Metabolites

27 pages, 1259 KB

Open AccessReview

The Impact of Gut Microbial Metabolomics on Type 2 Diabetes Development in People Living with HIV

by Yusnier Lázaro Díaz-Rodríguez, Elsa Janneth Anaya-Ambriz, Paula Catalina Méndez-Ríos, Jaime F. Andrade-Villanueva, Luz A. González-Hernández, Tania Elisa Holguín-Aguirre, Pedro Martínez-Ayala, Vida V. Ruiz-Herrera, Monserrat Alvarez-Zavala and Karina Sánchez-Reyes

Metabolites 2025, 15(9), 627; https://doi.org/10.3390/metabo15090627 - 19 Sep 2025

Abstract

Background/Objectives: HIV infection has been associated with an increased incidence of non-communicable comorbidities, including metabolic disorders. This phenomenon has been linked to gut microbiota dysbiosis, which involves not only changes in bacterial composition but also functional alterations in metabolite production. The objective of [...] Read more.

Background/Objectives: HIV infection has been associated with an increased incidence of non-communicable comorbidities, including metabolic disorders. This phenomenon has been linked to gut microbiota dysbiosis, which involves not only changes in bacterial composition but also functional alterations in metabolite production. The objective of this study was to describe the impact of intestinal microbial metabolomics on the development of type 2 diabetes in people living with HIV. Methods: This study provides a narrative synthesis of current evidence addressing the role of gut microbiota-derived metabolites in immunometabolic regulation and their implications in HIV-associated type 2 diabetes. Results: Microbial metabolites play a fundamental role in regulating key physiological processes such as intestinal permeability, systemic immune activation, and glucose metabolism. Compounds such as short-chain fatty acids, tryptophan catabolites, secondary bile acids, trimethylamine N-oxide, and imidazole propionate have been shown to significantly influence immunometabolic balance. In people living with HIV, these microbial products may exert diverse effects depending on their chemical nature and the molecular pathways they activate in peripheral tissues. The interaction between dysbiosis, chronic low-grade inflammation, and HIV-associated metabolic disturbances may contribute to the early onset of type 2 diabetes beyond traditional risk factors. Conclusions: Recognizing the role of microbial metabolites in the context of HIV infection is essential to broaden our pathophysiological understanding of associated metabolic comorbidities. It also opens opportunities to develop more comprehensive diagnostic and therapeutic strategies that include modulation of the gut microbiota and its metabolic activity for the prevention and management of type 2 diabetes in this population. Full article

(This article belongs to the Special Issue Targeting Microbiota and Metabolites for Prevention and Treatment of Human Diseases)

26 pages, 1439 KB

Open AccessArticle

Essential Amino Acid Supplementation May Attenuate Systemic Inflammation and Improve Hypoalbuminemia in Subacute Hemiplegic Stroke Patients

by Mirella Boselli, Roberto Aquilani, Roberto Maestri, Paolo Iadarola, Alessandro Magistroni, Chiara Ferretti, Antonia Pierobon, Matteo Cotta Ramusino, Alfredo Costa, Daniela Buonocore, Marco Peviani, Federica Boschi and Manuela Verri

Metabolites 2025, 15(9), 626; https://doi.org/10.3390/metabo15090626 - 19 Sep 2025

Abstract

Background: Post-stroke inflammation and hypoalbuminemia can negatively affect neurocognitive recovery. This study evaluated whether oral amino acid (AA) supplementation with prevalently essential amino acids (EAAs, 82.1%) could improve inflammation and albumin levels in post-stroke patients undergoing neurorehabilitation. Methods: Sixty-four patients with subacute stroke [...] Read more.

Background: Post-stroke inflammation and hypoalbuminemia can negatively affect neurocognitive recovery. This study evaluated whether oral amino acid (AA) supplementation with prevalently essential amino acids (EAAs, 82.1%) could improve inflammation and albumin levels in post-stroke patients undergoing neurorehabilitation. Methods: Sixty-four patients with subacute stroke (less than three 3 months from acute event) and elevated inflammation markers (C-reactive protein, CRP > 0.5 mg/dL) were enrolled. All underwent anthropometric assessments and blood tests for CRP (normal value < 0.5 mg/dL), albumin (normal range: 3.5–4.76 g/dL), prealbumin (18–32 mg/dL), and white blood cell count. Participants were randomly assigned to receive either oral EAAs (8.4 g/day) or placebo (maltodextrin, 8.4 g/day) for 55 days. Measurements were taken at baseline (T0) and at discharge (T1), approximately two months later. Results: At baseline, both groups had comparable levels of systemic inflammation, albumin and prealbumin: CRP, 2.13 ± 1.82 mg/dL (placebo) vs. 2.89 ± 2.12 mg/dL (EAAs), p = 0.13; albumin, 3.10 ± 0.46 g/dL (placebo) vs. 3.07 ± 0.57 g/dL (EAAs), p = 0.82; prealbumin, 18.3 ± 6.2 mg/dL (placebo) vs. 16.9 ± 3.9 mg/dL (EAAs), p = 0.28. During rehabilitation, only the EAA group showed significant reductions in CRP (p = 0.036 vs. placebo) and improvements in albumin (p = 0.033 vs. placebo) and prealbumin levels (p = 0.05 vs. placebo). However, full normalization of CRP and albumin was not achieved. Conclusions: This study demonstrates that a physiological dose of supplemented EAAs may attenuate, but not fully resolve, post-stroke inflammation and hypoalbuminemia. Further research is needed to determine whether higher EAA doses and/or modifications in EAA composition could enhance or normalize systemic inflammation. Full article

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

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11 pages, 763 KB

Open AccessArticle

Impact of Salivary Amino Acid Concentrations on 8 km Running Performance in Male Undergraduate Students: A Prospective Observational Study Based on HPLC

by Hai Zhao, Kangwei Shen, Wei Fan, Mengjie Li and Xuejun Kang

Metabolites 2025, 15(9), 625; https://doi.org/10.3390/metabo15090625 - 19 Sep 2025

Abstract

Purpose: To explore the potential relationship between salivary amino acid concentrations and 8 km running performance in male undergraduate students. Methods: Thirty male undergraduate students were recruited. Participants completed an 8 km run while wearing smart bracelets. Saliva samples were collected before, immediately [...] Read more.

