Antimicrobial resistance (AMR) is a worsening global health crisis that has arisen due to antibiotic overuse and misuse. Antibiotic resistance renders standard treatments less effective, making it difficult to control some infections, thereby increasing morbidity and mortality. Medicinal plants are sustainable treatment options that are becoming increasingly important as antibiotics lose their efficacies. The present study evaluates the antibacterial activity of aqueous, methanolic and ethyl acetate extracts prepared using Terminalia bellirica and Terminalia chebula fruit against six bacterial pathogens using disc diffusion and broth microdilution assays. The aqueous and methanol extracts of T. bellirica and T. chebula showed substantial zones of inhibition (ZOIs) against S. aureus and MRSA. The activity against those bacteria was determined to be strong, with minimum inhibitory concentrations (MIC) ranging from 94 µg/mL to 392 µg/mL. Additionally, the T. bellirica methanolic extract showed noteworthy antibacterial activity against E. coli and an ESBL E. coli strain (MIC values of 755 µg/mL for both). The aqueous T. bellirica and T. chebula extracts also inhibited K. pneumoniae growth (MIC values of 784 µg/mL and 556 µg/mL respectively), whilst the methanolic extracts of these plants also inhibited ESBL K. pneumoniae growth (MIC values of 755 µg/mL and 1509 µg/mL respectively). Eighteen additive interactions were observed when extracts were combined with reference antibiotics. Notably, strong antagonistic interactions occurred when any of the extracts were mixed with polymyxin B. All extracts were subjected to LC-MS analysis, revealing several interesting flavonoids and tannins, including 6-galloylglucose, 1,2,6-trigalloyl-β-D-glucopyranose, 6-O-[(2E)-3-phenyl-2-propenoyl]-1-O-(3,4,5-trihydroxybenzoyl)-β-D-glucopyranose, propyl gallate, methyl gallate, sanguiin H4, hamamelitannin, pyrogallol, gallic acid, ellagic acid, chebulic acid, and chebuloside II. All extracts were nontoxic when tested in brine shrimp assays. This lack of toxicity, combined with their antibacterial activities suggests that these plant species may be promising sources of antibacterial compound(s) that warrant further study.

Background/Objectives: Meconopsis has long been used in traditional Tibetan medicine to treat various diseases. However, blue-flowered Meconopsis (M. betonicifolia) is becoming increasingly scarce due to overharvesting. As a potential alternative, yellow-flowered Meconopsis (M. integrifolia) shows promise but requires comprehensive characterization. This study aimed to evaluate and compare the anti-inflammatory potential of yellow- and blue-flowered Meconopsis species. Methods: LC-MS was used to analyze the chemical profiles of yellow- and blue-flowered Meconopsis. Putative targets of shared constituents were subjected to GO and disease enrichment analysis. The LPS-induced RAW264.7 macrophage model was employed to assess anti-inflammatory effects. Metabolomics was applied to gain mechanistic insights. Results: LC-MS revealed over 70% chemical similarity between species. Enrichment analysis associated targets with inflammation-related pathways. In macrophage assays, both species demonstrated dose-dependent anti-oxidative and anti-inflammatory activities, with yellow Meconopsis exhibiting superior efficacy. Metabolomics showed modulation of key inflammatory metabolic pathways. Conclusions: This integrative study validated yellow-flowered Meconopsis as a credible alternative to its blue-flowered counterpart for anti-inflammatory applications. Metabolic profiling provided initial clues regarding their multi-targeted modes of action, highlighting clinical relevance and potential for sustainable utilization and biodiversity conservation.

Gastrointestinal parasites (GIP) are diverse parasitic organisms known to have coevolved with bacterial populations inside the gut of mammalian hosts. These helminths produce small molecules, peptides and proteins to evade or fight their hosts' immune systems. Small molecules include polar compounds, amino acids, lipids and carbohydrates. Metabolomics is an emerging field of research recently applied to study helminth infections and host-parasite interactions. This review comprehensively discusses metabolomics studies of small molecules of GIP in animals, providing insights into the available tools and techniques, databases, and analytical software. Most metabolomics investigations employed LC-MS, MS or MS/MS, NMR, or a combination thereof. Recent advancements in metabolomics platforms, including artificial intelligence (AI)-assisted software tools and databases, have propelled helminth metabolomics forward, offering new avenues to explore host-parasite interactions, immunomodulation, and the intricacies of parasitism. As our understanding of helminth metabolomics continues to expand, it promises to unveil novel perspectives and enrich the knowledge of these complex host-parasite relationships.

Metabolomics studies require a deep understanding of enzyme dynamics and their responses to environmental disturbances within a complex metabolic network. This paper presents a novel approach to modeling enzyme activity as a dynamic topological manifold, where each enzyme is represented as a node, and their interactions are described by differential equations. These equations account for both compensatory interactions and external perturbations, simulating how enzymes dynamically stabilize their activities in response to varying conditions. We explore the application of this model to visualize enzyme interactions, using graph theory to represent the network structure and color gradients to illustrate interaction intensities. Multiple disturbances are introduced to analyze the network's resilience and adaptability over time. The results provide insights into the compensatory mechanisms within enzymatic networks, offering a comprehensive visualization through both static and dynamic representations. Our approach allows for a better understanding of how enzymatic systems buffer against mutations and environmental stressors, contributing to the broader field of systems biology and metabolomics.

Polycystic ovary syndrome (PCOS) is a complex disorder that impacts both the endocrine and metabolic systems. The gut microbiota plays a crucial role in in metabolism regulation and immune responses through its interaction with the external environment. This article explores the intricate interplay between intestinal flora and the pathogenesis of PCOS, focusing on the pivotal role of microbial metabolites, specifically short-chain fatty acids (SCFAs). SCFA levels in fecal and blood samples from women with PCOS (n=69) and healthy controls (n=18) were analyzed using Gas Chromatography-Mass Spectrometry (GC/MS) for precise measurement. The results revealed that women with PCOS exhibited a significant reduction in beneficial bacteria alongside a notable overgrowth of opportunistic microorganisms. An overproduction of acetic acid (AA) and valeric acid (VA) in fecal samples suggests a link between elevated SCFAs and the development of obesity and PCOS. Interestingly, AA in the bloodstream might offer a protective effect against PCOS by ameliorating key symptoms such as high body mass index (BMI), insulin resistance (IR), and chronic inflammation. This finding points to the potential therapeutic value of maintaining optimal AA levels in the blood. Although serum SCFA levels showed non-significant changes following metformin treatment, the normalization of AA in the gut underscores that metformin exerts a more pronounced effect locally within the gastrointestinal tract. This treatment also led to an increase in beneficial gut bacteria and a reduction in opportunistic pathogens, suggesting a restoration of gut microbial balance. Furthermore, the study identified the most effective model for predicting the success of metformin therapy, based on serum concentrations of butyric acid (BA) and VA, achieving a 91% accuracy rate, 100% sensitivity, and 80% specificity. These promising findings highlight the potential for developing targeted interventions and personalized treatments, ultimately improving clinical outcomes for women with PCOS.

Keywords: cranberry, exercise, proteomics, oxylipins, gut microbiome, metabolomics, immunity

The field of personalized medicine is undergoing a transformative shift through the integration of multi-omics data, which encompasses genomics, transcriptomics, proteomics, and metabolomics. This synergy allows for a comprehensive understanding of individual health by analyzing genetic, molecular, and biochemical profiles. The generation and integration of multi-omics data enable more precise and tailored therapeutic strategies, improving the efficacy of treatments and reducing adverse effects. However, several challenges hinder the full realization of personalized medicine. Key hurdles include the complexity of data integration across different omics layers, the need for advanced computational tools, and the high cost of comprehensive data generation. Additionally, issues related to data privacy, standardization, and the need for robust validation in diverse populations remain significant obstacles. Looking ahead, the future of personalized medicine promises advancements in technology and methodologies that will address these challenges. Emerging innovations in data analytics, machine learning, and high-throughput sequencing are expected to enhance the integration of multi-omics data, making personalized medicine more accessible and effective. Collaborative efforts among researchers, clinicians, and industry stakeholders are crucial to overcoming these hurdles and fully harnessing the potential of multi-omics for individualized healthcare.

Porcine metabolomics research has been extensively conducted, primarily focusing on conventional cohorts or animal models. However, the composition and functions of fecal metabolites in pigs at various ages, particularly in the elderly, remain poorly understood. In the present study, an untargeted metabolomics approach was employed to analyze the fecal metabolomes of pigs at three distinct age stages, with the aim of elucidating age-associated changes in metabolite composition and functionality under standardized rearing conditions. Through the untargeted metabolomic analysis of fecal samples from young (one year), middle-aged (four years), and elderly (eight years) pig cohorts, a variety of age-related metabolites were identified. For example, L-methionine sulfoxide was observed to increase with age, while cytidine-5-monophosphate exhibited a concomitant gradual decrease during the aging process. These metabolites were found to undergo alterations across multiple biological pathways, including energy metabolism, pyrimidine metabolism, lipid metabolism, and amino acid metabolism. Furthermore, the age-dependent metabolic changes were associated with known senescence biomarkers, offering new insights into the mechanistic understanding of aging in pigs.

Considering the prevalence of cropping pattern in many Saffron cultivation regions, the continuous cropping obstacle caused the decline in growth and development. These effects justify the necessity of studying agronomic strategies to promote plant quality and production. Herein, the mono cropping, intercrop of Paulownia and Saffron, and intercrop of Soybean and Saffron patterns have been performed. The metabolites of Saffron under three cropping patterns were determined and identified using by an ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. Uni and multivariate statistical analysis were applied to examine the difference between groups and select the significant differential accumulated metabolites. The results showed that a total of 315 compounds were significantly changed in three comparison groups. Phenylalanine metabolism, linoleic acid metabolism, and flavonoid biosynthesis pathway has been greatly enriched by the changed metabolites. The phenyl lactate, trans-2-Hydroxy-cinnamate, γ-Linolenate, 9-oxo-octadecadienoic acid, 13-0xo-0ctadecadienoic acid, 9,12,13-TriHOME of those metabolites showed significant differential accumulation in Saffron under three cropping patterns. And the accumulation of safranal and picrocrocin related compounds, such as Crocetin, Crocin showed a similar variation regularity. These indicate that there may be a close internal relationship between the cropping pattern and the biosynthesis of metabolites related to endogenous substances and Saffron quality formation.

Identification of the individuals having impaired kidney function is essential in preventing the complications of this disease. We measured 1 009 metabolites at the baseline study in 10 159 Finnish men of the METSIM cohort and associated the metabolites with estimated glomerular filtration rate (eGFR). A total of 7 090 men participated in the 12-year follow-up study. Non-targeted metabolomics profiling was performed at Metabolon, Inc. (Morrisville, NC, USA) on EDTA plasma samples obtained after overnight fasting. We applied Liquid chromatography-mass spectrometry (LC-MS/MS) to identify the metabolites (the Metabolon DiscoveryHD4 platform). We performed association analyses between the eGFR and metabolites using linear regression adjusted for confounding factors. We found 108 metabolites significantly associated with a decrease in eGFR, and 28 of them were novel including 12 amino acids, 8 xenobiotics, 5 lipids, 1 nucleotide, 1 peptide, and 1 partially characterized molecule. The most significant associations were with five amino acids, N-acetylmethionine, N-acetylvaline, gamma-carboxyglutamate, 3-methylglutaryl-carnitine, and pro-line. We identified 28 novel metabolites associated with decreased eGFR in the 12-year follow-up study of the METSIM cohort.

