Metabolites

18 pages, 1886 KB

Open AccessArticle

Multi-Omics Feature Selection to Identify Biomarkers for Hepatocellular Carcinoma

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

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

Abstract

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

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

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

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15 pages, 838 KB

Open AccessArticle

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

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

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

Abstract

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

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

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

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20 pages, 2428 KB

Open AccessReview

Gastric Bypass Associated Hyperammonemia (GaBHA): A Case Study, Scoping Review of the Literature, and Proposed New Pathophysiologic Mechanism

by Andrew Z. Fenves, Dilara Hatipoglu, John C. Robinson and Michael M. Rothkopf

Metabolites 2025, 15(9), 573; https://doi.org/10.3390/metabo15090573 - 27 Aug 2025

Abstract

Background/Objectives: GaBHA syndrome (gastric bypass hyperammonemia) is an emerging new syndrome primarily in women who had prior Roux-en-Y gastric bypass surgery (RYGB) and then developed non-cirrhotic hyperammonemia with a high case–fatality ratio. Genetic and nutritional deficiencies have been implicated in the pathogenesis of [...] Read more.

Background/Objectives: GaBHA syndrome (gastric bypass hyperammonemia) is an emerging new syndrome primarily in women who had prior Roux-en-Y gastric bypass surgery (RYGB) and then developed non-cirrhotic hyperammonemia with a high case–fatality ratio. Genetic and nutritional deficiencies have been implicated in the pathogenesis of this clinical condition, but none has been proven. We present an illustrative case and do a scoping review of the current literature in 58 patients with this diagnosis. Methods: A retrospective scoping literature review was utilized to identify patients who fulfilled 1. RYGB surgery, and 2. Hyperammonemic encephalopathy following the PRISMA extended checklist. We searched PubMed, MedLine, SCOPUS, and Web of Science databases. Results: We described the classic presenting symptoms and laboratory findings of this syndrome. We confirmed the female predominance (93%) and the high case–fatality ratio (32%). We then presented a novel hypothesis contending that arginine deficiency ultimately leads to a functional deficiency of the ornithine transcarbamolyase (OTC) enzyme, leading to the non-cirrhotic life-threatening hyperammonemia. Our hypothesis may also explain the high incidence of hypoglycemia found in these patients as we found in our search. Our proposed hypothesis may also be relevant to the occurrence of hyperammonemia in some solid organ transplant recipients. Conclusions: GaBHA syndrome is emerging as an important potential adverse outcome after RYGB surgery. It has a female predominance and a high case–fatality ratio. Arginine deficiency may explain the emergence of a functional OTC deficiency, which then leads to the severe hyperammonemia, and may also explain the frequent occurrence of hypo-glycemia in these patients. Full article

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

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16 pages, 3642 KB

Open AccessArticle

miR-221-3p Exacerbates Obesity-Induced Insulin Resistance by Targeting SOCS1 in Adipocytes

by Nan Li, Liang Zhang, Qiaofeng Guo, Xiaoying Yang, Changjiang Liu and Yue Zhou

Metabolites 2025, 15(9), 572; https://doi.org/10.3390/metabo15090572 - 27 Aug 2025

Abstract

Objective: Insulin resistance (IR) is a complex and multifactorial disorder that contributes to type 2 diabetes and cardiovascular disease. MicroRNAs (miRNAs) play important roles in diverse developmental and disease processes. However, the molecular mechanisms of IR are unclear. This paper aims to explore [...] Read more.

Objective: Insulin resistance (IR) is a complex and multifactorial disorder that contributes to type 2 diabetes and cardiovascular disease. MicroRNAs (miRNAs) play important roles in diverse developmental and disease processes. However, the molecular mechanisms of IR are unclear. This paper aims to explore the role of miRNA in regulating IR and to elucidate the mechanisms responsible for these effects. Methods: IR models were created by feeding a high-fat diet (HFD) to mice or stimulating 3T3-L1 cells with palmitate. Twelve weeks of HFD trigger weight gain, leading to lipid accumulation and insulin resistance in mice. The expression profiles of miRNAs in adipose tissues (AT) from the HFD-induced mouse models were analyzed. The relationship between miR-221-3p and SOCS1 was determined using dual luciferase reporter gene assays. Metabolic alterations in AT were investigated by real-time PCR and Western blot. Results: miR-221-3p was significantly increased in AT. HFD-induced disturbances in glucose homeostasis were aggravated by miR-221-3p upregulation. The inhibition of miR-221-3p promoted insulin sensitivity including reduced lipid accumulation and the disruption of glucose metabolism. Of note, the 3′-UTR of SOCS1 was found to be a direct target of miR-221-3p. The SOCS1 inhibitor attenuated miR-221-3p-induced increases in IRS-1 phosphorylation, AKT phosphorylation, and GLUT4. miR-221-3p was considered to be involved in the PI3K/AKT signaling pathway, thus leading to increased insulin sensitivity and decreased IR in HFD-fed mice and 3T3-L1 adipocytes. Conclusions: The miR-221-3p/SOCS1 axis in AT plays a pivotal role in the regulation of glucose metabolism, providing a novel target for treating IR and diabetes. Full article

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

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14 pages, 1631 KB

Open AccessArticle

Urinary ¹H-NMR Metabolomics Highlights MIIA (Microbiota–Immune–Inflammation Axis) Activation by Organic Mediterranean Diet

by Laura Di Renzo, Simona Cesaroni, Giulia Frank, Barbara Pala, Daniel Oscar Cicero, Paola Gualtieri and Greta Petrella

Metabolites 2025, 15(9), 571; https://doi.org/10.3390/metabo15090571 - 26 Aug 2025

Abstract

Background: While the Mediterranean diet is well-established for its health benefits, the specific influence of organic versus conventional food sources within this pattern remains underexplored at the systemic metabolic level. Objective: This study investigated the metabolic effects of two matched Mediterranean diets, one [...] Read more.