Purpose: To explore the potential relationship between salivary amino acid concentrations and 8 km running performance in male undergraduate students. Methods: Thirty male undergraduate students were recruited. Participants completed an 8 km run while wearing smart bracelets. Saliva samples were collected before, immediately after, and 24 h after the run. Ultra-High Performance Liquid Chromatography (UHPLC) was used to quantify salivary amino acids. Results: The fast group (average speed > 12.80 km/h) had a significantly shorter running time (35.66 ± 1.30 min, p < 0.001) and higher speed (13.59 ± 0.46 km/h, p < 0.001) than the slow group. Before the run, salivary serine concentration (20.19 µg/mL, p = 0.013) was higher in the fast group. After 24 h, salivary glutamine concentration (6.65 µg/mL, p = 0.047) was lower in the fast group. Salivary threonine concentration was positively correlated with running speed. For every 1 µg/mL increase in salivary threonine concentration, average running speed increased by 0.011 km/h, and this correlation persisted after adjusting for age and heart rate. Conclusions: This study found a positive correlation between salivary threonine and 8 km running speed, along with differences in serine and glutamine concentrations among runners with different speeds. These findings provide preliminary evidence for the relationship between salivary amino acid concentrations and running performance, though further research with larger samples and diverse exercise types is needed. Full article

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

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36 pages, 505 KB

Open AccessReview

Dietary Modulation of Metabolic Health: From Bioactive Compounds to Personalized Nutrition

by Aleksandra Leziak, Julia Lipina, Magdalena Reclik and Piotr Kocelak

Metabolites 2025, 15(9), 624; https://doi.org/10.3390/metabo15090624 - 19 Sep 2025

Abstract

Metabolic health is a dynamic equilibrium influenced by diet and lifestyle. This review synthesizes evidence on how specific dietary patterns and bioactive nutrients modulate metabolic disorders. Diets like the Mediterranean and DASH plans consistently improve cardiometabolic markers: a Mediterranean diet can halve metabolic [...] Read more.

Metabolic health is a dynamic equilibrium influenced by diet and lifestyle. This review synthesizes evidence on how specific dietary patterns and bioactive nutrients modulate metabolic disorders. Diets like the Mediterranean and DASH plans consistently improve cardiometabolic markers: a Mediterranean diet can halve metabolic syndrome prevalence (~52% reduction) in as little as 6 months, while the DASH diet typically lowers systolic blood pressure by ~5–7 mmHg and modestly improves lipid profiles (LDL-C by ~3–5 mg/dL). Plant-based diets (vegetarian/vegan) are associated with lower BMI, improved insulin sensitivity, and reduced inflammation. Ketogenic diets induce rapid weight loss (~12% body weight vs. 4% on control diets) and improve glycemic control (reducing HbA1c and triglycerides), though long-term effects (elevated LDL) warrant caution. Bioactive compounds present in these diets play critical roles: polyphenols improve insulin signaling and reduce oxidative stress (resveratrol supplementation reduced HOMA-IR by ~0.5 units and fasting glucose by ~0.3 mmol/L); omega-3 fatty acids (fish oil) reduce triglycerides by ~25–30% and inflammation; and probiotic interventions modestly enhance glycemic control (lowering HOMA-IR and HbA1c) and gut health. Personalized nutrition approaches, which account for genetic and microbiome differences, are emerging to maximize these benefits. In conclusion, evidence-based dietary strategies rich in fiber, unsaturated fats, and phytochemicals can substantially improve metabolic health outcomes, underscoring the potential of tailored nutrition in preventing and managing obesity-related metabolic disorders. Full article

(This article belongs to the Special Issue Effects of Diet on Metabolic Health of Obese People)

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16 pages, 518 KB

Open AccessArticle

High-Intensity Interval Training (HIIT): Impact of Duration on Body Composition, Cardiometabolic Health, and Aerobic Capacity in Adolescent Women

by Mima Stankovic, Ilma Čaprić, Luka Pezelj, Emir Biševac, Raid Mekić, Armin Zećirović, Zerina Salihagić, Aldina Ajdinović and Igor Jelaska

Metabolites 2025, 15(9), 623; https://doi.org/10.3390/metabo15090623 - 19 Sep 2025

Abstract

Background: High-intensity interval training (HIIT) is a time-efficient approach that has been recognized to enhance cardiometabolic health and aerobic capacity in adolescents. The purpose of this study was to investigate the effects of various HIIT durations on cardiometabolic health and aerobic ability in [...] Read more.