Background/Objectives: The management of early breast cancer (BC) includes surgery, followed by adjuvant radiotherapy, chemotherapy, hormone therapy, or immunotherapy. However, the influence of these interventions in metabolic reprogramming remains unknown. This study explored alterations in the plasma metabolome of BC patients following distinct treatments to deepen our understanding of BC pathophysiology, outcomes, and the identification of potential biomarkers. Methods: We included 52 women diagnosed with BC and candidates for surgery as primary oncological treatment. Blood samples were collected at diagnosis, two weeks post-surgery, and one month post-radiotherapy. Plasma samples from 49 healthy women served as controls. Targeted metabolomics assessed 74 metabolites spanning carbohydrates, amino acids, lipids, nucleotide pathways, energy metabolism, and xenobiotic biodegradation. Results: Before treatment, BC patients exhibited notable changes in carbohydrate, nucleotide, lipid, and amino acid metabolism. We noticed a gradual restoration of specific metabolite levels (hypoxanthine, 3-phosphoglyceric acid, xylonic acid, and maltose) throughout different treatments, suggesting a normalization of nucleotide and carbohydrate metabolic pathways. Moreover, we observed increased dodecanoic acid concentrations, a metabolite associated with cancer protection. These variations distinguished patients from controls with high specificity and sensitivity. Conclusion: Oncological treatments modified the metabolism of patients towards a favorable profile with a decrease in the pathways that favor cell proliferation and an increase in the levels of anticancer molecules. These findings emphasize the pivotal role of metabolomics in recognizing the biological pathways influenced by each cancer treatment and the resulting metabolic consequences. Furthermore, it aids in identifying potential biomarkers for disease onset and progression.

Decidualization of the uterine endometrium is a critical process for embryo implantation in mammals, primarily occurring on gestational day 8 in pregnant mice. However, the interplay between the maternal gut microbiome, metabolism, and the uterus at this specific time point remains poorly understood. This study employed a multi-omics approach to investigate the metabolic, gut microbiome, and transcriptomic changes associated with early pregnancy (gestational day 8 (E8)) in mice. Serum metabolomics revealed a distinct metabolic profile in E8 compared to controls, with differential metabolites primarily enriched in amino acid metabolism pathways. Gut microbial composition showed that E8 mice exhibited higher alpha-diversity and a significant shift of beta-diversity. Specifically, the E8 group displayed a decrease in pathogenic Proteobacteria and an increase in beneficial Bacteroidetes and S24-7 taxa. Transcriptomics identified myriads of distinct gene between E8 and control mice. The differentially expressed genes were enriched in pathways involved in Alanine, Aspartate and Glutamate metabolism, PI3K-Akt signaling, and PPAR signaling pathway. Integrative analysis of the multi-omics data uncovered potential mechanistic relationships among the differential metabolites, gut microbiota, and uterine gene expression changes. Notably, the gene Asns showed strong correlations with specific gut S24-7 and metabolite L-Aspartatic acid, suggesting its potential role in mediating the crosstalk between the maternal environment and embryo development during early pregnancy. These findings provide valuable insights into the complex interplay between the maternal metabolome, gut microbiome, and uterine transcriptome in the context of early pregnancy, which may contribute to our understanding of the underlying mechanisms of embryo implantation and development.

Cyclocarya paliurus tea, also known as "sweet tea", a health substitute tea with Cyclocarya paliurus leaves as raw material, is famous for its unique nutritional benefits and flavor. However, due to the unique "bittersweet" of Cyclocarya paliurus tea, it is still unable to fully satisfy consumers' high-quality taste experience and oral pleasure. The taste and sensory quality of Cyclocarya paliurus tea are mainly determined by secondary metabolites. Therefore, this study aimed to explore the metabolites in Cyclocarya paliurus leaves during their growth process, particularly the composition and variation of sweet and bitter taste compounds, by combining multi-platform metabolomics analysis with an electronic tongue system and molecular docking simulation technology. The results indicated that there were significant differences in the contents of total phenols, flavonoids, polysaccharides and saponins of C. paliurus leaves in different growing months, among which the bioactive components in leaves harvested in July were the highest, and the best balance between sweetness and bitterness was achieved. A total of 575 secondary metabolites were identified as potential active metabolites related to sweet/bitter taste using nontargeted metabolomics based on UHPLC-MS/MS analysis. Molecular docking technology was utilized to study the interactions between candidate metabolites and the sweet receptor T1R2/T1R3 and the bitter receptor T2R4/T2R14. Six key compounds with high sweetness and low bitterness were successfully identified by using computational simulation analysis, including cis-Anethole, Gluconic acid, beta-D-Sedoheptulose, Asparagine, Proline, and Citrulline, which may serve as candidates for taste modification in Cyclocarya paliurus leaves. These findings provide a new perspective for understanding the sweet and bitter taste characteristics metabolites that contribute to the distinctive sensory quality of Cyclocarya paliurus leaves.

Medicinal plants produce various bioactive molecules with potential anticancer properties with favorable safety profiles. We investigated the comprehensive composition of Vernonia amygdalina leaf extract and its cytotoxic effects via apoptosis in HeLa cells. The metabolomics approach was conducted to gather the metabolite profile of the extract. Proteomics was performed to understand the comprehensive mechanistic pathways of action. The apoptosis was visualized by cellular staining and the apoptotic proteins were evaluated. V. amygdalina leaf extract exhibited dose-dependent cytotoxic effects on both HeLa and Vero cells after 24 h of exposure, however, a higher concentration was required for Vero cells cytotoxicity. The metabolomic profile indicated that majority of metabolites were alkaloids, phenolic compounds, and steroids. The cytotoxic pathways involved the response to stress and cell death which was similar to doxorubicin. The upstream regulatory proteins, PTEN and XBP1, were significantly altered supporting the regulation of apoptosis and cell death. The levels of apoptotic proteins, JNK, p53, and caspase-9 were significantly increased. These provided strong evidence that V. amygdalina leaf extract related to the induction of apoptosis and highlighted its potential for the development of chemotherapy.

3.9 million individuals rely on kidney replacement therapy worldwide. They experience height-ened susceptibility to cardiovascular diseases and mortality, alongside an increased risk of in-fections and malignancies, with inflammation being key to explaining this intensified risk. This study utilized semi-targeted metabolomics to explore novel metabolic pathways related to in-flammation in this populations. We collected pre and post-session blood samples of patients who had already undergone one year of chronic hemodialysis. And used liquid chromatography and high resolution mass spectrometry to perform a metabolomic analysis. Afterwards, we employed both univariate (Mann-Whitney test) and multivariate (logistic regression with LASSO regulari-zation) to identify metabolites associated with inflammation. In the univariate analysis, in-dole-3-acetaldehyde, 2-ketobutyric acid, and urocanic acid showed statistically significant de-creases in median concentrations in the presence of inflammation. In the multivariate analysis, metabolites positively associated with inflammation include allantoin, taurodeoxycholic acid, norepinephrine, pyroglutamic acid, and L-hydroorotic acid. Conversely, metabolites showing negative associations with inflammation include benzoic acid, indole-3-acetaldehyde, methio-nine, citrulline, alphaketoglutarate, n-acetyl-ornithine and 3-4-dihydroxibenzeneacetic acid. Non inflamed patients exhibit preserved autophagy and reduced mitochondrial dysfunction. Under-standing inflammation in this group hinges on the metabolism of arginine and the urea cycle. Additionally, the microbiota, particularly uricase-producing bacteria and those metabolizing tryptophan, play critical roles.

Differences in metabolic regulation among obesity phenotypes, specifically metabolically healthy obese (MHO) and metabolically unhealthy obese (MUO) women, may lead to varied responses to interventions, which could be elucidated through metabolomics. Therefore, this study aims to investigate the differences in metabolite profiles between MHO and MUO women and the changes following a lifestyle intervention. Serum from 36 MHO and 34 MUO women, who participated in a lifestyle intervention for weight loss were analyzed using an untargeted proton nuclear magnetic resonance spectroscopy (1H NMR) at baseline and 6 months post-intervention. Anthropometric, clinical and dietary intake parameters were assessed at both time points. Both groups showed differential metabolites profile at baseline and sixth month. Seven metabolites including trimethylamine-N-oxide (TMAO), arginine, ribose, aspartate, carnitine, choline and tyrosine significantly changed between group post-intervention, in which all showed a decreasing pattern in MHO. Significant reduction in body weight and BMI in the MUO correlated with changes in carnitine and tyrosine levels. In conclusion, metabolite profiles differed significantly between MHO and MUO women before and after a lifestyle intervention. Changes in carnitine and tyrosine levels in MUO correlated with weight loss, suggesting potential targets for therapeutic intervention.

The incidence of diabetes mellitus (DM) continues to rise worldwide and one of the most serious microvascular complications is diabetic kidney disease (DKD), which is the leading cause of end-stage renal disease. Current bi-omarkers such as urinary albumin excretion rate have limitation for early detection of DKD. In our study we used ultra-high-performance liquid chromatography coupled with electrospray ionization-quadrupole-time of flight-mass spectrometry (UHPLC-QTOF-ESI+-MS) techniques to quantify previously analyzed metabolites, such as tryptophan, kynurenic acid, taurine, l-acetylcarnitine, glycine, and tiglylglycine. We performed the targeted analy-sis of metabolites from urine and serum samples, collected from 110 subjects. Of these, 90 patients with type 2 DM (T2DM) were divided according to the urinary albumin/creatinine ratio (UACR) into normoalbuminuria 300 mg/g groups, respectively, while 20 subjects were rep-resented by healthy controls. Through various validation methods, we identified several metabolites as potential biomarkers, such as kynurenic acid, glycine, and l-tryptophan in serum and l-acetylcarnitine, tiglylglycine, and tau-rine in urine.

Abstract: Giant Cell Arteritis (GCA) is an autoimmune/autoinflammatory disease affecting large vessels in patients over 50 years old. The disease presents as an acute inflammatory response with two phenotypes, cranial-GCA and Large Vessel Vasculitis (LV)-GCA, involving the thoracic aor-ta and its branches. 18F-fluorodeoxyglucose positron emission tomography-computed tomogra-phy (18F-FDG PET-CT) is among the imaging techniques contributing to diagnosis of patients with systemic disease. However, its association with soluble inflammatory markers is still elu-sive. This proof-of-concept study aims to identify novel soluble serum biomarkers in PET/CT pos-itive patients with LV-GCA and associate them with active (0 months) and inactive disease (6 months following treatment), in sequential samples. The Most-Disease-Segment Target-to-Background Ratio (TBRMDS) was calculated for 9 LV-GCA patients, while 12 cranial-GCA and 7 Polymyalgia Rheumatica patients with negative initial PET/CT served as disease controls. Serum macrophage-related cytokines were evaluated by Cytometric Bead Array (CBA). Finally, previously published NMR-metabolomics data acquired at the same blood sampling were associated with PET/CT findings. TBRMDS was significantly increased in active versus inactive disease (3.45 vs. 2.55, p=0.008). The analysis identified 6 serum metabolites, as more sensitive to change from the active to inactive state. Among them, choline levels were exclusively altered in the LV-GCA group, but not the disease controls. Cytokine levels were not associated with PET/CT activity. Combining with CRP, ESR, and TBRMDS a composite index was generated to depict well the differences between active and inactive systemic LV-GCA (25.45 vs 11.45, p=0.0039). These preliminary results could pave the way for more extensive studies integrating serum metabolomic parameters with PET/CT imaging data to extract sensitive composite disease indexes useful for the everyday clinical practice.