Background: While the Mediterranean diet is well-established for its health benefits, the specific influence of organic versus conventional food sources within this pattern remains underexplored at the systemic metabolic level. Objective: This study investigated the metabolic effects of two matched Mediterranean diets, one based on organically produced foods (IMOD) and the other on conventionally produced equivalents (IMNOD), to assess the impact of food production methods on host metabolism and immune-inflammatory balance. Methods: Twelve healthy adults completed a crossover dietary intervention including IMOD and IMNOD phases. Urinary metabolite profiles were assessed via ¹H-NMR spectroscopy across 42 compounds. Multivariate and univariate analyses evaluated metabolic responses. Results: Both interventions normalized some out-of-range urinary metabolites. However, IMOD elicited broader and more significant changes, including increased levels of tricarboxylic acid (TCA) intermediates (e.g., isocitrate, trans-aconitate), plant-derived metabolites (e.g., trigonelline), and host–microbiota co-metabolites (e.g., N-phenylacetylglutamine, 1-methylnicotinamide). Simultaneously, fermentation-associated and xenobiotic-linked metabolites such as formate, acetate, and 2-furoylglycine decreased. These shifts collectively represent a beneficial modulation of the Microbiota–Immune–Inflammation Axis (MIIA effect). Conclusions: Organic food consumption within a Mediterranean framework promotes host–microbiota metabolic interplay and enhances immune-supportive biochemical pathways. The findings provide new mechanistic insight into how food production quality contributes to systemic metabolic health and support broader efforts to make organic foods more accessible. Full article

(This article belongs to the Special Issue Clinical Nutrition and Metabolic Diseases)

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14 pages, 5912 KB

Open AccessArticle

Effects of Macrococcus caseolyticus on the Volatile Flavor Substances of Chinese-Style Sausage

by Yuanqing Gu, Xinya Chen, Jingjing Mao, Xin Nie, Chenglin Zhu, Qin Zou, Qiqi Luo, Yudi Zeng, Luca Laghi, Gianfranco Picone and Zhiping Zhao

Metabolites 2025, 15(9), 570; https://doi.org/10.3390/metabo15090570 - 26 Aug 2025

Abstract

Objectives: The primary objective of this study was to investigate the effects of Macrococcus caseolyticus isolated from Chinese bacon on the quality of Chinese-style sausages. Methods: The physicochemical properties and volatile flavor compounds (VOCs) of sausages inoculated with M. caseolyticus at different concentrations [...] Read more.

Objectives: The primary objective of this study was to investigate the effects of Macrococcus caseolyticus isolated from Chinese bacon on the quality of Chinese-style sausages. Methods: The physicochemical properties and volatile flavor compounds (VOCs) of sausages inoculated with M. caseolyticus at different concentrations (10⁵, 10⁶, and 10⁷ CFU/g) were investigated. VOCs were detected using gas chromatography–ion mobility spectrometry (GC-IMS). Results: The sausages inoculated with M. caseolyticus showed progressive decreases in Aw, total volatile base nitrogen (TVB-N), malondialdehyde and carbonyl content during fermentation compared to the control sausage. A total of 90 VOCs were identified based on GC-IMS analysis, including 20 esters, 17 aldehydes, 22 alcohols, 12 ketones, 5 acids compounds, and 14 other compounds. M. caseolyticus-inoculated sausages exhibited elevated levels in alcohols and aldehydes, while the content of ketones was reduced compared to the control sausage. Multivariate statistical analysis indicated the significant differences in volatile flavor profiles among the sample and control sausages. Notably, seven VOCs in sausages, including 1-octen-3-ol, isoamyl alcohol, heptanal, hexanal, methyl 2-methylbutyrate, ethyl isovalerate and 2-pinene, were identified as the key aroma compounds (ROAV ≥ 1). Conclusions: The fermented sausages inoculated with different concentrations of M. caseolyticus exhibited significant differences in VOCs. This study provides the support for employing M. caseolyticus to improve the overall quality and flavor profile of Chinese-style sausage. Full article

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

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21 pages, 3294 KB

Open AccessArticle

The Utilization Value of Condensate Water from the Drying Process of Lonicera japonica via Metabolomics Analysis

by Da Li, Jiaqi Zhang, Yining Sun, Chongchong Chai, Fengzhong Wang, Bei Fan, Long Li, Shuqi Gao, Hui Wang, Chunmei Yang and Jing Sun

Metabolites 2025, 15(9), 569; https://doi.org/10.3390/metabo15090569 - 25 Aug 2025

Abstract

Background: Lonicerae japonicae flos (LJF), a traditional food and medicine with a history spanning thousands of years, undergoes drying as a critical processing step in modern applications after regular processing. While the by-products of this process are typically discarded as waste, the [...] Read more.