Background: High-intensity interval training (HIIT) is a time-efficient approach that has been recognized to enhance cardiometabolic health and aerobic capacity in adolescents. The purpose of this study was to investigate the effects of various HIIT durations on cardiometabolic health and aerobic ability in adolescent women aged 17 to 19 years. Methods: Participants were separated into two intervention groups: HIIT 1 (6 weeks) and HIIT 2 (8 weeks), along with a control group. Both HIIT regimens included two weekly sessions: warm-up (jogging, accelerated running, and dynamic stretching), major sets (2 × 6–9 bouts of 30 s training at 90–95% HR_max with active recovery), and cooldown. Pre- and post-intervention measurements included body mass, BMI, body fat percentage, lipid profile, blood pressure, fasting glucose, and VO_2max. Results: Both HIIT programs resulted in significant reductions in body weight, BMI, and body fat percentage (all p < 0.001), as well as improvements in total cholesterol, triglycerides, LDL cholesterol, and systolic and diastolic blood pressure (all p < 0.001), compared to the control group. The changes in glycemia (p = 0.078) and HDL cholesterol (p = 0.825) were not statistically significant. Both HIIT groups showed significantly higher VO_2max (p < 0.001). Conclusions: Adolescent women’s cardiometabolic health and aerobic capacity increased considerably following 6- and 8-week HIIT training. These findings emphasize HIIT as a practical and time-saving strategy for this population, highlighting its effectiveness in improving key health parameters within a relatively short period. Full article

(This article belongs to the Special Issue Effects of Various Exercise Methods on Metabolic Health)

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9 pages, 874 KB

Open AccessArticle

Paradoxical Regulation of α7nAChR and NLRP3 Inflammasome in Gastrointestinal Cancers and Ulcerative Colitis

by Gulten Ates, Ilker Ozgur and Ismail Cem Sormaz

Metabolites 2025, 15(9), 622; https://doi.org/10.3390/metabo15090622 - 18 Sep 2025

Abstract

Background: Gastrointestinal (GI) cancers are common and pose a major public health issue. An inflammatory microenvironment drives their development and progression. The α7nAChR receptor, known to suppress autoimmune and inflammatory bowel diseases, is also linked to colorectal cancer. It enhances anti-inflammatory activity, influences [...] Read more.

Background: Gastrointestinal (GI) cancers are common and pose a major public health issue. An inflammatory microenvironment drives their development and progression. The α7nAChR receptor, known to suppress autoimmune and inflammatory bowel diseases, is also linked to colorectal cancer. It enhances anti-inflammatory activity, influences tumor growth, metastasis, and treatment response, and is associated with tobacco use. NLRP3, a key inflammatory mediator, connects immunity and cancer. The α7nAChR receptor modulates tumorigenesis and therapy response by suppressing inflammatory pathways, while also regulating NLRP3 inflammasome activation through inhibition of mitochondrial DNA release. This study examines α7nAChR and NLRP3 expression in gastric and colorectal cancers, colitis, and normal tissues to clarify pathogenic mechanisms and identify therapeutic targets. Methods: Tissue samples of gastric tumor (S-Tm) (n = 10), colorectal tumor (C-Tm) (n = 10), colitis (UC) (n = 10), healthy stomach (S-C) (n = 10) and healthy colorectal tissue (C-C) (n = 10) taken during routine endoscopy protocols were homogenized. The α7nAChR and NLRP3 levels were examined using the ELISA method, and groups were compared. Results: We identified statistically significant differences in α7nAChR levels between the S-C and S-Tm (p < 0.05), C-C and C-Tm (p < 0.05), and S-C and C-Tm (p < 0.001) groups. The NRLP3 levels also differed significantly between the UC and C-Tm (p < 0.05), the S-C and C-Tm (p < 0.01), and the C-C and C-Tm groups (p < 0.01). Conclusions: Paradoxically, given the inflammatory regulatory role and oncogenic effects of α7nAChR, the relationship between α7nAChR and NLRP3 has become an important target for both oncological and inflammatory therapeutic approaches, particularly in inflammation-related GI cancers. Full article

(This article belongs to the Special Issue Metabolomic Insights: Interplay Between Metabolism and Immune Response in Cancer)

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18 pages, 400 KB

Open AccessArticle

The Effect of 9-Week Dietary Intervention on Anthropometric Parameters and Blood Pressure in Children with Excessive Body Weight

by Karolina Gajda, Marta Jeruszka-Bielak, Magdalena Górnicka, Irena Keser and Jadwiga Hamulka

Metabolites 2025, 15(9), 621; https://doi.org/10.3390/metabo15090621 - 18 Sep 2025

Abstract

Background/Objectives: The prevalence of pediatric overweight and obesity is steadily increasing, posing a tremendous problem and challenge to public health. Various strategies have been undertaken to combat this issue with mixed results. This study aimed at assessing the effect of a 9-week dietary [...] Read more.

Background/Objectives: The prevalence of pediatric overweight and obesity is steadily increasing, posing a tremendous problem and challenge to public health. Various strategies have been undertaken to combat this issue with mixed results. This study aimed at assessing the effect of a 9-week dietary intervention on anthropometric measurements and blood pressure among children aged 7–12 years with excessive body weight. Methods: The main aim of the intervention was to improve the children’s eating habits according to dietary guidelines for Polish children and adolescents with an individual approach and dietitian support. The intervention was completed by 68 children, 38 girls and 30 boys. Data on nutrition; anthropometrics, including body composition; and blood pressure were collected at baseline and after 3, 6, and 9 weeks of the dietary intervention. Results: The 9-week dietary intervention resulted in significant reductions in BMI z-score, fat mass, and body weight of 10.7%, 7.6%, and 4.0%, respectively. Blood pressure, especially diastolic blood pressure, also significantly decreased. Moreover, positive changes in dietary behaviors were noted. Conclusions: A 9-week dietary intervention based on an appropriate, high-quality diet in line with the Healthy Eating Pyramid guidelines, with individual counselling and constant monitoring of the implemented changes, an individual approach, support from a dietitian, and the involvement of parents or guardians, can be an effective tool for starting to improve the diets and health of overweight children. Full article

(This article belongs to the Special Issue Effects of Diet on Metabolic Health of Obese People)

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24 pages, 2191 KB

Open AccessArticle

NMR-Based Metabolomic Profiling Highlights Functional Nutritional Gaps Between Human Milk, Infant Formulas, and Animal Milks

by Gaia Meoni, Leonardo Tenori, Giovanni Niero, Massimo De Marchi and Claudio Luchinat

Metabolites 2025, 15(9), 620; https://doi.org/10.3390/metabo15090620 - 18 Sep 2025

Abstract

Background/Objectives: Human milk represents the gold standard for infant nutrition, providing a complex and bioactive metabolite profile essential for early development. Despite efforts to enrich infant and toddler formulas with functional ingredients, significant biochemical differences persist. This study aimed to characterize and compare [...] Read more.