The presence and localization of plant metabolites are indicative of physiological processes, e.g., under biotic and abiotic stress conditions. Further, the chemical composition of plant parts is related to their quality as food or for medicinal applications. Mass spectrometry imaging (MSI) has become a popular analytical technique for exploring and visualizing the spatial distribution of plant molecules within a tissue. This review provides a summary of mass spectrometry methods used for mapping and identifying metabolites in plant tissues. We present the benefits and the disadvantages of both vacuum and ambient ionization methods, considering direct and indirect approaches. Finally, we discuss the current limitations in annotating and identifying molecules and perspectives for future investigations.

The increasing use of chemicals requires a better understanding of their presence and their dynamics in the environment as well as their impact on ecosystems; it is therefore important to set up procedures. The aim of this study was to validate the first steps of an innovative multi-omics approach based on metabolomics and 16S metabarcoding data for future analyses of the contaminants fate and impact in Mediterranean lagoons. First, semi targeted analytical procedures for water and sediment matrices were set up to evaluate the lagoon contamination status. Forty-six compounds were detected, 28 could be quantified in both water (between 0.09 and 47.4 ng/L) and sediment (between 0.008 and 26.3 ng/g) samples using UHPLC-MS/MS instrument. Regarding the non-targeted metabolomics study (UHPLC-HRMS), four sample preparation protocols, based on solid/liquid extractions and an automated pressurized fluid extraction system (EDGE® extractions), were compared in terms of metabolome coverage, efficiency and reproducibility of the extraction methodology. A solid/liquid extraction using acetonitrile/methanol (50/50) solvent was the best protocol. On the other hand, in order to characterize the microbial diversity of the lagoon sediment using metabarcoding, five commercial kits for DNA extraction were evaluated. This study revealed that the DNeasy PowerSoil Pro Qiagen Kit (Promega, USA) was the best compromise for studies assessing microbial diversity in fresh sediment.

Astrocytes are considered to possess a noticeable role in brain metabolism and as a partners in neuron-glia cooperation contribute to synthesis, bioconversions and regulation of the flux of substrates for neuronal metabolism. With the aim to investigate to which extend are human astrocytes metabolizing amino acids and by which compounds are they enriching their surrounding we employed the metabolomics analysis of their culture media by 1H-NMR. In addition, we compered the composition of media with either 5 mM or 25 mM glucose. The quantitative analysis of culture media by 1H-NMR revealed that astrocytes readely dispose from their milieu glutamine, branched-chain amino acids, and pyruvate with significantly high rate, while they enrich the culture media with lactate, branched-chain keto acids, citrate, acetate, ketone bodies, and alanine. The hyperglycemia suppressed the capacity of astrocytes to release branched-chain amino acids while stimulating the generation of ketone bodies. Our results highlight the active involvement of astrocytes in metabolism of several amino acids, and the regulation of key metabolic intermediates. The observed metabolic activities of astrocytes provide valuable insights into their roles in supporting neuronal function, brain metabolism, and intercellular metabolic interactions within the brain. Understanding the complex metabolic interactions between astrocytes and neurons is essential for elucidating brain homeostasis and the pathophysiology of neurological disorders.

Abiotic stress is a significant factor restricting the normal growth and development of plants. Under abiotic stress, plants maintain their life and continuous growth by reconfiguring transcriptional regulation and metabolic networks. In recent years, with the development of sequencing technology and mass spectrometry technology, transcriptomics and metabolomics have emerged as new disciplines following genomics and proteomics, which are conducive to identifying metabolites and regulatory genes in plants under abiotic stress. In this review, we mainly analyzes the technical characteristics, advantages, and disadvantages of transcriptomics and metabolomics, focusing on reviewing the research progress in the field of plant responses to abiotic stress (temperature stress, salt stress, water stress, and heavy metal stress) using transcriptomics and metabolomics both domestically and internationally in recent years. It also provides a prospective view on current issues, which helps accelerate the understanding of the mechanisms of plant responses to abiotic stress and provides new ideas for breeding stress-resistant varieties in the future.

Lung cancer is the leading cause of cancer-related deaths globally, with non-small cell lung cancer (NSCLC) accounting for over 85% of cases and poor prognosis in advanced stages. This study explored shifts in circulating metabolite levels in NSCLC patients versus healthy controls and examined the effects of conventionally fractionated radiation therapy (CFRT) and stereotactic body radiation therapy (SBRT). We enrolled 91 NSCLC patients (38 CFRT and 53 SBRT) and 40 healthy controls. Plasma metabolite levels were assessed using semi-targeted metabolomics, revealing 32 elevated and 18 reduced metabolites in patients. Key discriminatory metabolites included ethylmalonic acid, maltose, 3-phosphoglyceric acid, taurine, glutamic acid, glycocolic acid, and d-arabinose, with a combined Receiver Operating Characteristics curve indicating perfect discrimination between patients and controls. CFRT and SBRT affected different metabolites, but both changes suggested a partial normalization of energy and amino acid metabolism pathways. In conclusion, metabolomics identified distinct metabolic signatures in NSCLC patients with potential as diagnostic biomarkers. The differing metabolic responses to CFRT and SBRT reflect their unique therapeutic impacts, underscoring the utility of this technique in enhancing NSCLC diagnosis and treatment monitoring.

Pseudomonas donghuensis P482 exhibits broad antibacterial and antifungal activity, primarily related to the production of 7-hydroxytropolone (7-HT). However, the restricted nutritional conditions (viz. mineral medium with single carbon source) diminished the antagonistic activity of P482. In this study, we unveil profiles of the secondary metabolites from P482 and its selected mutants, using nutrient-diluted (10% tryptone soy broth, TSB) and nutrient-restricted (M9 with either 0.4% glucose or 0.4% glycerol as a sole carbon source) media to explore differences in the quantity and quality of the secondary metabolites produced. No 7-HT was found to be synthetized by P482 under restricted nutritional conditions. However, both the wild-type and the tested mutants of P482 still did express some antagonistic activity towards the plant pathogenic bacteria tested. Based on these results, we postulate that 7-HT is not the sole antimicrobial compound produced by P. donghuensis P482 and that other antimicrobials may be involved in P482 antagonistic activity under limiting-nutrient conditions.

Gestational diabetes mellitus (GDM) triggers alterations in the maternal gut microbiome. Alongside metabolic shifts, microbial products may impact clinical factors and influence pregnancy outcomes. Here, we performed two separate analyses to integrate the maternal microbiome-metabolomic differences from a subset of the “Choosing Healthy Options in Carbohydrate Energy” (CHOICE) study. Women diagnosed with GDM were randomized to a diet higher in complex carbohydrates (CHOICE, n=18, 60% complex carbohydrate/25% fat/15% protein) or a conventional GDM diet (CONV, n=16, 40% carbohydrate/45% fat/15% protein). All meals were provided, diets were eucaloric, and fiber content was similar. CHOICE diet was associated with increases in TMAO, lysophosphotidylcholines, indoxyl sulfate, and several triglyceride (TG) species, while CONV diet was associated with higher plasma hippuric acid, aspartic acid, betaine, glutamic acid, indole propionic acid, and indoleacetic acid, suggesting that differences in lipid metabolism and tryptophan utilization pathways are linked to specific maternal diets. We also identified two latent metabolic groups not associated with either diet treatment: one metabolome associated with higher fasting glucose, and the other associated with higher fasting TGs after 7 weeks on either diet. Our study underscores the importance of utilizing dietary approaches to optimize maternal-fetal health outcomes in GDM treatment.

Methylmalonic acidemia (MMA), propionic acidemia (PA), and cobalamin C deficiency (cblC) share a defect in propionic acid metabolism. In addition, cblC is also involved in the process of homocysteine remethylation. These three diseases produce various phenotypes and complex downstream metabolic effects. In this study we used an untargeted metabolomics approach to investigate the biochemical differences and the possible connections with the pathophysiology of each disease. Untargeted urine metabolomic profiles of 21 patients (7 MMA, 7 PA, 7 cblC) were identified through statistical analysis (p<0.05; log2FC >|1|) and then used for the annotation. Annotated features were associated with different metabolic pathways potentially involved in the diseases development. Comparative statistic showed markedly different metabolomic profiles between MMA, PA and cblC, highlighting characteristic species for each disease. The most affected pathways were related to the metabolism of organic acids (MMA, PA, cblC), amino acids (MMA, PA, cblC), glycine and its conjugates (PA), transsulfuration pathway (cblC), oxidative processes (cblC) and neurosteroid hormones (cblC). The untargeted metabolomics study highlighted the presence of significant differences between the three diseases, pointing to the most relevant contrast of cblC profile compared to MMA and PA. Some new biomarkers are proposed for PA, while novel data regarding the alterations of steroid hormone profiles and biomarkers of oxidative stress were obtained for cblC disease. The elevation of neurosteroids in cblC may indicate a potential connection with the development of ocular and neuronal deterioration.

Plant-microbe interactions are essential for ecosystem health and agricultural productivity. Metabolomics has revolutionized our understanding of these interactions by providing powerful methods to decipher the complex chemical signals involved. This review highlights the various metabolomics techniques used to study plant-microbe interactions, such as mass spectrometry, nuclear magnetic resonance spectroscopy, and advanced imaging technologies. We also discuss the role of contemporary bioinformatics tools, extensive databases, and the increasing influence of artificial intelligence and machine learning in the analysis of metabolomics data. Integrating metabolomics with other omics fields, including transcriptomics, proteomics, and metagenomics, allows for a comprehensive understanding of the molecular mechanisms underlying plant-microbe interactions. The review emphasizes the significance of fluxomics in elucidating the dynamic nature of metabolic networks. While there are challenges in data analysis, integration, and interpretation, metabolomics has profoundly expanded our knowledge of the role metabolites play in shaping plant-microbe interactions. As metabolomics technologies advance and integrate further with other omics approaches, we anticipate groundbreaking discoveries that will provide deeper insights into these complex interactions, ultimately leading to innovative strategies for sustainable agriculture and biotechnology.

Agaricus bisporus is one of the most popular mushroom species in the world; however, mushrooms are highly susceptible to browning due to the absence of a protective cuticle layer and high respiration rate. The molecular mechanism underlying the process of mushroom browningneeds to be explored. Here, we analyzed the transcriptomic and metabolomic data from A. bisporusat ambient temperature. Specifically, a total of 263 significantly changed metabolites and 4492 differentially expressed genes were identified. Lipid metabolites associated with cell membrane degradation were predominantly up-regulated during ambient storage. Transcriptomic data further revealed the alterations of the expression of membrane lipid metabolism-related enzymes. Additionally, energy metabolic processes and products such as glycolysis and linoleic acid changed significantly during ambient storage, indicating their potential roles in the quality deterioration of A. bisporus. These findings provide new insights into the underlyingl ipidmetabolic mechanism of A. bisporus during postharvest ambient storage and will provide values for mushroom preservation techniques.