Background: Lonicerae japonicae flos (LJF), a traditional food and medicine with a history spanning thousands of years, undergoes drying as a critical processing step in modern applications after regular processing. While the by-products of this process are typically discarded as waste, the potential value of LJF condensate water (JYHC) remains largely unexplored. To address this gap and investigate its potential utilization, this study conducted widely targeted metabolome and volatile metabolomics profiling analyses of ‘JYHC’. Methods: This study analyzed the differential metabolites of ‘JYHC’ and dried Lonicerae japonicae flos (JYHG) based on widely targeted metabolomics using UPLC-MS/MS. Additionally, the metabolic differences between fresh Lonicerae japonicae flos (JYHX) and ‘JYHC’ based on GC-MS volatile metabolomics were comprehensively analyzed. Results: A total of 1651 secondary metabolites and 909 volatile metabolites were identified in this study. Among these, flavonoids and terpenoids were the predominant secondary metabolites, while esters and terpenoids dominated the volatile fraction. Further comparison of the ‘JYHC’ and ‘JYHG’ groups revealed that 58 differential metabolites with potential biological activities were significantly up-regulated, with the types being terpenoids, phenolic acids, and alkaloids, which included nootkatone, mandelic acid, sochlorogenic acid B, allantoin, etc. Notably, a total of 186 novel compounds were detected in ‘JYHC’ that had not been previously reported in LJF such as isoborneol, hinokitiol, agarospirol, 5-hydroxymethylfurfural, α-cadinol, etc. Conclusions: This study’s findings highlight the metabolic diversity of ‘JYHC’, offering new theoretical insights into the study of LJF and its by-products. Moreover, this research provides valuable evidence supporting the potential utilization of drying by-products from LJF processing, paving the way for further exploration of their pharmaceutical and industrial applications. Full article

(This article belongs to the Section Plant Metabolism)

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17 pages, 663 KB

Open AccessReview

Gut Microbiota in Acute Myeloid Leukemia: From Biomarkers to Interventions

by Meifen Ji, Meixia Ji, Yebo Zhong and Lewen Shao

Metabolites 2025, 15(9), 568; https://doi.org/10.3390/metabo15090568 - 25 Aug 2025

Abstract

Acute myeloid leukemia (AML), the most common acute leukemia among adults, poses significant therapeutic challenges due to diagnostic limitations and the frequent development of treatment resistance. While genomics-based approaches have advanced, DNA aberrations do not always reflect the expression levels of genes and [...] Read more.

Acute myeloid leukemia (AML), the most common acute leukemia among adults, poses significant therapeutic challenges due to diagnostic limitations and the frequent development of treatment resistance. While genomics-based approaches have advanced, DNA aberrations do not always reflect the expression levels of genes and proteins, which are more tightly connected to disease phenotypes. Recently, the role of the gut microbiota in AML has gained increasing attention. AML patients often exhibit gut microbiota dysbiosis, which is linked to disease progression and heightened infection risk. Mounting evidence indicates that gut microbiota metabolism influences hematopoiesis and immune function via the “gut-bone marrow axis,” with microbiota composition and diversity significantly affecting treatment outcomes and prognosis. High-throughput sequencing and metabolomics have identified correlations between gut microbiota composition and its metabolic products with AML clinical characteristics, paving the way for new biomarkers in diagnosis and prognosis. Additionally, treatments such as fecal microbiota transplantation (FMT) show promise in enhancing chemotherapy efficacy and improving patient outcomes. This review highlights recent advances in understanding the role of the gut microbiota in AML and explores new perspectives for its diagnosis and treatment. Full article

(This article belongs to the Special Issue Advancing Metabolic/Microbial Biomarker Applications in Disease Prevention, Diagnosis and Public Health)

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13 pages, 425 KB

Open AccessArticle

Phytochemical Analysis and Appraisal of Antiproliferative Activity of Magnolia alejandrae

by José E. Caballero-Chávez, Alma D. Paz-González, Diana V. Navarrete-Carriola, Fabián E. Olazarán-Santibañez, María Miriam Estevez-Carmona, Benjamín Nogueda-Torres, Fernando Emiliano Jiménez-Mondragón, Melany X. Márquez-Aguilar, Carmen Michelle Pineda-Alcala, Diego Cisneros-Juárez, Álvaro Marín-Hernández, Debasish Bandyopadhyay and Gildardo Rivera

Metabolites 2025, 15(9), 567; https://doi.org/10.3390/metabo15090567 - 22 Aug 2025

Abstract

Background: Magnolia alejandrae is a tree endemic to Tamaulipas, Mexico, distributed in the forests of the Sierra Madre Oriental. Objective: Our objective was to analyze the secondary metabolite profile of different parts of M. alejandrae and evaluate their antiproliferative activity in vitro. [...] Read more.