Background/Objectives: Human milk represents the gold standard for infant nutrition, providing a complex and bioactive metabolite profile essential for early development. Despite efforts to enrich infant and toddler formulas with functional ingredients, significant biochemical differences persist. This study aimed to characterize and compare the metabolomic composition of human milk, cow’s milk (both conventional and lactose-free), goat’s milk, and a variety of commercial formulas, including both infant (0–12 months) and toddler (1–3 years) formulations, using ¹H NMR-based metabolomics. Methods: A total of 90 milk samples were analyzed, including eight formula milk brands, four human milk samples, four goat milk brands, and seven cow milk products. ¹H NMR spectra were acquired and processed to identify 54 metabolites. Multivariate and univariate statistical analyses were used to assess compositional similarities and differences among milk types. Results: Human milk displayed a unique metabolic signature, enriched in fucosylated oligosaccharides (2′-FL, 3′-FL), N-acetylated carbohydrates, and amino acids such as glutamine and glutamate. Goat milk was characterized by higher levels of creatine, carnitine, and succinate, whereas cow milk showed elevated orotate, butyrate, and mannose. Formulations exhibited a relatively homogeneous composition across brands but differed from human and animal milk, particularly in choline, formate, and added micronutrients. Toddler formulas contained more energy-related compounds (e.g., creatine, maltose) compared to infant formulas. Conclusions: While modern formulas provide nutritional adequacy, they remain metabolically distinct from human milk. NMR-based metabolomics offers a powerful tool for guiding future improvements in formula composition toward more biomimetic profiles. Full article

(This article belongs to the Special Issue NMR-Based Metabolomics in Biomedicine and Food Science)

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19 pages, 2713 KB

Open AccessArticle

Comparative Proteomic Analysis of Extracellular Vesicles from Donkey Colostrum and Mature Milk

by Simonetta Caira, Sandra Buratta, Silvia Vincenzetti, Raffaella Latella, Matteo Seccaroni, Sabrina De Pascale, Cristina Federici, Luana Lugini, Stefano Giovagnoli, Anna Maria Salzano, Carla Emiliani, Andrea Scaloni and Elisabetta Chiaradia

Metabolites 2025, 15(9), 619; https://doi.org/10.3390/metabo15090619 - 18 Sep 2025

Abstract

Background/Objectives: Donkey milk (DM) has been considered a valuable alternative to human and bovine counterparts as well as to infant formulas. Milk extracellular vesicles (EVs) have been proposed to influence key biological processes. The purpose of this study is to provide a comprehensive [...] Read more.

Background/Objectives: Donkey milk (DM) has been considered a valuable alternative to human and bovine counterparts as well as to infant formulas. Milk extracellular vesicles (EVs) have been proposed to influence key biological processes. The purpose of this study is to provide a comprehensive characterization of the protein composition of extracellular vesicles (EVs) by extending quantitative proteomic comparisons to EVs derived from donkey colostrum (DC) and mature donkey milk (MDM). Methods: The EVs were isolated from DC and MDM samples, characterized, and subjected to proteomic analysis using the tandem mass tag-based quantitative approach. Results: In addition to typical milk proteins and EV markers, EVs from DC and MDM both contain components associated with the immune system, immune response, or promoting tissue repair, and assisting with communication between the infant and their environment. The EVs from DC were enriched in proteins associated with protein turnover, specific defense functions, and regenerative processes. Conclusions: Overall, the results can contribute to the broader characterization of the overall protein composition of DC and MDM and might help to predict the beneficial effects of the corresponding EVs on various mammalian cells. They may also provide valuable insights for the development of novel DM-based products for food, pharmaceutical, and biotechnological applications. Full article

(This article belongs to the Special Issue The Molecular Cargo of Extracellular Vesicles: A Key to Understanding Their Biological Role)

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17 pages, 4890 KB

Open AccessArticle

Yigong San Extract Modulates Metabolism, Antioxidant Status, and Immune Function to Improve Health in Diarrheic Calves

by Sijuan Huang, Chao Han, Jianyu Lv, Xiaosong Zhang, Xuan Ni, Xin Wang, Jianfei Wang, Yunfei Ma and Zhihui Hao

Metabolites 2025, 15(9), 618; https://doi.org/10.3390/metabo15090618 - 18 Sep 2025

Abstract

Background/Objectives: Calf diarrhea is a serious health problem in dairy farming, which seriously affects their production performance in adulthood. Diarrhea in calves is usually treated with antibiotics, which may lead to issues of antibiotic residue and resistance. Therefore, finding antibiotic alternatives is of [...] Read more.

