabolic demand was quantified via the τ-axis; execution capacity was assessed using cytosolic and mitochondrial energy compensation ratios (CECR, MECR). Induction–execution mismatch was captured by three Gap metrics (Cytosolic, Warburg, Global). Functional validation correlated these metrics with transcriptional signatures of folate transport, one-carbon metabolism, receptor-mediated micronutrient uptake (LRP2–CUBN–AMN), cobalamin processing, and vitamin D activation across both platforms. Results: Six immunometabolic CD4+ subtypes were identified within ASD. τ-axis discrimination was strongest for Tr1-like (AUC = 0.811) and Tfh (AUC = 0.825) states, while TH17 profiles were indistinguishable from controls. Despite variation in metabolic demand, CECR and MECR remained relatively preserved, indicating decoupling between induction and execution capacity. Global Gap values were most negative in Tfh and TH1 states and positive in TH17 and controls. Negative Gap states showed coordinated suppression of ATP-intensive micronutrient acquisition pathways, including folate transport (FOLR1/2, SLC19A1), megalin–cubilin-mediated uptake (r ≈ 0.77–0.79), and vitamin D activation (CYP27B1). Intracellular cobalamin processing was upregulated in proportion to metabolic demand (r > 0.9). Findings were directionally replicated across both datasets. Conclusions: These data demonstrate that ASD exhibits structured immunometabolic heterogeneity characterized by subtype-specific demand–capacity imbalance. The Global Gap framework provides transcriptomic evidence of energetic deficit in Tfh- and Tr1-like-dominant states. Future clinical studies should incorporate subtype-stratified assessment of micronutrient status and metabolic execution capacity.

Metabolites doi: 10.3390/metabo16060415

Authors: Sofia Tamini Adele Bondesan Diana Caroli Francesca Frigerio Alessandro Sartorio

Background/Objectives: Pediatric obesity is closely associated with metabolic syndrome (MetS), a condition linked to increased cardiometabolic risk. Early identification of high-risk individuals remains challenging. This study aimed to evaluate the diagnostic performance of selected anthropometric, metabolic dysfunction and insulin resistance indexes for identifying MetS in children and adolescents with obesity. Methods: In this retrospective, cross-sectional, single-center study, 758 children and adolescents with obesity (mean age 14.8 ± 2.1 years; 59.9% females) hospitalized for a body weight-reduction program were included. MetS was defined according to International Diabetes Federation criteria, in which central obesity is a mandatory diagnostic component. The triglyceride–glucose (TyG), TyG–waist circumference (TyG-WC), body adiposity index (BAI), fasting glucose-to-insulin ratio (FGIR), and quantitative insulin sensitivity check index (QUICKI) were calculated. Receiver operating characteristic curve analysis was used to assess their discriminative ability. Results: The prevalence of MetS was 27.8% and was significantly higher in males than females (34.9% vs. 23.1%, p < 0.0001). TyG and TyG-WC showed the best discriminative performance (AUC 0.75 and 0.76, respectively), although with only moderate sensitivity and specificity. FGIR and QUICKI demonstrated lower accuracy (AUC 0.64 and 0.63), whereas BAI showed no discriminative ability (AUC 0.48). These findings were consistent across sexes, although sex-specific differences in both MetS prevalence and optimal cut-off values were observed. Correlation analyses confirmed moderate associations between TyG-based indexes and MetS, whereas other indexes showed weaker relationships. Conclusions: In the present cohort of children and adolescents with obesity, TyG and TyG-WC showed the best performance in identifying MetS compared with the other evaluated indexes. However, their performance remained moderate, and the proposed cut-off values require validation in independent populations. These indexes may represent simple supportive screening and risk-stratification tools but should be used alongside comprehensive clinical assessment and established diagnostic criteria rather than as stand-alone diagnostic measures.

Metabolites doi: 10.3390/metabo16060414

Authors: Anita Dittrich Sofie Amalie Andersson Aage Kristian Olsen Alstrup Pernille Lajer Sørensen Mette Irene Theilgaard Simonsen Maibritt Hald Arildsen Rasmus Roost Aabling Henrik Lauridsen