Background: Magnolia alejandrae is a tree endemic to Tamaulipas, Mexico, distributed in the forests of the Sierra Madre Oriental. Objective: Our objective was to analyze the secondary metabolite profile of different parts of M. alejandrae and evaluate their antiproliferative activity in vitro. Methods: Different extracts of leaf, bark, and fruit were obtained using conventional and unconventional extraction methods with solvents of different polarity. The extracts were analyzed by Ultra-Performance Liquid Chromatography-Mass Spectra (UPLC-MS), and their antiproliferative activity against cancer cell lines was determined. Results: The primary yields of the extracts obtained from M. alejandrae ranged from 8.32% to 36.19%. Three hundred and twelve secondary metabolites previously reported from the Magnolia genus were detected. The most frequent were magnone A, pinoresinol, and yangambin. Honokiol and magnolol were not detected. Two of the extracts (FSW and BSW) had antiproliferative activity (IC₅₀ < 140 µg/mL) against HeLa, MCF-7, A549, U373, and PC3 cancer cell lines. The higher activity was against the A549 cell line. Conclusions: M. alejandre extracts showed secondary metabolites previously reported and unreported in other species. Interestingly, some extracts had antiproliferative activity against cancer cell lines. Therefore, M. alejandrae is a source of molecules that could be explored to develop new drugs. Full article

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

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23 pages, 3539 KB

Open AccessArticle

Unraveling the Metabolic Mechanisms and Novel Biomarkers of Vulvar Lichen Simplex Chronicus Using Skin Biopsy and Tape Stripping Samples

by Tian He, Fanrui Xu, Jing Liang, Qing Feng, Dan Cheng, Linlin Xiao, Maoyu Liu, Xuerui Zhang, Xin Wang, Yang Yang, Dan Zhu, Sergey Tumanov, Richard D. Cannon, Ting-Li Han and Shufang Chang

Metabolites 2025, 15(9), 566; https://doi.org/10.3390/metabo15090566 - 22 Aug 2025

Abstract

Background/Objectives: Lichen simplex chronicus (LSC) of the vulva is a chronic dermatologic disorder characterized by persistent pruritus, compulsive scratching, and progressive thickening of the vulvar skin. Currently, LSC diagnosis primarily relies on clinical presentation, with histopathological examination performed when the diagnosis is unclear. [...] Read more.

Background/Objectives: Lichen simplex chronicus (LSC) of the vulva is a chronic dermatologic disorder characterized by persistent pruritus, compulsive scratching, and progressive thickening of the vulvar skin. Currently, LSC diagnosis primarily relies on clinical presentation, with histopathological examination performed when the diagnosis is unclear. However, the precise pathogenic mechanisms driving the disease remain poorly understood. This study aimed to investigate the pathogenesis of LSC and evaluate the feasibility of tape stripping as a non-invasive diagnostic technique. Methods: Skin specimens were obtained using both traditional biopsy and tape stripping methods, and the metabolites and oxidized lipids in these samples were analyzed using advanced mass spectrometry techniques. Results: Our findings suggest that 20-hydroxyeicosatetraenoic acid (20-HETE), an oxidized derivative of arachidonic acid (AA), activates the TRPV1 receptor, thereby exacerbating the itch–scratch cycle. This activation upregulates energy metabolism and promotes epidermal hyperplasia, providing new insights into the disease’s pathophysiology. Conclusions: Our study suggests that tape stripping could serve as a viable non-invasive diagnostic tool for LSC, with linoleic acid (LA) and AA potentially acting as biomarkers for the disease. Full article

(This article belongs to the Section Advances in Metabolomics)

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13 pages, 7066 KB

Open AccessArticle

Metabolomic Analysis of Feces vs. Cecum Content in Animals: A Comparative Study Investigated by ¹H-NMR

by Xiexin Li, Yang Li, Xin Nie, Chenglin Zhu, Qiqi Luo, Luca Laghi and Gianfranco Picone

Metabolites 2025, 15(9), 565; https://doi.org/10.3390/metabo15090565 - 22 Aug 2025

Abstract

Background: Feces and cecum content are commonly involved in metabolomic analysis to understand the gut metabolic profile of the host, while, in fact, they are different. Feces represent the terminal excretory product after extensive host enzymatic digestion, absorption, and significant modification by [...] Read more.