Background/Objectives: Calf diarrhea is a serious health problem in dairy farming, which seriously affects their production performance in adulthood. Diarrhea in calves is usually treated with antibiotics, which may lead to issues of antibiotic residue and resistance. Therefore, finding antibiotic alternatives is of critical importance. Yigong San (YGS) is a traditional Chinese medicine formula traditionally indicated for inflammatory gastrointestinal disorders. This study aimed to investigate whether YGS can be used as an alternative to antibiotics for the effective treatment of calf diarrhea and the underlying mechanisms. Methods: Ten healthy Holstein calves served as the control (Ctrl) group, while twenty diarrheic calves were randomly assigned to either a natural diarrhea (ND) group or a YGS treatment (YGS) group, which received YGS for seven days. Serum samples were collected post-treatment and analyzed for biochemical parameters, oxidative stress indicators, cytokine levels, and metabolomic profiles. Results: The results showed that YGS effectively alleviated diarrhea and improved abnormal biochemical indicators. YGS significantly increased serum levels of CAT, GSH-PX, and SOD, while reducing MDA levels. In addition, YGS also suppressed the expression of multiple proinflammatory cytokines, including IL-1α, TNF-α, IL-1β, IL-17A, IL-18, IL-21, IFN-γ, as well as chemokines CXCL9 and CXCL10. Metabolomic analysis revealed that YGS treatment significantly improved metabolic disorders and enriched the Arginine and Proline Metabolism pathways. The metabolites 1-methylhydantoin and ornithine were significantly and negatively correlated with pro-inflammatory cytokine levels. Conclusions: YGS effectively treats calf diarrhea by enhancing antioxidant capacity, reducing inflammatory factor levels, regulating immune function, and modulating serum metabolites. It provided valuable insights for the development of safe and effective antibiotic alternatives for preventing and treating calf diarrhea. Full article

(This article belongs to the Topic Recent Advances in Veterinary Pharmacology and Toxicology)

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14 pages, 1048 KB

Open AccessArticle

Molecular Characterization, Identification of the Volatile Organic Compounds by GC–MS, and Assessment of the Cytotoxic Activity of Leaves of Pimenta dioica L. Merrill Trees from Mexico

by Isis Montalvo-López, María del Rosario García-Mateos, Juan Martínez-Solís, Ramón Marcos Soto-Hernández and Ma Carmen Ybarra-Moncada

Metabolites 2025, 15(9), 617; https://doi.org/10.3390/metabo15090617 - 18 Sep 2025

Abstract

Background: Pimenta dioica is a medicinal plant rich in various natural compounds, giving it significant potential for applications in the pharmaceutical, cosmetic, food, and agricultural industries. However, little is known about the metabolites present in the leaves of female and male trees, [...] Read more.

Background: Pimenta dioica is a medicinal plant rich in various natural compounds, giving it significant potential for applications in the pharmaceutical, cosmetic, food, and agricultural industries. However, little is known about the metabolites present in the leaves of female and male trees, as well as their toxicity and genetic variability. Therefore, in this study, molecular characterization was conducted, the volatile compounds in the leaves of female and male trees were identified, and their cytotoxicity was assessed. Methods: For molecular characterization, a clustering analysis was performed using Ward’s minimum variance method; genetic distances were determined using Jaccard’s coefficient (similarity) and an analysis of molecular variance. Hexane extracts were obtained using the Soxhlet method and analyzed by gas chromatography coupled to mass spectrometry (GC–MS). The cytotoxicity of the extracts was evaluated by a bioassay with Artemia salina. Results: Forty-two metabolites were identified in leaf extracts from female and male trees, of which 17 are reported for the first time in this tissue. The female tree exhibited a distinct metabolite profile compared to the male tree and was slightly more toxic than the male tree. However, both were considered to be moderately toxic (282.00 and 222.87 μg/mL, respectively). Conclusions: Pimenta dioica has a high potential for various uses, primarily for anthropocentric purposes due to its composition of specific metabolites and moderate toxicity. The sampled trees showed a high molecular genetic variability among individuals. Full article

(This article belongs to the Special Issue Bioactive Metabolites from Plants)

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20 pages, 1558 KB

Open AccessArticle

Targeted Isolation of Prenylated Flavonoids from Paulownia tomentosa Fruit Extracts via AI-Guided Workflow Integrating LC-UV-HRMS/MS

by Tomas Rypar, Lenka Molcanova, Barbora Valkova, Ema Hromadkova, Christoph Bueschl, Bernhard Seidl, Karel Smejkal and Rainer Schuhmacher

Metabolites 2025, 15(9), 616; https://doi.org/10.3390/metabo15090616 - 17 Sep 2025

Abstract

Objectives: This study presents a versatile, AI-guided workflow for the targeted isolation and characterization of prenylated flavonoids from Paulownia tomentosa (Thunb.) Steud. (Paulowniaceae). Methods: The approach integrates established extraction and chromatography-based fractionation protocols with LC-UV-HRMS/MS analysis and supervised machine-learning (ML) custom-trained classification models, [...] Read more.

Objectives: This study presents a versatile, AI-guided workflow for the targeted isolation and characterization of prenylated flavonoids from Paulownia tomentosa (Thunb.) Steud. (Paulowniaceae). Methods: The approach integrates established extraction and chromatography-based fractionation protocols with LC-UV-HRMS/MS analysis and supervised machine-learning (ML) custom-trained classification models, which predict prenylated flavonoids from LC-HRMS/MS spectra based on the recently developed Python package AnnoMe (v1.0). Results: The workflow effectively reduced the chemical complexity of plant extracts and enabled efficient prioritization of fractions and compounds for targeted isolation. From the pre-fractionated plant extracts, 2687 features were detected, 42 were identified using reference standards, and 214 were annotated via spectra library matching (public and in-house). Furthermore, ML-trained classifiers predicted 1805 MS/MS spectra as derived from prenylated flavonoids. LC-UV-HRMS/MS data of the most abundant presumed prenyl-flavonoid candidates were manually inspected for coelution and annotated to provide dereplication. Based on this, one putative prenylated (C5) dihydroflavonol (1) and four geranylated (C10) flavanones (2–5) were selected and successfully isolated. Structural elucidation employed UV spectroscopy, HRMS, and 1D as well as 2D NMR spectroscopy. Compounds 1 and 5 were isolated from a natural source for the first time and were named 6-prenyl-4′-O-methyltaxifolin and 3′,4′-O-dimethylpaulodiplacone A, respectively. Conclusions: This study highlights the combination of machine learning with analytical techniques to streamline natural product discovery via MS/MS and AI-guided pre-selection, efficient prioritization, and characterization of prenylated flavonoids, paving the way for a broader application in metabolomics and further exploration of prenylated constituents across diverse plant species. Full article