Limited research has been conducted on the metabolites present in the essential oils (EOs) of Phlomoides rotata (Benth. ex Hook. f.) Mathiesen (PR, syn. Lamiophlomis rotata (Benth.) Kudô), and their potential pharmacological activities, such as antioxidant properties, are often overlooked. We conducted a metabolomics-based screening to identify the characteristic metabolites (CMs) in the EOs extracted from PR. Meanwhile, we evaluated their in vitro antioxidant activities (AOAs). The EOs obtained through hydro-distillation are characterized by a light yellow color and a fresh, elegant fragrance. Cryoprecipitation was used to separate the crystals (Crs) from the EOs, resulting in the crystal-free EOs (CFs). A total of 121 components are identified and quantified in the EOs, Crs, and CFs. Among them, 84 were reported for the first time from such EOs. The major compounds include long-chain fatty acids (LCFAs) and their esters, such as palmitic acid (PA), myristic acid (MA), linoleic acid (LA), oleic acid (OA), stearic acid, and methyl palmitate (MP). Furthermore, 11 kinds of apocarotenoids (also called norisoprenoids) were first systematically investigated. Among them, eight C13-norisoprenoids, with trans-β-damascenone (DN) being particularly notable for its flavor, were identified. A sum of 11 CMs are screened , including PA, MA, LA, OA, MP, hexahydrofarnesyl acetone, phytol (PT), DN, stearic acid, linalool, and hexanal. These CMs are biosynthesized through FAs and 2-C-Methyl-D-erythritol 4-phosphate/1-Deoxy-D-xylulose 5-phosphate pathways. The in vitro AOAs of EOs, Crs, CFs, and seven selected CMs (PA, MA, LA, OA, MP, PT, and DN) were evaluated. Generally, PA and MA exhibited pro-oxidant activities (POAs) or weak AOAs. LA and OA demonstrated POAs or weak AOAs at lower concentrations, but at higher concentrations, they displayed medium to strong AOAs. Importantly, the CFs typically exhibited stronger AOAs compared to the corresponding EOs and Crs, potentially due to variations in their PA content. Overall, this study provides valuable insights into the potential utilization of EOs from PR.

Metabolites present in the hemolymph of honey bees play a crucial role in modulating the metamorphic process within the species. However, the precise alterations in metabolite composition, along with the associated variances and regulatory pathways implicated during the larvae-to-pupae metamorphosis of honey bees, remain incompletely elucidated. In this investigation, we gathered hemolymph samples from honey bee larvae at three distinct physiological stages-feeding, prepupal, and pupae and subjected them to metabolite analysis utilizing the liquid chromatography-mass spectrometry (LC-MS) technique. Employing principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA), we identified significant differential metabolites and conducted a metabolic pathway analysis on those differentially up-regulated during the prepupal and pupae stages. Notably, metabolites up-regulated in the hemolymph of prepupal stage larvae primarily governed glucose metabolism and fat digestion and absorption, while those in pupae stage larvae were involved in regulating chitin and lipopolysaccharide precursor formation, as well as the biosynthesis of phenylalanine, tyrosine, and tryptophan. These findings bear significant implications for advancing our comprehension of the metamorphic processes in honey bees.

Methylmercury (MeHg) intoxication is a global health concern. Although MeHg neurotoxicity is well-recognized, less is known about MeHg's effects on metabolism. In this study, we evaluated MeHg intoxication (20mg/L in drinking water for 20 days) effects on liver and epididymal white fat (EWF) in young ApoE knockout (ko) and wild-type mice. The former is well-known to show spontaneous dyslipidemia. Hg levels in hair, liver, and EWF were measured to assess the degree of MeHg exposure. We also evaluated body weight gain, plasma triglycerides, total cholesterol levels, and liver injury by assessing steatosis score, AST, ALT, SOD, and TBAR levels. To evaluate EWF, we analyzed mean wet weight and adipocyte diameter, plasma leptin levels and metabolomics. Hg levels were markedly higher among intoxicated mice. ApoE ko mice showed higher Hg in the hair but lower levels in the liver and EWF than wild-type controls. Among wild-type mice, MeHg compromised weight gain and increased liver TBAR levels compared to non-challenged controls. Among non-intoxicated mice, ApoE deficiency significantly increased triglyceride, total cholesterol, and liver transaminases with reduced EWF wet weight, hepatic SOD, and plasma leptin levels. MeHg accumulation together with ApoE deficiency elevated total cholesterol, triglycerides, hepatic transaminases, and TBARS. We found distinct EWF metabolite activity in different scenarios of ApoE deficiency and MeHg intoxication, highlighting increased cardiovascular risk especially when both challenges occur. Further studies are required to elucidate the underlying mechanisms involved in these effects and the target nutritional interventions in most need to ameliorate them.

As critical biocontrol agents, Trichoderma and Metarhizium have demonstrated vast potential in disease prevention and pest control respectively. Current applications, however, are predominantly confined to singular use or simplistic combinations of the two fungi. This study innovatively utilizes Metarhizium and Trichoderma as experimental subjects, employing non-targeted metabolomics to compare the differences in metabolites between co-culture and separate fermentation. The metabolite distinctions in co-culture are meticulously analyzed using sample correlation, least squares discriminant analysis, cluster analysis, and KEGG enrichment analysis. Metabolome sequencing analysis is then applied to compare the co-culture fermentation filtrate with Trichoderma atroviride and Metarhizium anisopliae. Differential metabolite analysis found that co-culture had significantly up-regulated or down-regulated metabolites compared to singular cultures.However,significant metabolite discrepancies are discovered in singular cultures, notably the up-regulated metabolites such as osthole and spirocyclic amine, which have documented antibacterial functions that may prove effective against Fusarium graminearum. Ultimately, the findings from this research contribute to the exploration of synergistic applications of biocontrol fungi and serve as a valuable reference for future development of bio-pesticides for disease and pest control.

Acute coronary syndrome (ACS) is a life-threatening condition that requires a prompt diagnosis and therapeutic intervention. Although serum troponin T and creatinine kinase-MB (CK-MB) are established biomarkers for ACS, it may take several hours to reach diagnostic values for ACS. In this study, we attempted to explore novel biomarkers for ACS with higher sensitivity than that of troponin T and CK-MB. The metabolomic profiles of 18 patients with ACS upon hospital arrival and those of the age-matched control (HC) group consisted of 24 healthy volunteers were analyzed using liquid chromatography-time-of-flight mass spectrometry. Volcano plots showed 24 metabolites whose concentrations differed significantly between the ACS and HC groups. Using these data, we developed a multiple logistic regression model for the ACS diagnosis, in which lysine, isocitrate, and tryptophan were selected as minimum-independent metabolites. The area under the receiver operating characteristic curve value for discriminating ACS from HC was 1.00 (95% confidence interval [CI]: 1.00-1.00). In contrast, those for troponin T and CK-MB were 0.917 (95% confidence interval [CI]: 0.812-1.00) and 0.988 (95% CI: 0.966-1.00), respectively. This study showed the potential of combining three plasma metabolites to discriminate ACS from HC with a higher sensitivity than that of troponin T and CK-MB.

Background: The pathophysiology of functional dyspepsia (FD) remains insufficiently understood, and the pain and economic constraints associated with endoscopic examinations hinder the precise definition and treatment of this disorder. Exploring the potential of multi-omics biomarkers for FD could yield promising targets for effectively diagnosing and treating this condition. Methods: We recruited 54 FD patients and 29 healthy volunteers and characterized their gut microbiota by shotgun metagenomic sequencing and their serum and urine metabolites by liquid chromatography-mass spectrometry (LC-MS). Results: We identified the changes in circulating metabolites associated with FD and linked to the gut microbial alterations. Among the differential circulating metabolites, we particularly highlighted the strong association of L-glutamate deficiency with the severity of FD symptoms and its strong predictive value for FD. Although no significant changes were noted in the gut microbial community structure of the FD samples, this might be attributed to symptom overlap between epigastric pain syndrome (EPS) and postprandial distress syndrome (PDS). However, significant alterations in the abundance of certain species were observed, including a substantial increase in the abundance of Streptococcus in the digestive tract of patients with FD. Finally, a cross-omics correlation network integrating metabolomic data with microbial community abundance was established, uncovering potential host-microbe-metabolite interactions. Conclusions: This work provides the first comprehensive description of the disrupted state of blood and urine metabolite composition and gut microbiota in patients with FD. These findings potentially offer promising targets for the diagnosis and treatment of this condition through a multi-omics approach, with particular emphasis on serum metabolomics.

This study investigates the effects of xylitol, a natural sugar alcohol, on tumor progression in syngeneic mouse cancer models. Xylitol has been known for its dental health benefits, but emerging evidence suggests broader biological roles, including potential anti-cancer properties. We explored xylitol's impact on two mouse cancer models: 4T1 mammary carcinoma and B16F10 melanoma. Xylitol's efficacy in inhibiting cancer cell lines and modulating tumor progression was assessed using immunocompetent female mice. The experiments involved intratumoral and peri-tumoral administration of a 20% xylitol solution in two mouse strains: BALB/c (4T1 mammary carcinoma) and C57BL/6 (B16F10 melanoma). Tumor volume, histopathology, and metabolomic analyses were conducted to gauge xylitol's influence. The study revealed that xylitol administration initially reduced tumor growth in the B16F10 melanoma model, accompanied by alterations in tumor metabolism. However, similar effects were not observed in the 4T1 mammary carcinoma model, and melanoma tumor growth re-commenced after stroma deterioration permitted xylitol solution leakage. These findings suggest that xylitol may have potential as an adjunct therapy in cancer treatment, specifically in melanoma. The differential response between the two cancer models underscores the complexity of cancer biology and the need for further investigation into xylitol's mechanisms of action and its role in cancer therapy.