Background: Feces and cecum content are commonly involved in metabolomic analysis to understand the gut metabolic profile of the host, while, in fact, they are different. Feces represent the terminal excretory product after extensive host enzymatic digestion, absorption, and significant modification by the distal gut microbiota. In contrast, cecum content reflects the localized, in situ metabolic microenvironment at that specific site. However, it is worth noting that feces are the most accessible sample type for non-invasive studies, which could be considered proxies for cecum content in some specific cases. Unfortunately, the validity of fecal samples as an alternative to cecum content has rarely been assessed. Methods: The current study attempted to illustrate the distinct metabolomic and microbiota features of feces and cecum content in eight animals (mouse, pig, chicken, duck, rabbit, Gansu yak, Sichuan yak, and sheep) by means of ¹H-NMR and 16S rRNA, respectively. Results: A total of 116 molecules were characterized in feces and cecum content samples. Among them, 22 molecules were shared in all groups. Taking advantage of the univariate analysis, twenty-seven of the quantified molecules were significantly different between feces and cecum content, mainly pertaining to amino acids and organic acids. Moreover, in terms of mammals and non-mammals, short-chain fatty acids could be considered the main factor discriminating the metabolomic profiles between feces and cecum content. Furthermore, to better understand the mechanism of their metabolomic differences, 16S rRNA sequencing analysis was performed on feces and cecum content samples of mice, which is the most widely used animal model. The result showed that the Ace, Shannon, and Sobs indexes in feces were significantly higher than those of cecum content (p < 0.05). At the phylum and genus levels, the microbiota structures of feces and cecum content were similar, while the relative abundances of their microbiota exhibited distinct features. Conclusions: The present study could reduce this gap in information by characterizing, for the first time, the metabolomic differences between feces and cecum content using ¹H-NMR. Moreover, this study is meant as a reference guide for researchers wishing to apply a metabolomics approach to the gut of the host. Full article

(This article belongs to the Section Animal Metabolism)

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18 pages, 8498 KB

Open AccessArticle

Plasma Metabolomic Profiling Reveals Systemic Alterations in a Mouse Model of Type 2 Diabetes

by Masuma Akter Brishti, Fregi Vazhappully Francis and M. Dennis Leo

Metabolites 2025, 15(9), 564; https://doi.org/10.3390/metabo15090564 - 22 Aug 2025

Abstract

Background: Type 2 diabetes (T2D), the most common form of diabetes, is associated with a significantly elevated risk of cardiovascular and cerebrovascular complications. However, circulating metabolic signatures that reliably predict the transition to insulin resistance, and are potentially linked to increased vascular risk, [...] Read more.

Background: Type 2 diabetes (T2D), the most common form of diabetes, is associated with a significantly elevated risk of cardiovascular and cerebrovascular complications. However, circulating metabolic signatures that reliably predict the transition to insulin resistance, and are potentially linked to increased vascular risk, remain incompletely characterized. Rodent models, particularly those induced by a high-fat diet (HFD) combined with low-dose streptozotocin (STZ), are widely used to study the progression of T2D. However, the systemic metabolic shifts associated with this model, especially at the plasma level, are poorly defined. Methods: In this study, we performed untargeted liquid chromatography–mass spectrometry (LC-MS)-based metabolomic profiling on plasma samples from control, HFD-only (obese, insulin-sensitive), and HFD + STZ (obese, insulin-resistant) C57BL/6 mice. Results: In the HFD + STZ cohort, plasma profiles showed a global shift toward lipid classes; depletion of aromatic and branched-chain amino acids (BCAAs); accumulation of phenylalanine-derived co-metabolites, consistent with gut–liver axis dysregulation; elevations in glucose, fructose-6-phosphate, and nucleoside catabolites, indicating impaired glucose handling and heightened nucleotide turnover; increased free fatty acids, reflecting membrane remodeling and lipotoxic stress; and higher cAMP, thyroxine, hydrocortisone, and uric acid, consistent with endocrine and redox imbalance. By contrast, HFD-only mice exhibited elevations in aromatic amino acids and BCAAs relative to controls, a pattern compatible with early obesity-associated adaptation while insulin signaling remained partially preserved. KEGG analysis revealed disturbances in carbohydrate metabolism, amino acid degradation, nucleotide turnover, and hormone-related pathways, and HMDB mapping linked these changes to T2D, obesity, heart failure, and renal dysfunction. Conclusion: Collectively, these findings delineate insulin resistance-specific plasma signatures of metabolic inflexibility and inflammatory stress in the HFD + STZ model, distinguishing it from HFD alone and supporting its utility for mechanistic studies and biomarker discovery. Importantly, this plasma metabolomics study shows that insulin-sensitive and insulin-resistant states exhibit distinct variation in circulating metabolites and cardiovascular risk factors, underscoring the translational value of plasma profiling. Full article

(This article belongs to the Topic Animal Models of Human Disease 3.0)

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26 pages, 2295 KB

Open AccessArticle

Retrospective Urine Metabolomics of Clinical Toxicology Samples Reveals Features Associated with Cocaine Exposure

by Rachel K. Vanderschelden, Reya Kundu, Delaney Morrow, Simmi Patel and Kenichi Tamama

Metabolites 2025, 15(9), 563; https://doi.org/10.3390/metabo15090563 - 22 Aug 2025

Abstract

Background/Objectives: Cocaine is a widely used illicit stimulant with significant toxicity. Despite its clinical relevance, the broader metabolic alterations associated with cocaine use remain incompletely characterized. This study aims to identify novel biomarkers for cocaine exposure by applying untargeted metabolomics to retrospective urine [...] Read more.