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

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17 pages, 2618 KB

Open AccessArticle

Metabolomic Analysis of Key Metabolites and Regulatory Mechanisms in the Transition of Uterine Receptivity in Water Buffalo (Bubalus bubalis)

by Xingrong Lu, Jingyuan Song, Gan Liang, Huapei Zhong, Yuanyuan Xu, Yingxue Xie, Deshun Shi and Chan Luo

Metabolites 2025, 15(9), 615; https://doi.org/10.3390/metabo15090615 - 17 Sep 2025

Abstract

Background: While economically vital, buffalo exhibits low reproductive efficiency largely due to embryonic losses during implantation. Successful implantation requires precise embryo–maternal communication and metabolic/immune adaptations in the endometrium. We aimed to identify key serum metabolic signatures and associated peripheral immune responses that characterize [...] Read more.

Background: While economically vital, buffalo exhibits low reproductive efficiency largely due to embryonic losses during implantation. Successful implantation requires precise embryo–maternal communication and metabolic/immune adaptations in the endometrium. We aimed to identify key serum metabolic signatures and associated peripheral immune responses that characterize the endometrial receptivity window during early pregnancy in water buffalo. Methods: Blood samples from pregnant (Preg, n = 12) and non-pregnant (Non-P, n = 10) buffaloes were collected on days 15, 18, and 21 post-artificial insemination (AI). We measured leukocyte counts and hormone levels and performed untargeted serum metabolomic profiling using LC-MS. Results: Pregnant buffaloes showed significantly reduced total white blood cell count, lymphocyte (LYM%), and neutrophil (NEU%) percentages, indicating immune remodeling at the beginning of pregnancy establishment. Metabolomic analysis identified 131 differentially expressed metabolites (DEMs) associated with pregnancy status at different stages. Enriched pathways included steroid hormone synthesis, retinol metabolism, starch/sucrose metabolism, and phenylalanine biosynthesis. Crucially, alterations in unsaturated fatty acids, retinol, and phenylalanine metabolism, along with monocyte (MON%)/LYM% ratios, were strongly linked to receptivity changes and successful implantation. Conclusions: Endometrial receptivity in buffalo during the embryonic implantation window was associated with changes in immune cells and metabolism in the blood, suggesting that immunometabolism may play an essential role in modulating endometrial receptivity during the implantation window. This study provides potential clues and a metabolic framework for understanding the underlying mechanisms of buffalo embryonic implantation. Full article

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

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15 pages, 1254 KB

Open AccessReview

Ethnomedicinal Applications, Phytochemistry, and Pharmacological Properties of Zanthoxylum caribaeum Lam.: A Comprehensive Review

by Ahissan Innocent Adou, Ebed Fleurima, Valendy Thesnor, Ander Urrutia, Alain Fournet, Marie-Noëlle Sylvestre, Muriel Sylvestre, Zohra Benfodda and Gerardo Cebrián-Torrejón

Metabolites 2025, 15(9), 614; https://doi.org/10.3390/metabo15090614 - 16 Sep 2025

Abstract

Zanthoxylum caribaeum Lam. is a member of the Rutaceae Family that can be naturally found in South and central America (Brazil, Paraguay, Bolivia, Caribbean, etc.). Its traditional medicinal uses are well documented among native communities, such as that of the Guarani, in Paraguay. [...] Read more.

Zanthoxylum caribaeum Lam. is a member of the Rutaceae Family that can be naturally found in South and central America (Brazil, Paraguay, Bolivia, Caribbean, etc.). Its traditional medicinal uses are well documented among native communities, such as that of the Guarani, in Paraguay. More than 60 metabolites, including alkaloids, terpenoids, coumarins, and alkylamides, have been identified in its leaves, bark, and fruits. The biological activities and mechanisms of action of several of these compounds, as well as those of crude extracts, have also been investigated by previous studies. As a medicinal and edible plant, Z. caribaeum shows promising applications in the pharmacological industry. For the last 25 years, a significant amount of research has been conducted with Z. caribaeum to better understand its toxicity and complex mechanisms of action, bringing science-based clinical safety to its traditional uses. This review integrates available knowledge chemical and biological data on this species. It emphasizes the diversity of bioactive metabolites, their associated bioactivities, and provides an updated overview of the plant’s advances in ethnopharmacology, phytochemistry, pharmacology, agricultural exploitation, and potential utilization. Full article

(This article belongs to the Special Issue Bioactive Plant Extracts: Phytochemical Characterization, Isolation and Biological Evaluation)

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35 pages, 1357 KB

Open AccessReview

Relationship of Ageing to Insulin Resistance and Atherosclerosis

by Xiaoyu Hao, Siying Tu, Da Pan, Wang Liao, Ligang Yang, Shaokang Wang and Guiju Sun

Metabolites 2025, 15(9), 613; https://doi.org/10.3390/metabo15090613 - 15 Sep 2025

Abstract

Ageing drives a vicious cycle of insulin resistance (IR) and atherosclerosis through shared pathological pathways. This review aims to synthesise the current understanding of the molecular mechanisms that connect ageing, IR, and atherosclerosis, with a particular focus on oxidative stress, chronic inflammation, and [...] Read more.