Ovarian cancer is among the most common causes of female mortality. Despite improvements in diagnostic methods, non-specific symptoms and delayed gynecological exams can lead to late-stage ovarian tumor discovery. In this study, the effect of an anti-cancer compound, 3-amino-N-(3-chloro-2-methylphenyl)-5-oxo-5,6,7,8-tetrahydrothieno[2,3-b]quinoline-2-carboxamide (Compound 1) was examined. Cytotoxicity, apoptosis, and metabolomic changes in ovarian cancer cell lines SK-OV-3 and OVCAR-3, as well as glycosphingolipid (GSL) expression, both on cancer stem cells (CSCs), marked as CD49f+ and non-CSCs (CD49f-) were explored. Treatment with Compound 1 reduced the percentage of CSCs compared to non-treated cells (P < 0.001). The expression of eight GSLs on CSCs and non-CSCs was examined using flow cytometry. Both cell lines showed a change in the glycophenotype of the cells, either up or down of its expression, after the treatment. These findings raise the possibility of specifically targeting CSCs in ovarian cancer therapy. Additionally, treatment of Compound 1 resulted in a statistically significant increase in both early and late apoptosis (P<0.001) suggesting a pivotal role in initiating programmed cell death by the apoptotic pathway. The metabolic analysis revealed that the treated cancer cells showed reduced metabolic activity compared to the control group (P < 0.001)

High-density olive groves, despite their interesting production potential, have several limitations, also due to the high fruit load and the irrigation requirements.The study aimed to evaluate the effects of fruit load and deficit irrigation on oil yield and fruit quality, and on olive chemical composition in a high-density olive grove (cv Sikitita). Our main hypothesis was that the primary metabolism, as influenced by crop load and stress, could modify the accumulation of different phenolic classes.Different fruit loads were generated through flower thinning (66%, 50%, 33%, 0%) and two deficit irrigation treatments (-60%, -75%) were compared to the well-watered control (920 m3/ha).Thinning treatments had a limited effect on oil yield, on the other hand, deficit irrigation caused considerably less oil accumulation in the fruit on all sampling dates.Thinning 66% and deficit irrigation 75% were considered with the control for untargeted metabolomic analysis, considering three sampling dates. 233 different phenolic compounds were annotated. Multivariate HCA results indicated the impact of harvest time on the phenolic profile of olive fruits, yielding two separate clusters grouping t1 and t2 together and apart from t3. Regarding agronomic techniques, they played a differential role in the phenolic profile (supervised OPLS – DA). Fruit load mostly affected flavonoid glycosides. In contrast, the phenolic response to deficit irrigation is more heterogeneous, with phenolic acids (35%), flavonoids (25%), LMW, and other phenols (25%).

Glioblastoma is a highly malignant brain tumor consisting of heterogeneous cellular population. The transformed metabolism of glioblastoma cells supports their growth and division on the background of their milieu. One might hypothesize that the transformed metabolism of a primary glioblastoma could be well adapted to limitations in the variety and number of substrates imported into the brain parenchyma and present it their microenvironment. Additionally, the phenotypic heterogeneity of cancer cells could promote the variations among their metabolic capabilities regarding the utilization of available substrates and release of metabolic intermediates. With the aim to identify the putative metabolic footprint of different types of glioblastoma cells, we exploited the possibility for separation of polar and ionic molecules present in culture media or cell lysates by hydrophilic interaction liquid chromatography (HILIC). The mass spectrometry (MS) was then used to identify and quantify the eluted compounds. The introduced method allows the detection and quantification of more than 150 polar and ionic metabolites in single run, those may be present either in culture media or cell lysates and provide data for polaromic studies within metabolomics. The method was applied to analyze the culture media and cell lysates derived from two types of glioblastoma cells, T98G and U118. The analysis revealed that even the both types of glioblastoma cells share several common metabolic aspects, they also exhibit differences in their metabolic capability. This finding agrees with the hypothesis about metabolic heterogeneity of glioblastoma cells. Furthermore, the combination of both analytical methods, HILIC-MS, provides a valuable tool for metabolomic studies based on the simultaneous identification and quantification of a wide range of polar and ionic metabolites - polaromics.

Graft injury affects over 50% of liver transplant (LT) recipients, but non-invasive biomarkers to diagnose and guide treatment are currently limited. We aimed to develop a biomarker of graft injury by integrating serum metabolomic profiles with clinical variables. Serum from 55 LT recipients with biopsy confirmed metabolic-dysfunction associated steatohepatitis (MASH), T-cell mediated rejection (TCMR) and biliary complications was collected and processed using a combination of LC-MS/MS assay. The metabolomic profiles were integrated with clinical information using a multi-class Machine Learning (ML) classifier. The efficacy of the model was assessed through the evaluation of the Out-of-Bag (OOB) error estimate. Our ML model yielded an overall accuracy of 79.66% with an OOB estimate of the error rate at 19.75%. The model exhibited a maximum ability to distinguish MASH, with an OOB error estimate of 7.4% compared to 22.2% for biliary and 29.6% for TCMR. The metabolites serine and serotonin emerged as the topmost predictors. When predicting binary outcomes using 3 models: Biliary (biliary vs. rest), MASH (MASH vs. rest) and TCMR (TCMR vs. rest), the AUCs were 0.882, 0.972 and 0.96 respectively. Our ML tool integrating serum metabolites with clinical variables shows promise as a non-invasive, multi-class serum biomarker of graft pathology.

Exposure to ionizing radiation, accidental or intentional, may lead to delayed effects of acute radiation exposure (DEARE) that manifest as injury to organ systems including kidney, heart, and brain. This study examines the role of activated protein C (APC), a known mitigator of radiation-induced early toxicity, in long-term plasma metabolite and lipid panels that may be associated with DEARE. Male and female cohorts of C57BL/6N wild-type and APCHi transgenic mice were exposed to 9.5 Gy γ-rays with their hind-legs shielded to allow long-term survival that is necessary to monitor DEARE, and plasma was collected at 6 months for LC-MS based metabolomics and lipidomics. We observed significant dyslipidemia, indicative of inflammatory phenotype, upon radiation exposure. Additionally, observance of several other metabolic dysregulations was suggestive of gut damage, perturbations in TCA and urea cycles, and arginine metabolism. We also observed gender and genotype modulated metabolic perturbations post radiation exposure. The APCHi mice showed near normal abundance for several lipids. Moreover, restoration of plasma levels of some metabolites including amino acids, citric acid, and hypoxanthine in APCHi mice are indicative of APC-mediated protection from radiation injuries. With the help of these findings the role of APC in plasma molecular events after acute -radiation exposure in a gender-specific manner can be established for the first time.

Lung cancer is the leading cause of cancer related mortality worldwide. In order to improve its overall survival, early diagnosis is required. Since current screening methods still face some pitfalls, such as high false positive rates for low-dose computed tomography, researchers are still looking for early biomarkers to complement existing screening techniques in order to provide a safe, faster and more accurate diagnosis. Biomarkers are biological molecules found in body fluids, such as plasma, that can be used to diagnose a condition or disease. Metabolomics has already shown to be a powerful tool in the search for cancer biomarkers since cancer cells are characterised by impaired metabolism, resulting in an adapted plasma metabolite profile. The metabolite profile can be determined using nuclear magnetic resonance, or NMR. Although metabolomics and NMR metabolite profiling of blood plasma are still under investigation, there is already evidence for its potential for early-stage lung cancer diagnosis, therapy response, and follow-up monitoring. This review highlights some key breakthroughs in this research field, where the most significant biomarkers will be discussed in relation with their metabolic pathways and in light of the altered cancer metabolism.

The Australian tropical montane cloud forest (TMCF) is home to approximately 18 percent of the nation’s total vascular plant species. Over the past century, human activity and industrial development have caused global climate changes, posing a severe and irreversible danger to the entire land-based ecosystem, and WTWHA is no exception. The current average annual temperature of WTWHA in FNQ is 24 °C. However, in the coming years (by 2030), the average annual temperature increase is estimated to be between 0.5 and 1.4 °C compared to the climate observed between 1986 and 2005. Looking further ahead to 2070, the anticipated temperature rise is projected to be between 1.0 and 3.2 °C, with the exact range depending on future emissions. We identified 84 plant species endemic to the WTWHA in FNQ, which are already experiencing climate change threats. Few of these plants are used in herbal medicines. This study comprehensively reviewed metabolomics studies conducted on these 84 plant species until now toward understanding their physiological and metabolomics responses to global climate change. This review also discusses: i) recent developments in plant metabolomics studies that can be applied to study and understand the interactions of wet tropical plants with climatic stress, ii) medicinal plants and isolated phytochemicals with structural diversity, and iii) reported biological activities of crude extracts and isolated compounds.

Abstract: Patient blood samples are invaluable in clinical omics databases, yet current methodologies often fail to fully uncover the molecular mechanisms driving patient pathology. While Genome-scale Metabolic Models (GEMs) show promise in systems medicine by integrating various omics data, having only exometabolomic data remains a limiting factor. To address this gap, we introduce a comprehensive pipeline integrating GEMs with patient plasma metabolome. This pipeline constructs case-specific GEMs using literature-based and patient-specific metabolomic data. Novel computational methods, including adaptive sampling and an in-house developed algorithm for the rational exploration of the sampled space of solutions, enhance integration accuracy while improving computational performance. Model characterization involves task analysis in combination with clustering methods to identify critical cellular functions. The new pipeline was applied to a cohort of trauma patients to investigates shock-induced endotheliopathy using patient plasma metabolome data. By analyzing endothelial cell metabolism comprehensively, the pipeline identified critical substrates and contributed to the development of targeted therapeutic strategies. Our study demonstrates the efficacy of integrating patient plasma metabolome data into computational models to analyze endothelial cell metabolism in disease contexts. This approach offers a deeper understanding of metabolic dysregulations and provides insights into diseases with metabolic components and potential treatments.

A total of 473 metabolites were identified from 4 sour cherry genotypes using UPLC-TOF-MS. Untargeted metabolomics revealed the dominant chemical groups present in sour cherries. PCA showed that the diversity in sour-cherry metabolites was due to the genotype differences indicating iditol, malic acid, chlorobenzene, 2-mercaptobenzothiazole, and pyroglutamic acid as the predominant contributors. The variable importance in the projection (VIP > 1.0) in partial least-squares–discriminant analysis described 20 biomarker metabolites, representing the cherry metabolome profiles. A heatmap of Pearson’s correlation analysis between the 20 biomarker metabolites and antioxidant activities identified seven antioxidant determinants that displayed the highest correlations with different types of antioxidant activities. This study of correlating metabolomics and antioxidant activities elucidated that the higher nutritional value and biological functions of select sour cherry genotypes can be useful for the development of nutraceutical and functional foods.

Ischemic stroke is one of the leading causes of death and permanent disability in the world. Rapid diagnosis and intervention are crucial for reducing its consequences on individuals and societies. Identifying reliable biomarkers for early detection, prognostics and therapy is a criti-cal imperative for improving the stroke patient treatment. Metabolomics has been shown as a promising tool for biomarker discovery since many of the post-ischemic metabolites can found in the plasma or serum of the patient. In this research, we have performed comparative targeted metabolomic analysis of stroke thrombi, patient serums and healthy control serums in order to determine the alteration in the patients’ metabolome. The most statistically altered metabolites characterized in patient compared to control serums were glutamate and serotonin, followed by several lipid metabolites (phospholipids and triacylglycerols) and glucose. In stroke thrombi compared to patient’s serums, the most significantly altered metabolites were classified as li-pids, with choline-containing phospholipids and sphingomyelins having the highest discrimi-natory score. The results of this study could help in understanding the roles of different meta-bolic changes occurring during thrombosis and cerebral ischemia and possibly suggest new metabolic biomarkers of the ischemic stroke.