Background/Objectives: Cocaine is a widely used illicit stimulant with significant toxicity. Despite its clinical relevance, the broader metabolic alterations associated with cocaine use remain incompletely characterized. This study aims to identify novel biomarkers for cocaine exposure by applying untargeted metabolomics to retrospective urine drug screening data. Methods: We conducted a retrospective analysis of a raw mass spectrometry (MS) dataset from urine comprehensive drug screening (UCDS) from 363 patients at the University of Pittsburgh Medical Center Clinical Toxicology Laboratory. The liquid chromatography–quadrupole time-of-flight mass spectrometry (LC-qToF-MS) data were preprocessed with MS-DIAL and subjected to multiple statistical analyses to identify features significantly associated with cocaine-enzyme immunoassay (EIA) results. Significant features were further evaluated using MS-FINDER for feature annotation. Results: Among 14,883 features, 262 were significantly associated with cocaine-EIA results. A subset of 37 more significant features, including known cocaine metabolites and impurities, nicotine metabolites, norfentanyl, and a tryptophan-related metabolite (3-hydroxy-tryptophan), was annotated. Cluster analysis revealed co-varying features, including parent compounds, metabolites, and related ion species. Conclusions: Features associated with cocaine exposure, including previously underrecognized cocaine metabolites and impurities, co-exposure markers, and alterations in an endogenous metabolic pathway, were identified. Notably, norfentanyl was found to be significantly associated with cocaine -EIA, reflecting current trends in illicit drug use. This study highlights the potential of repurposing real-world clinical toxicology data for biomarker discovery, providing a valuable approach to identifying exposure biomarkers and expanding our understanding of drug-induced metabolic disturbances in clinical toxicology. Further validation and exploration using complementary analytical platforms are warranted. Full article

(This article belongs to the Special Issue Applications of Mass Spectrometry in Elucidating Human Drug Metabolism: From the Preclinical Phase to Real-World Studies)

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15 pages, 1441 KB

Open AccessArticle

Secondary Metabolites Predict Diazotrophic Cyanobacteria: A Model-Based Cheminformatic Approach

by James Young, Taufiq Nawaz, Liping Gu and Ruanbao Zhou

Metabolites 2025, 15(9), 562; https://doi.org/10.3390/metabo15090562 - 22 Aug 2025

Abstract

Background: Nitrogen fixation (diazotrophy) is a desirable trait present in some cyanobacteria with potential applications in sustainable agriculture and chemical feedstock production. This study discovers a predictive relationship modeled between secondary metabolites and diazotrophic cyanobacteria by leveraging chemical structure similarity to identify diazotrophic [...] Read more.

Background: Nitrogen fixation (diazotrophy) is a desirable trait present in some cyanobacteria with potential applications in sustainable agriculture and chemical feedstock production. This study discovers a predictive relationship modeled between secondary metabolites and diazotrophic cyanobacteria by leveraging chemical structure similarity to identify diazotrophic strains. Methods: An algorithm was developed using chemical fingerprint similarity of metabolites curated from CyanoMetDB and evaluated with leave-one-out cross-validation on 133 manually labeled metabolites. Results: The model demonstrated strong predictive performance, achieving 88% accuracy and a ROC-AUC of 0.96. We then applied this approach to prioritize likely diazotrophic strains among 1980 unlabeled metabolites and their associated organisms, providing a rank order of most likely undetected diazotrophic strains. Toxicity analysis showed that diazotrophic-associated metabolites show similar toxicity to non-diazotrophic metabolites in rats, with less toxicity in Daphnia magna, suggesting that these metabolites are not playing a defensive role. However, these metabolites did have relatively high nitrogen presence, and many were cyclic peptides, potentially serving as signaling molecules. Conclusions: This study underscores the potential of secondary metabolites in identifying diazotrophs, even when they may not be actively demonstrating diazotrophic physiology. Discovering more diazotrophic cyanobacteria has strong implications for advancing agricultural biotechnology towards the goal of self-fertilizing crops. Full article

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

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15 pages, 1327 KB

Open AccessArticle

Tentative Identification of Chemical Constituents in Liuwei Dihuang Pills Based on UPLC-Orbitrap-MS

by Lanxiang Yang, Min Tao, Rongping Tao, Mingzhu Cao and Rui Wang

Metabolites 2025, 15(8), 561; https://doi.org/10.3390/metabo15080561 - 21 Aug 2025

Abstract

Background: Liuwei Dihuang Pills, a classic traditional Chinese medicine formula, has been widely used in clinical practice for its multiple pharmacological effects. However, the systematic characterization and identification of its chemical constituents, especially the aqueous decoction, remain insufficient, which hinders in-depth research on [...] Read more.