Background/Objectives: Cardiac regenerative ability varies in vertebrates. Adult mammals cannot mount a regenerative response, while fetal mammals and some salamanders and teleosts fully regenerate the heart after a cryoinjury mimicking a myocardial infarction. This contrast is suggested to be regulated in part by metabolism, with high regenerative capacity correlating with a comparatively lower mass-specific metabolic rate, ectothermy rather than endothermy and a metabolic phenotype favoring glycolysis in cardiac muscle. Methods: In this physiological study on axolotl salamanders, we altered the housing temperatures from the standard 20 °C to 10 °C, 25 °C and 30 °C and assayed key metabolic parameters as well as cardiac function, survival and regenerative capacity. Results: Our study demonstrated that while axolotls could be housed at temperatures ranging from 10 °C to 30 °C in an uninjured state, signs of a pathological response involving cardiac and metabolic insufficiency and mortality, especially after cryoinjury, increased progressively with increasing temperatures. We observed several metabolic effects, including differences in oxygen consumption, plasma metabolites and cardiac function. Cardiac regeneration after cryoinjury progressed as expected with only a small remaining injury after 60 days at the standard housing temperature of 20 °C. Regeneration was highly reduced in a reversible manner at 10 °C while regenerative rate was not affected at 25 °C. At 30 °C, cardiac regeneration could not be evaluated as the majority of animals (five out of six) did not survive the injury, likely reflecting insufficient cardiac reserve capacity to simultaneously sustain thermal metabolic effects and support tissue repair. Conclusions: The ectothermic axolotl undergoes several metabolic changes when exposed to different housing temperatures, with heart regeneration showing a narrower permissive temperature range than survival of the axolotl in an uninjured state.

Metabolites doi: 10.3390/metabo16060413

Authors: Xuefei Chen Jie Su Wenhua Huang Yanjun Li Jing Zhang

Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) has emerged as a global metabolic disorder. As a non-pharmacological intervention, the effects of high-intensity interval training (HIIT) on MASLD and its molecular mechanisms remain poorly understood. This study aimed to investigate whether HIIT could ameliorate high-fat diet (HFD)-induced liver fibrosis by recalibrating the intrahepatic lactate metabolic axis. Methods: An HFD-induced murine MASLD model combined with HIIT intervention was utilized to evaluate the therapeutic efficacy and underlying mechanisms. Hepatosomatic indices, histological architecture and fibrosis severity were examined. Lactate concentrations within the systemic circulation and hepatic parenchyma, alongside comprehensive lipid profiles, were measured. The expressions of genes and proteins involved in hepatic lactate metabolism were delineated via qPCR and Western blotting. Results: The 8-week HIIT intervention effectively improved liver lipid accumulation, hepatocellular injury, and oxidative stress caused by a high-fat diet. Fibrotic expansion and suppressed hepatic stellate cell activation were restricted markedly, as evidenced by the downregulation of collagen type I alpha 1 chain and alpha-smooth muscle actin(α-SMA). HIIT reversed the HFD-induced accumulation of lactate in both systemic circulation and liver tissues, which was found to positively correlate with hepatic α-SMA. Mechanistically, HIIT regulated the expression of the lactate metabolism-related proteins lactate dehydrogenase A and monocarboxylate transporter 1, while selectively enhancing the expression of the gluconeogenic enzymes. Conclusions: Our findings indicate that HIIT effectively ameliorated MASLD and associated hepatic fibrosis by remodeling the hepatic lactate metabolic axis, specifically through the suppression of lactate production and the enhancement of its clearance. These results indicate that targeting lactate homeostasis might be a promising therapeutic strategy for MASLD.

Metabolites doi: 10.3390/metabo16060412

Authors: Torbjørn Norberg Myhre Terkel Hansen Tetiana Lutchyn Marie Mardal Terje Vasskog

Background: Metabolite identification and annotation remain major bottlenecks in untargeted metabolomics because mass spectral features often lack sufficient specificity. High-confidence annotation requires experimental validation using authentic standards analyzed under matched chromatographic and ionization conditions, providing greater reliability than in silico predictions or database matching alone. This study aimed to develop a practical and scalable workflow for constructing a high-quality mass spectral library using a commercially available analytical standards kit. Methods: A total of 603 metabolites from the MSMLS kit were organized into 42 mixtures, each containing approximately 15 compounds. Mixture design was based on molecular mass and distribution coefficient values, specifically logD at pH 3.1, with a minimum logD spacing of 0.15 to improve chromatographic separation and reduce co-elution. This strategy was used to minimize the total number of injections while maintaining spectral quality. The resulting spectra were evaluated against online spectral resources and in silico fragmentation predictions. A preliminary proof-of-concept analysis was also performed using human serum samples. Results: Using this workflow, 471 metabolites, corresponding to approximately 78% of the standards, were successfully detected and incorporated into the spectral library. Comparison with online resources and in silico fragmentation predictions demonstrated improved spectral quality and reliability. The proof-of-concept serum analysis enabled identification of endogenous metabolites using the constructed library. In addition, the robustness and applicability of the workflow were further supported by a method validation study using metabolites derived from this library. Conclusions: This workflow provides a scalable strategy for constructing mass spectral libraries that balances spectral quality with analytical throughput. By using rational mixture design and authentic standards analyzed under matched experimental conditions, the approach enables substantial metabolite coverage while maintaining data reliability and minimizing experimental effort.