Plants can utilize the different forms of nitrogen (N), including inorganic and organic N nutrients, and show the great difference in the utilizing efficiency of N-form among species and genotypes within a species. In our previous study, we found that Tibetan wild barley (XZ16) was better in utilization of organic nitrogen in comparison with cultivated barley (Hua30). In this study, metabolite profiles of the two barley genotypes were comprehensively compared in their response to four N forms, including nitrate (NO3-), ammonium (NH4+), urea and glycine. Macro-and micro-nutrient concentrations in shoots were mostly found higher in nitrate and urea treatments than in ammonium and glycine in both the genotypes. XZ16 had higher concentrations of nutrient ions in glycine treatment, but Hua30 accumulated more nutrients in ammonium treatment. Among the total 163 differentially expressed metabolites, highest up-regulation and highest down-regulation was found in XZ16 in glycine and urea treatments respectively. Some important metabolites such as proline, glutamine, serine, asparagine, L-homoserine, aspartic acid, putrescine, ornithine, 4-aminobutyrate were up-regulated in glycine treatment in both the genotypes with higher fold change in XZ16 than in Hua30. Similarly, fructose-6-PO4, aconitic acid and isocitrate were only up-regulated in XZ16 in glycine treatment. Here, we concluded that the genotype XZ16 exhibited higher response to glycine treatment, while Hua30 showed higher response to NH4+ treatment which is attributed to their better utilization of glycine-N and NH4+-N, respectively. .

Chronic kidney disease (CKD) affects approximately 12% of the global population posing a significant health threat. Inflammation plays a crucial role in the uremic phenotype of CKD contributing to elevated cardiovascular and overall mortality in affected individuals. This study aimed to explore novel metabolic pathways in non-dialysis dependent stage 5 CKD patients using semitargeted metabolomics. In a prospective observational design involving 50 patients, blood samples collected before the initial hemodialysis session underwent liquid chromatography and high resolution mass spectrometer analysis. Univariate (Mann-Whitney test) and multivariate (logistic regression with LASSO regularization) methods identified metabolomic variables associated with inflammation. Notably, adenosine-5’-phosphosulfate (APS), dimethylglycine, pyruvate, lactate, and 2-ketobutyric acid exhibited significant differences in the presence of inflammation. Cholic acid, homogentisic acid, and 2-phenylpropionic acid displayed opposing patterns. Multivariate analysis indicated increased inflammation risk with certain metabolites (N-Butyrylglycine, dimethylglycine, 2-Oxoisopentanoic acid, and pyruvate), while others (homogentisic acid, 2-Phenylpropionic acid, and 2-Methylglutaric acid) suggested decreased probability. These findings unveil potential inflammation-associated biomarkers related to defective mitochondrial fatty acid beta oxidation and branched-chain amino acid breakdown in CKD, shedding light on cellular energy production and offering insights for further clinical validation.

Prolonged ethanol (EtOH) consumption is associated with male infertility with a decreased spermatogenesis rate as one cause. Defective maturation and development of sperm during their storage in the cauda epididymis and transit in the seminal vesicle can be another cause, possibly occurring before the drastic spermatogenesis disruption. Herein, we demonstrated that the cauda epididymis and seminal vesicle of rats, orally fed with EtOH under a regimen that spermatogenesis was still ongoing, showed histological damage, including lesion and decreased height of the epithelial cells, and increased collagen fibers in the muscle layer, which implicated fibrosis. Lipid peroxidation (shown by malondialdehyde (MDA) levels) was observed, indicating that reactive oxygen species (ROS) was produced along with acetaldehyde during EtOH metabolism by CYP2E1. MDA, acetaldehyde and other lipid peroxidation products could further damage cellular components of the cauda epididymis and seminal vesicle and this was supported by increased apoptosis (shown by TUNEL assay and caspase 9/caspase 3 expression) in these two tissues of EtOH-treated rats. Consequently, functionality of the cauda epididymis and seminal vesicle in EtOH-treated rats was impaired, as demonstrated by decreases in 1H NMR-analyzed metabolites (e.g., carnitine, fructose), which were important for sperm development, metabolism and survival in their lumen.

Thymomas (TH) are a unique group of heterogeneous tumors of the thymic epithelium. In particular, the subtypes B2 and B3 tend to be aggressive and metastatic. Radical tumor resection remains the only curative option for localized tumors, while more advanced TH require multimodal treatment. Deep sequencing analyses have failed to identify known oncogenic driver mutations in TH, with the notable exception of the GTF2I mutation, which occurs predominantly in type A and AB TH. However, there are multiple alternative non-mutational mechanisms (e.g., perturbed thymic developmental programs, metabolism, non-coding RNA networks) that control cellular behavior and tumorigenesis through deregulation of critical molecular pathways. Here, we attempted to show how the results of studies investigating such alternative mechanisms could be integrated into a current model of TH biology. This model could be used to focus ongoing research and therapeutic strategies.

Metabolites are at the end of the gene-transcript-protein-metabolism cascade. As such, metabo-lomics is the omic approach that offers the most direct correlation with phenotype. This allows that, where genomics, transcriptomics and proteomics fail to explain a trait, metabolomics might give an answer. Complex phenotypes, which are determined by the influence of multiple small effect alleles, are an example of these situations. Consequently, the interest in metabolomics has increased ex-ponentially in the last years. As a newer discipline, the metabolomics bioinformatics analysis pipe-lines are not as standardized as in the other omic approaches. In this review we synthesized the different steps that need to be carried out to obtain biological insight from the annotated metabolite abundance raw data. These steps were grouped in three different modules: preprocessing, statistical analyses and metabolic pathway enrichment. We included within each one of them the different state-of-the art procedures and tools that can be used depending on the characteristics of the study, providing details about the characteristics of each method has, as well as the issues the reader might encounter. Finally, we introduce genome scale metabolic modeling as a tool for obtaining pseu-do-metabolomic data in situations where its acquisition is difficult, being possible to analyze the resulting data with the modules of the described workflow.

Lactobacilli are considered an inexhaustible source of potentially bioactive substances; indeed, several products from their metabolism are known to have immunomodulatory and anti-inflammatory activity. Recently, we demonstrated that cell-free supernatants (CFS) obtained from Lactobacillus (L.) acidophilus, L. plantarum, L. rhamnosus and L. reuteri can impair Candida pathogenic potential in an in vitro model of epithelial vaginal infection. This effect could be ascribed to a direct effect of living lactobacilli on Candida virulence and to the production of metabolites which are able to impair fungal virulence. In the present work, stemming from those data, we deepened our knowledge on the CFS from these 4 lactobacilli by performing a metabolomic analysis to better characterize their composition. By using an untargeted metabolomic approach, we detected consistent differences in the metabolites produced by these four different lactobacilli. Interestingly, L. rhamnosus showed the most peculiar metabolic profile. Specifically, after a hierarchical clustering analysis in positive and negative ionization mode, L. rhamnosus showed a specific area of significant overexpressed metabolites that strongly differed from the same area in other lactobacilli. In this area, inosine was identified among the overexpressed metabolites of L. rhamnosus. This molecule has been described to have antioxidant, anti-inflammatory, anti-infective and neuroprotective properties. The biological significance of its overproduction by L. rhamnosus might be important in its probiotic and/or postbiotic activity.

Salmonella Typhimurium infection in pigs is characterized by an intense inflammatory response in early infection which seems to dysregulate host physiology including the gut microbiota. Both, changes in host physiology and microbiome composition, must entail modifications within the gut environment. This study analyzes the gut metabolome in early infected pigs (48 hours after infection) and non-infected controls by untargeted metabolomics (LC–QTOF MS/MS and GC–TOF MS), supported with microbiome data (16S rRNA abundance and prediction functional analyses). The metabolomic profile in Salmonella-infected pigs differed from healthy controls in 39 of these metabolites, including eight amino acids, four bile acids and carboxylic acids, three carnitines and sugar derivates, eleven fatty acids and six other compounds. Changes in amino acids abundance and the observed decrease of proteolytic bacteria such as Lactobacillus or Bacteroides could favor the niche colonization by Desulfovibrionaceae. In addition, the decrease in short chain fatty acids and tricarboxylic acids cycle was correlated to a decrease in beneficial bacteria in infected pigs. Interestingly, we observed an increase of bile acids concentration and compounds such as succinic acid or pantothenic acid, which may boost the inflammatory response. Altogether, the results reveal how S. Typhimurium infection alters the gut microbiome composition and prompts changes in the metabolism with a potential interaction between intestinal metabolism and microbiota abundance.

Chrysanthemum tea, a typical health tea with the same origin as medicine and food, is famous for its unique health benefits and flavor. To clarify the influence of metabolites of different varieties of chrysanthemum tea on the formation of taste and quality differences, nontargeted metabolomics combined with electronic tongue analysis were used to characterize the correlation between metabolites profiles and taste characteristics of different quality chrysanthemum tea. Thirteen metabolites were identified as the key metabolites of the sensory quality difference between Huangju and Jinsi Huangju tea. Kaempferol, luteolin, genistein, and some quinic acid derivatives were correlated with the ‘astringent’ and taste attributes. In contrast, l-(-)-3 phenyllactic acid and L-malic acid were found to be the ‘bitterness’ and ‘umami’ in chrysanthemum tea. KEGG pathway enrichment analysis showed that the flavonoid and flavonol biosynthesis pathway had important effects on the sensory quality of chrysanthemum tea.

Metastatic castration-resistant prostate cancer (mCRPC) remains a lethal disease due to the absence of effective therapies. A more comprehensive understanding of molecular events, encompassing the dysregulation of microRNAs (miRs) and metabolic reprogramming, holds the potential to unveil precise mechanisms underlying mCRPC. This study aims to assess the expression of selected serum exosomal miRs (miR-15a, miR-16, miR-19a-3p, miR-21, and miR-141a-3p) alongside serum metabolomic profiling and their correlation in patients with mCRPC and benign prostate hyperplasia (BPH). Blood serum samples from mCRPC patients (n=51) and BPH patients (n=48) underwent metabolome analysis through 1H-NMR spectroscopy. The expression levels of serum exosomal miRs in mCRPC and BPH patients were evaluated using quantitative real-time polymerase chain reaction (qRT‒PCR). The 1H-NMR metabolomics analysis revealed significant alterations in lactate, acetate, citrate, 3-hydroxybutyrate, and branched-chain amino acids (BCAAs, including valine, leucine, and isoleucine) in mCRPC patients compared to BPH patients. MiR-15a, miR-16, miR-19a-3p, and miR-21 exhibited a down-regulation of more than twofold in the mCRPC group. Significant correlations were predominantly observed between lactate, citrate, acetate, and miR-15a, miR-16, miR-19a-3p, and miR-21. The importance of integrating metabolome analysis of serum with selected serum exosomal miRs in mCRPC patients has been confirmed, suggesting their potential utility as clinical diagnostic markers.