Background: Liuwei Dihuang Pills, a classic traditional Chinese medicine formula, has been widely used in clinical practice for its multiple pharmacological effects. However, the systematic characterization and identification of its chemical constituents, especially the aqueous decoction, remain insufficient, which hinders in-depth research on its pharmacodynamic material basis. Thus, there is an urgent need for a comprehensive analysis of its chemical components using advanced analytical techniques. Methods: After screening chromatographic columns, the ACQUITY UPLC™ HSS T3 column (100 mm × 2.1 mm, 1.8 μm) was selected. The column temperature was set to 40 °C, and the mobile phase consisted of 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile (B). A gradient elution program was adopted, and the separation was completed within 20 min. Ultra-high performance liquid chromatography–Orbitrap mass spectrometry (UPLC-Orbitrap-MS) combined with a self-established information database was used for the analysis. Results: A total of 80 compounds were tentatively identified, including 13 monoterpenoids, 6 phenolic acids, 16 iridoids, 11 flavonoids, 25 triterpenoids, and 9 other types. Triterpenoids are mainly derived from Poria cocos and Alisma orientale; iridoids are mainly from Rehmannia glutinosa; monoterpenoids are mainly from Moutan Cortex; and flavonoids are mainly from Dioscorea opposita. Among them, monoterpenoids, iridoids, and triterpenoids are important pharmacodynamic components. The cleavage pathways of typical compounds (such as pachymic acid, catalpol, oxidized paeoniflorin, and puerarin) are clear, and their mass spectral fragment characteristics are consistent with the literature reports. Conclusions: Through UPLC-Orbitrap-MS technology and systematic optimization of conditions, this study significantly improved the coverage of chemical component identification in Liuwei Dihuang Pills, providing a comprehensive reference for the research on its pharmacodynamic substances. However, challenges remain in the identification of trace components and isomers. In the future, analytical methods will be further improved by combining technologies such as ion mobility mass spectrometry or multi-dimensional liquid chromatography. Full article

(This article belongs to the Special Issue Analysis of Specialized Metabolites in Natural Products)

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12 pages, 821 KB

Open AccessArticle

Antiparasitic Effect of Polyphenols and Terpenes from Natural Products Against Trypanosoma cruzi and Leishmania mexicana

by Diana V. Navarrete-Carriola, Gildardo Rivera, Eyra Ortiz-Pérez, Alma D. Paz-González, Ana Verónica Martínez-Vázquez, Laura Victoria Aquino-González, Liliana Argueta-Figueroa, Michael P. Doyle and Adriana Moreno-Rodríguez

Metabolites 2025, 15(8), 560; https://doi.org/10.3390/metabo15080560 - 21 Aug 2025

Abstract

Background: Worldwide, the number of cases of parasitic diseases has been increasing; however, available treatments have variable adverse effects and low efficacy, mainly in Neglected Tropical Diseases such as Chagas disease and Leishmaniasis. Therefore, the development of new and more effective antiparasitic [...] Read more.

Background: Worldwide, the number of cases of parasitic diseases has been increasing; however, available treatments have variable adverse effects and low efficacy, mainly in Neglected Tropical Diseases such as Chagas disease and Leishmaniasis. Therefore, the development of new and more effective antiparasitic drugs is important. Natural products are the source of secondary metabolites with different biological activities, such as antibacterial, anticancer, anti-inflammatory, and antiparasitic. Objectives: In this work, secondary metabolites (phenols and terpenes) from natural products were selected to be evaluated against the epimastigotes of NINOA and A1 strains of Trypanosoma cruzi and the promastigotes of M379 strain and FCQEPS native isolate of Leishmania mexicana. Additionally, their cytotoxicity and selectivity index were determined. Methods: Eighteen secondary metabolites were evaluated in vitro against T. cruzi epimastigotes and L. mexicana promastigotes; additionally, their cytotoxicity on the J774.2 macrophage cell line was determined. Results: The compounds l-(-)-menthol (14, IC₅₀ = 24.52 µM) and β-citronellol (11, IC₅₀ = 21.54 µM) had higher trypanocidal activity than the reference drug (benznidazole) against NINOA and A1 strains of T. cruzi, respectively. On the other hand, para-anisyl alcohol (4, IC₅₀ = 34.89 µM) had higher leishmanicidal activity than the reference drug (glucantime^®) against M379 and the FCQEPS native isolate of L. mexicana. Finally, in silico, the determination of their pharmacokinetic and toxicological properties showed that they are promising candidates for oral and topical uses. Conclusions: This study opens the possibility of using secondary metabolites as scaffolds for access to the development of new molecules for the treatment of parasite diseases. Full article

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

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18 pages, 1585 KB

Open AccessArticle

Modeling the Sensory Characteristics of Japanese Sake Using the Sake Metabolome Analysis Method

by Takuji Kobayashi, Yuko Komatsu-Hata, Ryota Saito, Hisashi Yazawa, Masayuki Takahashi, Ken Oda and Kazuhiro Iwashita

Metabolites 2025, 15(8), 559; https://doi.org/10.3390/metabo15080559 - 20 Aug 2025

Abstract

Background/Objectives: The components of food and beverages are important elements that determine their palatability. Although the components of sake, a traditional Japanese alcoholic beverage, have been studied for many years, their correlation with sensory characteristics is unclear. Methods: We investigate the correlation with [...] Read more.