Metabolites doi: 10.3390/metabo16060411

Authors: Fanjia Cheng Chenghao Lv Yuhang Yi Dongsheng Wang Wenbo Wang Tao Li Runze Zhou Qili Li Si Qin

Background/Objectives: Metabolic syndrome (MetS) is a pressing global health challenge comprising obesity, hyperglycemia, hypertension, and hyperlipidemia. Conventional polypharmacy often presents long-term compliance issues and side effects. Eucommia ulmoides Oliv., a traditional medicinal and edible plant rich in iridoids, lignans, flavonoids, and polysaccharides, has emerged as a promising natural intervention. This review aims to systematically summarize the bioavailability and multifaceted pharmacological mechanisms of E. ulmoides and its bioactive components in alleviating MetS. Methods: We comprehensively reviewed the recent in vitro and in vivo literature to map the functional evidence, specific signaling pathways, and gut microbiota–host interactions associated with E. ulmoides extracts and its key phytochemicals (e.g., asperuloside) against various metabolic dysfunctions. Results: Current evidence indicates that E. ulmoides operates through a “multi-component, multi-target, and multi-pathway” paradigm. For hyperlipidemia and obesity, it activates hepatic lipid metabolism (PPARα/CPT1A, FXR/CYP7A1) and mitigates oxidative stress (Nrf2/ARE). Furthermore, it dose-dependently reshapes the gut microbiota by enriching beneficial bacteria like Akkermansia and increasing butyrate production, exerting profound gut–liver axis regulation. It also ameliorates hypertension by activating the ACE2-Ang-(1–7)-Mas axis, improves insulin resistance via the AMPK/PI3K/Akt cascade, and manages hyperuricemia by modulating XOD and renal transporters. Notably, the low oral bioavailability of its glycosides highlights the crucial role of gut microbial hydrolysis in its efficacy. Conclusions: E. ulmoides holds substantial therapeutic potential as a multi-target natural supplement for MetS. However, future translational applications necessitate large-scale randomized clinical trials, multi-omics studies to further clarify host–microbiome interactions, and the development of standardized formulations to ensure clinical efficacy.

Metabolites doi: 10.3390/metabo16060410

Authors: Vladimír Kraus Anna Birková Miroslava Majerníková Beáta Čižmárová

Background/Objectives: Phytoestrogens are secondary plant metabolites produced via the phenylpropanoid pathway. They include a broad spectrum of chemical compounds, such as phenolics, flavonoids, isoflavones, coumestans, lignans, and others. Their chemical structures resemble those of estradiol, and they exhibit biological effects similar to those of human estrogens, influencing many physiological processes throughout life in both men and women—including the timing and progression of puberty. Methods: The literature search included databases such as PubMed, Scopus, Web of Science, and Google Scholar with the use of specific keywords. Studies were considered eligible if they reported original findings from observational studies (cohort, case–control, and cross-sectional) or from experimental studies. Results: Phytoestrogens can modulate estrogenic activity and interact with a variety of biological pathways. These compounds may play a role in human development and pubertal processes, contribute to overall health, and potentially help alleviate menopausal symptoms and reduce the risk of certain cancers. Conclusions: Phytoestrogens have numerous positive effects on the human body across various stages of life. Their overall impact and potency, however, seem to be influenced by factors such as intake level, individual genetic variability, and the specific phytoestrogen class consumed.