Ageing drives a vicious cycle of insulin resistance (IR) and atherosclerosis through shared pathological pathways. This review aims to synthesise the current understanding of the molecular mechanisms that connect ageing, IR, and atherosclerosis, with a particular focus on oxidative stress, chronic inflammation, and metabolic disturbances. We systematically summarise evidence demonstrating how age-related mitochondrial dysfunction promotes IR, which in turn accelerates atherosclerotic progression. Based on this integration, we conclude that the intertwined nature of these processes reveals promising therapeutic targets. Targeting these shared pathways, such as with senolytic agents or anti-inflammatory agents, may offer novel strategic insights for concurrently mitigating IR and atherosclerosis in the ageing population. Full article

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

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19 pages, 3707 KB

Open AccessArticle

An NMR Metabolomics Analysis Pipeline for Human Neutrophil Samples with Limited Source Material

by Grace Filbertine, Genna A. Abdullah, Lucy Gill, Rudi Grosman, Marie M. Phelan, Direkrit Chiewchengchol, Nattiya Hirankarn and Helen L. Wright

Metabolites 2025, 15(9), 612; https://doi.org/10.3390/metabo15090612 - 15 Sep 2025

Abstract

Background/Objectives: Untargeted ¹H NMR metabolomics is a robust and reproducible approach used to study the metabolism in biological samples, providing unprecedented insight into altered cellular processes associated with human diseases. Metabolomics is increasingly used alongside other techniques to detect an instantaneous altered [...] Read more.

Background/Objectives: Untargeted ¹H NMR metabolomics is a robust and reproducible approach used to study the metabolism in biological samples, providing unprecedented insight into altered cellular processes associated with human diseases. Metabolomics is increasingly used alongside other techniques to detect an instantaneous altered cellular function, for example, the role of neutrophils in the inflammatory response. However, in some clinical settings, blood samples may be limited, restricting the amount of cellular material available for a metabolomic analysis. In this study, we wanted to establish an optimal 1D ¹H NMR metabolomic pipeline for use with human neutrophil samples with low amounts of input material. Methods: We compared the effect of different neutrophil isolation protocols on metabolite profiles. We also compared the effect of the absolute cell counts (100,000 to 5,000,000) on the identities of metabolites that were detected with an increasing number of scans (NS) from 256 to 2048. Results/Conclusions: The variance in the neutrophil profile was equivalent between the isolation methods, and the choice of isolation method did not significantly alter the metabolite profile. The minimum number of cells required for the detection of neutrophil metabolites was 400,000 at an NS of 256 for the spectra acquired with a cryoprobe (700 MHz). Increasing the NS to 2048 increased metabolite detection at the very lowest cell counts (<400,000 neutrophils); however, this was associated with a significant increase in the analysis time, which would be rate-limiting for large studies. The application of a correlation-reliability-score-filtering method to the spectral bins preserved the essential discriminatory features of the PLS-DA models whilst improving the dataset robustness and analytical precision. Full article

(This article belongs to the Special Issue NMR-Based Metabolomics in Biomedicine and Food Science)

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13 pages, 1005 KB

Open AccessArticle

Association of Gla-Rich Protein (GRP) with Inflammatory Markers in Critically Ill Patients: A Cross-Sectional Observational Study

by Elif Eygi, Sinem Bayrakçı, Onur Bayrakçı, Nazire Ates Ayhan, Ahmet Atlas, Metin Kilinc and Recep Dokuyucu

Metabolites 2025, 15(9), 611; https://doi.org/10.3390/metabo15090611 - 13 Sep 2025

Abstract

Objectives: Gla-rich protein (GRP), a vitamin K-dependent protein, has been increasingly recognized for its dual role in modulating inflammation and inhibiting pathological calcification. Despite its emerging importance in chronic conditions, limited evidence exists regarding its behavior during acute critical illness. This study aimed [...] Read more.

Objectives: Gla-rich protein (GRP), a vitamin K-dependent protein, has been increasingly recognized for its dual role in modulating inflammation and inhibiting pathological calcification. Despite its emerging importance in chronic conditions, limited evidence exists regarding its behavior during acute critical illness. This study aimed to investigate the association between GRP, systemic inflammatory markers, oxidative stress (via total thiol oxidation-reduction ratio, TORR), and calcium metabolism in critically ill patients. Materials and Methods: This cross-sectional observational study included 93 critically ill patients admitted to the intensive care unit (ICU) and 60 age- and sex-matched non-critically ill volunteers. Serum GRP levels were measured using ELISA. Other biomarkers including TORR, C-reactive protein (CRP), procalcitonin (PCT), white blood cell count (WBC), immature granulocytes (IGs), and serum calcium were also analyzed. Pearson’s correlation, multivariate linear regression, and ROC analysis were performed to assess the relationships among GRP and biochemical markers, as well as their capacity to differentiate ICU patients from controls. Results: GRP, TORR, CRP, PCT, WBC, IGs, and ferritin levels were significantly elevated in ICU patients compared to the control group, whereas serum calcium levels were markedly reduced (all p < 0.05). GRP levels demonstrated moderate positive correlations with WBC (r = 0.47), neutrophils (r = 0.51), TORR (r = 0.42), CRP (r = 0.30), and IGs (r = 0.46), and a strong negative correlation with calcium (r = −0.63). In multivariate regression, TORR, CRP, WBC, IGs, PCT, and calcium levels showed significant correlations with GRP levels in univariate analysis. ROC analysis revealed that CRP had the highest discriminatory power (AUC = 0.88; 95% CI: 0.82–0.94), followed by TORR (AUC = 0.79; 95% CI: 0.71–0.86), GRP (AUC = 0.76; 95% CI: 0.68–0.84), and IGs (AUC = 0.77; 95% CI: 0.69–0.85), for distinguishing ICU patients from non-critically ill individuals. Conclusions: Our findings demonstrated that GRP is significantly associated with systemic inflammation, oxidative stress, and calcium metabolism disturbances in critically ill patients. The combined evaluation of GRP and TORR may enhance the understanding of inflammatory and oxidative mechanisms in acute critical illness. Although this study did not assess patient outcomes, these biomarkers could serve as promising candidates for future prognostic research in ICU settings. Full article

(This article belongs to the Special Issue Metabolite Profiles in Inflammatory Diseases)