Background/Objectives: The components of food and beverages are important elements that determine their palatability. Although the components of sake, a traditional Japanese alcoholic beverage, have been studied for many years, their correlation with sensory characteristics is unclear. Methods: We investigate the correlation with the sake metabolome analysis method developed by our group using ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry. We constructed orthogonal projections to latent structure models to predict sensory evaluation data obtained through the quantitative descriptive analysis method from the sake metabolome data. Results: For two years of study, 8 sensory evaluation models of the 2016 brewing year and 11 sensory evaluation models of the 2017 brewing year, including color, ethyl hexanoate, Hine-ka, Nama hine-ka, ethyl acetate, grainy/sweet aroma, sweetness, sourness, body, astringency, harsh taste/acrid taste, aftertaste, and overall quality, demonstrated a predictive performance with Q² > 0.5. Liquid chromatography-based analytical data indicated that it is possible to predict not only taste but also aroma. Additionally, the generalization performance of the prediction models for sensory evaluation attributes common to both years was verified. Conclusions: These results provide a new option for explaining the sensory characteristics of sake from its components and contribute to a deeper understanding of them. Full article

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

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13 pages, 2522 KB

Open AccessArticle

Metabolomic Variation in Sugarcane Maturation Under a Temperate Climate

by Yasuhiro Date, Chiaki Ishikawa and Hiroshi Ono

Metabolites 2025, 15(8), 558; https://doi.org/10.3390/metabo15080558 - 20 Aug 2025

Abstract

Background: Metabolomics is a powerful tool used for the evaluation of sugarcane components which are key factors influencing its response to biotic and abiotic stresses. However, little is known about the compositional variability and diversity of the sugarcane juice metabolome under practical field [...] Read more.

Background: Metabolomics is a powerful tool used for the evaluation of sugarcane components which are key factors influencing its response to biotic and abiotic stresses. However, little is known about the compositional variability and diversity of the sugarcane juice metabolome under practical field conditions in temperate climates. Methods: In this study, we characterized metabolomic differences and variability in sugarcane juice components during the maturation stage of nine cultivars grown in a temperate climate in Japan using a nuclear magnetic resonance-based metabolomics approach, aiming to provide insights into genotype-dependent adaptability to environmental and climate changes. Results: Principal component analysis revealed distinct metabolic profiles based on cultivar and maturation level. Notably, sucrose levels increased from September to December accompanied by decreased glucose and fructose levels across all cultivars. Early-maturing cultivars had high sucrose content even with shorter growing periods, suggesting particular advantages for sugar production in temperate climates. Additionally, 4-aminobutyric acid accumulated in all cultivars as maturation progressed. On the other hand, trans-aconitic acid, choline, and branched-chain amino acids showed cultivar-dependent trends. In one example, choline concentrations increased significantly in specific cultivars during maturation. Conclusions: These findings support a deeper understanding of metabolic adaptation and may aid in identifying cultivars better suited to environmental fluctuations. Full article

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

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16 pages, 2557 KB

Open AccessArticle

Differential Impacts of Environmentally Relevant Microplastics on Gut Barrier Integrity in Mice Fed High-Fat Diet Versus Normal Chow Diet

by Huixia Niu, Ying Yang, Yuting Zhou, Xue Ma, Zhehao Ding, Manjin Xu, Lizhi Wu, Xueqing Li, Mingluan Xing, Qin Zhang, Hao Chen, Xiongwei Tao, Zhe Mo, Zhijian Chen, Pengcheng Tu and Xiaoming Lou

Metabolites 2025, 15(8), 557; https://doi.org/10.3390/metabo15080557 - 20 Aug 2025

Abstract

Background: Despite escalating global pollution from microplastics (MPs) and the concurrent surge in high-fat food consumption, the health impacts of MP exposure on individuals under different dietary patterns remain poorly understood. Methods: This study investigated the differential effects of environmentally relevant concentrations of [...] Read more.

Background: Despite escalating global pollution from microplastics (MPs) and the concurrent surge in high-fat food consumption, the health impacts of MP exposure on individuals under different dietary patterns remain poorly understood. Methods: This study investigated the differential effects of environmentally relevant concentrations of polystyrene microplastics (5 μm, 8 mg/kg) on gut barrier function in mice fed either a normal chow diet (CD) or a high-fat diet (HFD). Results: Key findings revealed that, in HFD-fed mice, MP exposure significantly reduced (p < 0.05) the transcriptional levels of genes encoding the tight junction proteins (ZO-1, Occludin, and Claudin-1), as well as the mucin protein Muc-2, accompanied by decreased protein expression levels of these markers in both colonic and ileal tissues. In contrast, no significant differences were observed in CD-fed mice exposed to MPs. Analysis of the gut microbiota and measurement of short-chain fatty acid (SCFA) metabolites showed that MPs induced significant alterations in the composition and diversity indices of the gut microbiota, along with a marked decrease (p < 0.05) in the levels of the characteristic metabolite butyrate in HFD-fed mice. Conversely, butyrate levels remained unchanged in CD-fed mice following MP exposure. Quantitative PCR (qPCR) and immunofluorescence staining of colonic tissues demonstrated that MP exposure significantly downregulated (p < 0.05) both the transcription and protein expression of peroxisome proliferator-activated receptor γ (PPARγ) in HFD-fed mice. Again, no significant changes were detected in CD-fed mice. Conclusions: These results collectively indicate that the impact of microplastics on the intestinal barrier differs significantly between mice fed normal and high-fat diets. The gut microbiota and its metabolites, particularly butyrate, may play a critical role, possibly through modulating PPARγ signaling. This study contributes valuable insights into understanding the toxicity profiles of microplastics and establishing crucial links between dietary patterns and the health effects of emerging pollutants. Full article

(This article belongs to the Special Issue Effects of Environmental Exposure on Host and Microbial Metabolism)

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