Background: Although previous studies have implicated a role for the stool microbiome in cancer cachexia, the fecal microbiome has not been previously characterized for patients with pancreatic ductal adenocarcinoma (PDAC) and cachexia treated with nutritional interventions such as enteral feeding. Methods: The PANCAX-1 (NCT02400398) prospective trial enrolled 31 cachectic advanced PDAC patients to receive jejunal tube peptide-based diet for 12 weeks who were planned for palliative chemotherapy. Out of 16 evaluable patients, 62.5% receiving enteral feeding met the primary endpoint of weight stability at 12 weeks. As part of an exploratory analysis of the PANCAX-1 trial, serial stool and blood samples were collected at 0 (C1D1), 6 (C2D1), and 12 (C3D1) weeks over the 12-week period of enteral feeding. Stool samples were analyzed using 16S v4 sequencing of the microbiome. Up to 219 plasma metabolites were analyzed by mass spectrometry and high-performance liquid chromatography. Results: A total of 29 stool samples were prospectively collected from 16 subjects with PDAC enrolled in PANCAX-1 who were evaluable for weight stability. Over 12 weeks of enteral feeding, statistically significant increases in the abundance of bacterial genera such as Veillonella (p=0.0150) and Actinomyces (p=0.0390) were observed, while there was a lower abundance of Bacteroides (p=0.0150) and Butyricicoccus (p=0.0390). Greater abundance of Veillonella and reduced Bifidobacterium at baseline were linked to greater weight stability. Plasma metabolomics in 10 subjects showed that weight unstable patients had significantly decreased levels of essential (L-histidine, L-phenylalanine) and non-essential amino acids (L-citrulline, L-tyrosine, all p<0.05) at the end of 12 weeks of enteral feeding. High stool Veillonella abundance was significantly associated with increases in the nucleotide 2-deoxycytidine 5-diphosphate and essential amino acid L-isoleucine but decreased TCA cycle metabolite alpha-ketoglutarate (all p<0.05). Conclusions: We are the first to demonstrate the feasibility of stool microbiome profiling and plasma metabolomics in paired stool and plasma samples from a prospective cohort of advanced PDAC patients on enteral feeding as their primary source of nutrition. Our findings are hypothesis-generating in that metabolites unique to weight stability and abundance of stool bacterial genera may inform future studies of anti-cachexia therapies involving enteral feeding or microbial modulation.

Polygonatum cyrtonema Hua. is an important medicinal and edible food in China and the traditional processing method of nine-steaming and nine-drying has been used to process its rhizome. However, the global dynamic changes in secondary metabolites during the processing and whether this method could enhance the accumulation of functional components remain unclear. This study aimed to explore the processing-induced mechanisms involved in the accumulation of secondary metabolites and provide theoretical support for the pharmacological study on P. cyrtonema. Results showed the first 6 processing cycles induced drastic changes in the accumulation of secondary metabolites, while the last 3 did not induce further changes. The accumulation of most secondary metabolites significantly increased after the first 3 cycles and stabilized after 6 cycles. The first 3 cycles led to numerous newly added metabolites while the last 6–9 cycles led to a small number of disappeared metabolites. Processing enhanced the biosynthesis of various secondary metabolites and significantly affected the metabolisms of amino acids. Together, a short period of processing was helpful for enhancing the biosynthesis of secondary metabolites. However, the enhancing effects will be reversed or weakened under continuous processing. The processing cycles should be reduced to 3–6 to maintain the enhancing effects.

Intrauterine growth restriction (IUGR) pigs are characterized by long-term growth failure, metabolic disorders, and intestinal microbiota imbalance. The characteristics of the negative effects of IUGR at different swine growth stages are still unclear. Therefore, this study explored whether intrauterine growth restriction (IUGR) model damaged the intestinal barrier function and altered the colonization and metabolic profiles of the colonic microbiota in growing-finishing pigs by the multi-omics method. Seventy-two piglets (36 IUGR and 36 NBW) were selected for this trial to analyze physiological and plasma biochemical parameters, oxidative damage, and inflammatory response in the colon. Moreover, the colonic microbial communities were examined using 16s rRNA sequencing and metabolomics to reveal the intestinal characteristics of pigs at different growth stages (25, 50, and 100 kg). IUGR altered the plasma concentrations of glucose, total protein triglyceride, and cholesterol. Colonic tight junction proteins were markedly inhibited by IUGR. IUGR decreased plasma T-AOC, SOD, and GSH levels, and colonic SOD-1, SOD-2, and GPX4 expressions by restraining the Nrf2/Keap1 signaling pathway. Moreover, IUGR increased the colonic IL-1β and TNF-α levels while reducing IL-10, possibly activating the TLR4-NF-κB/ERK pathways. Notably, IUGR pigs had lower colonic Streptococcus abundance and Firmicutes-to-Bacteroidetes ratio at the 25 kg BW stage while having higher Firmicutes abundance at the 100 kg BW stage; moreover, IUGR pigs had lower SCFAs concentrations. Metabolomics analysis showed that IUGR increased colonic lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic concentrations and enriched three differential metabolic pathways, including linoleic acid, sphingolipid, and purine metabolisms throughout the trial. Collectively, IUGR altered the nutrient metabolism, redox status, and colonic microbial community and metabolite profiles of pigs and continued to disrupt colonic barrier function by reducing antioxidant capacity via the Nrf2/Keap1 pathway and activating inflammation via the TLR4-NF-κB/ERK pathway during the growing-finishing stage. Colonic Firmicutes and Streptococcus could be potential regulatory targets for modulating the metabolism and health of IUGR pigs.

This study investigated whether metabolomic fingerprints of bovine embryo growth media improve the prediction of successful embryo implantation. In this prospective cohort study, the metabolome from in vitro produced Day 7 blastocysts with successful implantation (n=11), blas-tocysts with failed implantation (n=10), and plain culture media without embryos (n=5) was in-cluded. Samples were analyzed using AbsoluteIDQ® p180 Targeted Metabolomics Kit with LC-MS/MS, and a total of 189 metabolites were analyzed from each sample. Blastocysts that re-sulted in successful embryo implantation had significantly higher levels of methionine sulfoxide (p<0.001), DOPA (p<0.05), spermidine (p<0.001), acetylcarnitine to free carnitine ratio (p<0.05), C2+C3 to free carnitine ratio (p<0.05), and lower levels of threonine (nep<0.001) and phosphati-dylcholine PC ae C30:0 (p<0.001) compared to control media. However, when compared to embryos that failed to implant, only DOPA, spermidine, C2/C0, (C2+C3)/C0 and PC ae C30:0 levels differentiated significantly. In summary, our study identifies a panel of differential metabolites in the culture media of bovine blastocysts that could act as potential biomarkers for the selection of viable blastocysts before embryo transfer.

Long Covid or post-acute sequelae of SARS-CoV-2 infection (PASC) can manifest as long-term symptoms in multiple organ systems, including respiratory, cardiovascular, neurological, and metabolic systems. In patients with severe COVID-19, immune dysregulation is significant, and the relationship between metabolic regulation and immune response is of great interest in determining the pathophysiological mechanisms. We aimed to characterize the metabolomic footprint for recovering severe COVID-19 patients in three consecutive time points and compare metabolite levels to controls. Our findings add proof of dysregulated amino acid metabolism in the acute phase, and dyslipidemia, glycoprotein level alterations, and energy metabolism disturbances in severe COVID-19 patients 3-4 months post hospitalization.

Hydrogen sulfide (H2S) is an environmental toxicant of health concern. The brain is a major target in acute H2S poisoning. This study was to test the hypothesis that acute and subchronic ambient H2S exposures alter the brain metabolome. Male 7-8 week-old C57BL/6J mice were exposed by whole-body inhalation to 1000 ppm H2S for 45 min and euthanized at 5 min or 72 h for acute exposure. For subchronic study, mice were exposed to 5 ppm H2S 2 h/day, 5 days/week for 5 weeks. The brainstem was removed for metabolomic analysis. Enrichment analysis showed the metabolomic profiles in acute and subchronic H2S exposures matched with those of cerebral spinal fluid from patients with seizures or Alzheimer’s disease. Acute H2S exposure decreased excitatory neurotransmitters, aspartate and glutamate, while the inhibitory neurotransmitter, serotonin, was increased, which may explain H2S-induced loss of consciousness. Branched-chain amino acids and glucose were increased by acute H2S exposure. Subchronic H2S exposure within OSHA guideline surprisingly decreased serotonin altering central nervous system. In subchronic H2S exposure, glucose was decreased while polyunsaturated fatty acids, inosine, and hypoxanthine were increased. Collectively, these results provide important mechanistic clues of acute and subchronic ambient H2S poisonings and show that H2S alters brainstem metabolome.

Background: Estrogen homeostasis is crucial for bladder function, and estrogen deprivation resulting from ovarian removal or ovarian dysfunction may lead to various bladder dysfunctions. However, the specific mechanisms are not fully understood. Methods: We simulated estrogen deprivation using a rat ovariectomy model and supplemented estrogen through subcutaneous injections. The metabolic characteristics of bladder tissue were analyzed using non-targeted metabolomics, followed by bioinformatics analysis to preliminarily reveal the association between estrogen deprivation and bladder function. Results: We successfully established a rat model with estrogen deprivation and, through multivariate analysis and validation, identified several promising biomarkers represented by 3, 5-tetradecadiencarnitine, lysoPC (15:0), and cortisol. Furthermore, we explored estrogen deprivation-related metabolic changes in the bladder primarily characterized by amino acid metabolism imbalance. Conclusions: This study, for the first time, depicted the metabolic profile of bladder resulting from estrogen deprivation, providing an important experimental basis for future research on bladder dysfunctions caused by estrogen deprivation.

Background: Physiological changes of blood amino acids and acylcarnitines during healthy child development are not well studied. The LIFE Child study offers a platform with a large cohort of healthy children to investigate these dynamics. We aimed to assess the intra-person variability of these blood metabolites and associations with anthropometric parameters related to excess body fat and IGF1 serum levels. Methods: Concentrations of 23 amino acids, 5 acylcarnitines and free carnitine of 2213 children aged between 3 months and 19 years were analyzed using liquid chromatography/tandem mass spectrometry. Standard deviation score values were used to account for physiological sex- and age-related differences. The stability of metabolites was assessed through the coefficient of determination. Associations with parameters for body composition and IGF1 serum levels were determined by Pearson correlation and linear regression. Results: Our research reveals substantial fluctuations in metabolite concentrations in the same person during childhood and adolescence. Most metabolites had a positive correlation with parameters of body composition with notable influence of sex, pubertal status and weight group specific differences. Glycine exhibited negative associations with parameters of body fat distribution especially in normal weight girls, overweight/obese boys and during puberty. Conclusions: The observed alterations in metabolite concentrations contribute to our knowledge on the complex interplay between blood amino acid and acylcarnitine levels and metabolic health in children and adolescents.

Osteoarthritis (OA) is a pathology of great impact worldwide which its physiopathology is not completely known and usually diagnosed by imaging techniques performed at advanced stages of the disease. The aim of this study was to evaluate early serum metabolome changes and identify the main metabolites involved in an inflammatory OA animal model. The study was performed with thirty rats, OA in all animals was induced by intra-articular injection of monoiodoacetate into the knee joint. Blood samples were taken from all animals and analyzed by mass spectrometry before OA induction, and 28, 56 and 84 days following induction. Histological study confirmed OA in all samples. The results of this study allow the identification of several changes in the serum metabolome over time, including organic acids, benzenoids, heterocyclic compounds and lipids at T28, organic acids at T56 and lipid classes at T84. We conclude that OA induces serological changes in the metabolome and, more specifically, 18 metabolites which could serve as potential biomarkers. However, it was not possible to establish a relationship between the identified metabolites and the time at which the samples were taken. Therefore, these findings should be confirmed in future OA studies.