Metabolites doi: 10.3390/metabo16060409

Authors: Zhangqun Li Ling Zhang Xiaofang Li Mingjie Li Haiyang Xia

Background: Doramectin (CHC-B1) is an excellent antiparasitic drug produced by feeding cyclohexanecarboxylic acid (CHC) to Streptomycesavermitilis bkd− mutants. AveC, a bifunctional enzyme encoded by aveC (sav_0940), catalyzes the stereospecific spiroketalization and selective dehydration of dihydroxy ketone polyketide intermediates and modulates both the yield and the proportion of avermectin/doramectin in Streptomyces avermitilis. In our previous work, we constructed a strain harboring a synthetic aveC* gene encoding ten amino acid mutations, which produced nearly pure doramectin. However, the doramectin yield achieved only approximately 60% of the total doramectin and CHC-B2 output observed in the parental strain. Methods: To investigate the roles of Ser138 and Ala139 of AveC in the biosynthesis of doramectin and avermectin, site-directed mutagenesis was performed at both sites. The production and proportion of avermectin and doramectin were determined using high-performance liquid chromatography (HPLC). AlphaFold2-based molecular docking simulations were used to interpret the results. Results: Among the tested mutants, S138G, S138T, and A139H exhibited the highest doramectin production, achieving 143.87%, 151.22%, and 153.36% of the control level, respectively. Unfortunately, almost none of the tested mutants showed a positive effect on avermectin production. Molecular docking simulations revealed distinct affinities of these mutants for the dihydroxy ketone polyketide intermediate, both with and without a cyclohexyl group. Notably, all three mutants displayed larger substrate-binding cavity volumes compared with the wild-type enzyme, which likely facilitates doramectin synthesis by effectively accommodating the cyclohexyl moiety. Docking results further indicated that Ser138 and Ala139 are positioned within the binding cavity but probably do not directly participate in the dehydration activity. Conclusions: These findings suggest that optimizing cavity size through residue substitutions can enhance substrate specificity for doramectin production while preserving catalytic functionality.

Metabolites doi: 10.3390/metabo16060408

Authors: Zuzanna Chęcińska-Maciejewska Ewa Pruszyńska-Oszmałek Paweł Kołodziejski Andrzej Ciborek Hanna Krauss

Elabela (ELA/APELA/Toddler) is an endogenous peptide ligand of the apelin receptor APLNR (also known as APJ) and, together with apelin, forms the apelinergic signalling system. Its role in embryonic development, the cardiovascular system, the kidneys and the endothelium is becoming increasingly well characterised, whilst its function in metabolic regulation remains unresolved. Elabela activates pathways essential for metabolic homeostasis—PI3K/Akt, AMPK-related pathways, redox regulation, inflammatory control and pro-survival cascades—but no study has shown that it directly regulates adipocyte lipid metabolism. This narrative review categorises the evidence at the receptor, organ, immunometabolic and intra-adipocyte levels, and also considers the adipose tissue microenvironment as a distinct level of potential relevance. The available data support a role for Elabela as a candidate mediator of lipid-related metabolic dysfunction—via anti-inflammatory, antioxidant and tissue-protective mechanisms—with macrophage lipid metabolism representing the most informative immunometabolic interface. Human studies remain scarce, heterogeneous and limited by a lack of standardisation in assay methods and the unresolved specificity of isoforms. Elabela should therefore be regarded as a candidate indirect modulator of metabolic homeostasis and a candidate biomarker of cardiometabolic stress or adaptation—not as a confirmed direct regulator of adipocyte lipid metabolism.

Metabolites doi: 10.3390/metabo16060407

Authors: Melih Okcu Zuhal Okcu Funda Kaya Kamil Haliloglu

Background/Objectives: Soil salinity is a major constraint on legume productivity worldwide, threatening forage pea (Pisum sativum L.) cultivation in semiarid regions. This study evaluated the effect of exogenous melatonin in attenuating NaCl-induced salinity stress across diverse forage pea genotypes. Methods: A three-factor factorial experiment was conducted under greenhouse conditions, testing three NaCl levels (0, 100 and 200 mM) and four melatonin concentrations (0, 100, 150 and 200 µM) across 13 genotypes with three replications (468 pots). Nine vegetative traits were measured and analyzed by factorial ANOVA and Tukey’s HSD test. Results: Increasing NaCl from 0 to 200 mM reduced plant height by ~28% and node number by ~32%. Application of 100 µM melatonin under 100 mM NaCl reduced canopy temperature from 28.1 °C to 23.7 °C and restored SPAD values from 21.7 to 26.5 under 200 mM NaCl. By contrast, 200 µM melatonin under severe salinity paradoxically suppressed SPAD to 8.9 and reduced root length. Emirbey and Kirazlí showed the greatest vegetative growth, while Özkaynak exhibited the highest chlorophyll content. Conclusions: 100 µM melatonin emerged as the optimal concentration for alleviating moderate salt stress in forage pea, and genotype selection is critical when deploying melatonin as a biostimulant under saline conditions. Direct measurement of biomass, yield, and forage quality under field conditions remains an essential next step before agronomic deployment.