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20 pages, 21922 KB

Open AccessArticle

SnRK-PP2C-PYL Gene Families in Citrus sinensis: Genomic Characterization and Regulatory Roles in Carotenoid Metabolism

by Pengjun Lu, Zhenting Shi, Tao Liu, Jianqiu Ji, Jing Li, Wentao Li and Chongbo Sun

Metabolites 2025, 15(9), 610; https://doi.org/10.3390/metabo15090610 - 12 Sep 2025

Abstract

Background/Objectives: Carotenoids in citrus are vital nutritional compounds and precursors of the stress hormone abscisic acid (ABA). SNF1-related kinases (SnRKs)—key regulators of plant stress signaling that phosphorylate is targeting proteins for post-transcriptional regulation—mediate ABA signaling through its subfamily SnRK2-phosphatase type-2C (PP2C)-PYR1-LIKE (PYL) [...] Read more.

Background/Objectives: Carotenoids in citrus are vital nutritional compounds and precursors of the stress hormone abscisic acid (ABA). SNF1-related kinases (SnRKs)—key regulators of plant stress signaling that phosphorylate is targeting proteins for post-transcriptional regulation—mediate ABA signaling through its subfamily SnRK2-phosphatase type-2C (PP2C)-PYR1-LIKE (PYL) cascades. This study aims to identify the SnRK-PP2C-PYL family members and decipher their underlying post-transcriptional regulatory mechanisms which control carotenoid metabolism in Citrus sinensis for improved nutrition and stress resilience. Methods: SnRK, PP2C, and PYL were identified by integrated HMMER-blastp-CDD pipeline in the Citrus genome. Using two carotenoid-divergent cultivars, ‘Newhall’ (yellow) and ‘Cara Cara’ (red, hyperaccumulating linear carotenoids), we conducted spatiotemporal expression profiling and integrated transcriptomic and metabolomic data via Weighted Gene Co-expression Network Analysis (WGCNA) to identify modules correlated with accumulation. Results: We identified 26 CsSnRKs (1 SnRK1, 7 SnRK2, 18 SnRK3), 57 CsPP2Cs, and 7 CsPYLs in Citrus sinensis. Despite a >26-fold difference in linear carotenoids, structural gene expression was similar among cultivars, strongly implicating post-transcriptional control. WGCNA identified a key turquoise module highly correlated with linear carotenoid content. This module contained phosphorylation-related genes (CsSnRK1/3.5/3.6/3.16, CsPP2C14/15/33/35/38/40/43/56, and CsPYL6), biosynthetic genes (CsPSY1, CsZISO, and CsZDS), and candidate transcription factors. Network analysis predicted that CsSnRKs, CsPP2Cs, and CsPYLs regulate phytoene-derived carotenoid biosynthesis. Conclusions: We propose a novel phosphorylation-mediated post-transcriptional regulatory network in carotenoid accumulation. This mechanism bridges ABA signaling and metabolic adaptation, providing crucial molecular targets for engineering nutrient-dense and climate-resilient citrus varieties. Full article

(This article belongs to the Section Plant Metabolism)

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18 pages, 5707 KB

Open AccessArticle

Comparison of the Metabolic and Flavor Characteristics of the Egg Yolks of BIAN Chicken and Hy-Line Brown Chicken Using LC-MS and GC × GC-TOF MS Techniques

by Bochi Zhang, Xianyi Song, Kaige Li, Kai Zhang, Rui Zhao, Chunlei Yang and Liying Du

Metabolites 2025, 15(9), 609; https://doi.org/10.3390/metabo15090609 - 12 Sep 2025

Abstract

Objectives: This study systematically compared the differences in egg quality between the BIAN chicken, an indigenous breed of Shanxi Province, and the Hy-Line Brown, a commercial breed, through the integration of non-targeted metabolomics and volatile flavoromics methods. Methods: A total of 675 metabolites [...] Read more.

Objectives: This study systematically compared the differences in egg quality between the BIAN chicken, an indigenous breed of Shanxi Province, and the Hy-Line Brown, a commercial breed, through the integration of non-targeted metabolomics and volatile flavoromics methods. Methods: A total of 675 metabolites and 84 volatile flavor compounds were identified in eggs from 300-day-old laying hens using LC-MS and GC × GC-TOF MS techniques. Results: BIAN chicken eggs exhibited notable advantages in flavor quality. The relative odor activity value (ROAV) of 1-octen-3-ol, a key flavor component, was 27.01 in BIAN compared with 13.46 in Hy-Line Brown, contributing to the characteristic mushroom aroma of BIAN eggs. Furthermore, the levels of heptaldehyde, 2-pentylfuran, and styrene in BIAN chicken eggs were significantly elevated, contributing to its characteristic flavor profile. Metabolomic analysis identified 40 breed-specific metabolites in BIAN chicken, with 21 up-regulated and 19 down-regulated. These metabolites were primarily involved in biological processes such as α-linolenic acid metabolism, cholesterol metabolism, and unsaturated fatty acid biosynthesis, highlighting the distinctive lipid metabolism regulation in BIAN chicken. Sensory evaluation based on relative odor activity values (ROAV) demonstrated that BIAN chicken eggs exhibited enhanced sweet, fruity, herbal, and citrus aromas, which correlated with the enriched lipid metabolism pathways. Conclusions: This study elucidates the molecular basis of distinctive egg quality characteristics in local chicken breeds, offering a scientific rationale for the conservation and utilization of indigenous breeds and the documentation of their unique metabolic and sensory properties. Furthermore, it furnishes a theoretical framework for understanding breed-specific flavor development and provides baseline data for future genetic selection and nutritional intervention strategies. Full article

(This article belongs to the Special Issue Metabolomics in Food Science and Nutrition Using GC-MS)

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