Plants have developed unique mechanisms to cope with the harsh environmental conditions to compensate for their lack of mobility. A key part of their coping mechanisms is the synthesis of secondary metabolites. In addition to their role in plants’ defense against pathogens, they also possess therapeutic properties against diseases, and their use by humans predates written history. Viruses are a unique class of submicroscopic agents, incapable of independent existence outside a living host. Pathogenic viruses continue to pose a significant threat on global health, leading to unprecedented fatalities on a yearly basis. The use of medicinal plants as a natural source for an-tiviral agents has been widely reported in literature in the past decades. Metabolomics is a powerful research tool for the identification of plant metabolites with antiviral potentials and can be used to isolate compounds with antiviral activities in plants and study the biosynthetic pathways involved in viral disease progression. This review discusses the use of medicinal plants as antiviral agents, with a special focus on the metabolomics evidence supporting their efficacy. Additionally, suggestions are made for the optimization of various metabolomics methods for characterizing the bio-active compounds in plants and subsequent understanding of the mechanism of their operation.

Microbial competition within plant tissues affects invading pathogens' fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierce's disease (PD) in grapevines, secretes various virulence factors including cell wall degrading enzymes, adhesion proteins, and quorum sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. LC-MS and MAGI were used to detect and map metabolites to genomes revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of a functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-Aminoisobutyric acid and Gibberellic Acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.

Microbial community succession in raw milk determines its quality and storage period. In this study, carbon dioxide (CO2) at 2000 ppm was used to treat raw milk to investigate the mechanism of extending the shelf life of raw milk by CO2 treatment from the viewpoint of microbial colonies and metabolites. The results showed that the shelf life of CO2-treated raw milk was extended to 16 days at 4 ℃, while that of the control raw milk was only 6 days. Microbiomics analysis identified 221 Amplicon Sequence Variants (ASVs) in raw milk, and the alpha diversity of microbial communities increased (P < 0.05) with the extension of storage time. Among them, Pseudomonas, Actinobacteria and Serratia were the major microbial genus responsible for the deterioration of raw milk, with a percentage of 85.7%. A combined metagenomics and metabolomics analysis revealed that microorganisms altered the levels of metabolites, such as pyruvic acid, glutamic acid, 5'- cmp, arginine, 2-propenoic acid, and phenylalanine in the raw milk through metabolic activities, such as ABC transporters, pyrimidine metabolism, arginine and proline metabolism and phenylalanine metabolism, and reduced the shelf life of the raw milk. CO2 treatment prolonged the shelf life of the raw milk by inhibiting the abundance of Gram-negative aerobic bacteria, such as Acinetobacter guillouiae, Pseudomonas fluorescens, Serratia liquefaciens and Pseudomonas simiae.

Hypoxic-ischemic encephalopathy (HIE) is one of the most common causes of childhood disability. Hypothermic therapy is currently the only approved neuroprotective approach. However, early diagnosis of HIE can be challenging, especially in the first hours after birth when the decision to treat with hypothermic therapy is critical. Differentiating HIE from other neonatal conditions, such as sepsis, further complicates the diagnosis. This study investigated the utility of a metabolomic-based approach using the NeoBase 2 MSMS kit to diagnose HIE using dry blood stains in a Rice-Vannucci model of HIE in rats. We evaluated the diagnostic accuracy of this method between 3 and 6 hours after the onset of HIE, including in the context of systemic inflammation and concomitant hypothermic therapy. Discriminant analysis revealed several metabolite patterns associated with HIE. A logistic regression model using glycine levels achieved high diagnostic accuracy with areas under the curve (AUC) of 0.94 at 3 hours and 0.96 at 6 hours after the onset of HIE. In addition, orthogonal partial least squares discriminant analysis, which included five metabolites, achieved 100% sensitivity and 80% specificity within 3 hours of HIE. These results highlight the significant potential of the NeoBase 2 MSMS kit for the early diagnosis of HIE and could improve patient management and outcomes in this serious illness.

The latest life-origin literature is reviewed, along with grouping and classification of the most enduring models of abiogenesis. New trends are identified in origin-of-life thought. Astrobiology continues to deal mostly with inorganic and very elementary organic reactions in extreme environments. Nonequilibrium thermodynamics has received a great deal of attention. Attempts have been made to relate Bejan’s Constructal Law to life and abiogenesis. RNA World preclusions only seem to have grown, while ribozyme/peptide models have expanded. The biosemiotic movement and code biology is gaining influence in refining a more complete description of life. Prof James Tour at Rice University in a fourteen-lecture series lists a number of synthetic biochemical hurtles remaining that still need to be overcome. But the need for some sort of informational recipe, instruction, steering and control now seems to be the most prominent area of focus and concern. Even a protometabolism needed active selection and controls rather than mere constraints or law. The latest literature still does not elucidate how protometabolism was orchestrated in an inanimate, pre-evolutionary environment.

Model animals are employed in experiments as substitutes for human tissues and fluids, particularly when accessing particular human samples (such as cerebrospinal fluid, brain, ocular tissues, etc.) poses significant challenges or is ethically constrained. Nonhuman primates are frequently regarded as superior animal models for investigating human ophthalmological diseases. However, despite this recognition, the metabolomic composition of ocular tissues in non-human primates remains predominantly unexplored. In this work, we present a dataset on metabolite concentrations in serum and ocular tissues, including aqueous humor (AH), vitreous humor (VH), and lens, in two Macaque species: crab-eating macaque (Macaca fascicularis) and rhesus macaque (Macaca mulatta). A total of 99 compounds were quantified in 45 samples, shedding light on the previously unknown metabolomic profiles of primate eye tissues.

Hypsizygus marmoreus has become one of the most popular edible mushrooms due to its high nu-tritional and economic value. Previous researchers found that Serratia odorifera could promote the growth of H. marmoreus by producing and secreting some of its inducers. However, the specific mechanism of action was still unclear. In this study, we found that exogenous addition of sterile fermentation filtrate (HZSO-1), quorum sensing (QS signaling molecules, 3-oxo-C6-HSL, cy-clo(Pro-Leu), and cyclo(Tyr-Leu) could significantly promote the growth of H. marmoreus, increase the number of clamp junctions, and the diameter of mycelium (P < 0.05). In addition, non-targeted metabolomic analysis has revealed that 706 metabolites were detected in the treated group. Of these, 307 metabolites were significantly different (P < 0.05). Compared with the control, 54 and 86 metabolites were significantly increased and decreased in the HZSO-1 group, respec-tively (P < 0.05). We speculated that the sterile fermentation filtrate of S. odorifera could mediate the carbohydrate and amino acid metabolism of H. marmoreus by influencing the pentose phosphate pathway (PPP) to increase the energy supply for the growth and development of the mycelium. The above results will further reveal the growth-promoting mechanism of S. odorifera on H. mar-moreus.

Benign Paroxysmal Positional Vertigo (BPPV) represents the most frequent cause of peripheral vertigo. In most cases it is successfully treated by canalith repositioning procedure (CRP), but it is often followed by a continuous lightheadedness in absence of vertigo or nystagmus (residual dizziness, RD). Our aim is to describe the clinical effectiveness and the urine metabolomics profile treating these patients by a polyphenol compound supplementation. We enrolled 30 patients reporting RD after BPPV successfully treated using CRP. A supplementation with a Polyphenol compound was administered for 60 days, and patients were evaluated after 30 and 60 days of treatment by a self-administered questionnaires (Visual Analog Scales for Dizziness and Nausea, Dizziness Handicap Inventory, DHI) and by urine metabolomics analysis performed by 1H-NMR spectroscopy and multivariate followed by univariate analysis. Most patients reported an excellent or good efficacy of RD with a significant decrease for VAS and DHI values. The metabolomics analysis identified six significant metabolites related to the treatment: 1-methylnicotinamide, anserine, Hippurate, lysine, methyl succinate, and urea indicating an inflammatory activities and antioxidant properties of the polyphenol compound. These preliminary data suggest that supplementation with a polyphenol compound cold induces some metabolic changes that can help recover RD. However, the future steps will require confirmation with a more significant cohort of patients and an extension of the metabolomic evaluation to other problems concerning the different clinical aspects of BPPV, such as the high relapse found in a high percentage of patients.

Ionizing radiation exposure is known to induce molecular and cellular injury, inflicting a cascade of potentially catastrophic events leading to tissue and organ damage. Metabolomic analysis allows for the identification and quantification of small molecules downstream of genomic changes induced by radiation exposure. We aimed to characterize metabolomic changes that underscore the prefinal stage of lethally irradiated rhesus nonhuman primates (NHPs). Peripheral blood was drawn at baseline, post-exposure as well as at the preterminal stage of NHPs (immediately prior to death in moribund NHPs), which did not survive exposure with 7.2 Gy total-body radiation (LD70/60). Herein, we analyzed global metabolomic changes using ultra-performance liquid chromatography (UPLC) quadrupole time-of-flight mass spectrometry (QTOF-MS) in plasma samples of NHPs collected at various timepoints in relation to irradiation. The overall goal was to identify metabolic shifts present immediately prior to death. Our findings, for the first time, show that radiation induced significant time dependent metabolic perturbations when compared to pre-irradiation samples, particularly in the glycerophospholipid metabolism and steroid hormone biosynthesis and metabolism pathways. These findings provide valuable insights for identifying biomarkers for lethality, which may be helpful for triage during a mass casualty scenario.

China Xihu Longjing tea famous for its good flavor and quality. However, the related metabolites information except flavonoids is largely deficient. Different processing methods of China Xihu Longjing tea fixing both by machine at first and second step(A1), first step by machine and second step by hand(A2), first step by hand and second step by machine(A3), both by hand at first and second step (A4) were compared using a UHPLC-QE-MS-based metabolomics approach. Liquid chromatography-mass spectrometry was used to analyze the metabolic profiles of the processed samples. A total of 490 metabolites (3 alkaloids, 3 anthracenes, 15 benzene and substituted derivatives, 2 benzopyrans, 13 coumarins and derivatives, 128 flavonoids, 4 furanoid lignans, 16 glycosides and derivatives, 5 indoles and derivatives, 18 isocoumarins and derivatives, 4 chalcones and dihydrochalcones, 4 naphthopyrans, 3 nucleosides, 78 organic acids and derivatives, 55 organooxygen compounds, 5 phenols, 109 prenol lipids, 3 saccharolipids, 3 steroids and steroid derivatives, 17 tannins) were identified. The different metabolism profiles were distinguished using PCA and OPLS-DA. There were differences in the types and contents of metabolites, especially flavonoids, furanoid lignans, glycosides and derivatives, organic acids and derivatives and organooxygen compounds. There was a positive correlation between flavonoid metabolism and amino acid metabolism. However, there was a negative correlation between flavonoid metabolism and amino acid metabolism, which had the same trend as prenol lipids metabolism, tannin.This study provides new valuable information for regarding differences in the metabolite profile of China Xihu Longjing tea processed based on machine fixing and manual fixing methods.

For Lentinula edodes, its characteristic flavor is the key determinant for consumer pref-erences. However, the tissue-specific volatile flavor variations of the fruiting body have been overlooked. Here, we comprehensively investigated volatile flavor profiles of different tissues including the pileus skin, context, gill and stipe of the fruiting body of two widely cultivated L. edodes strains (T2 and 0912). We show that the eight-carbon and sulfur com-pounds, which represented 43.2-78.0% and 1.4-42.9% to the total volatile emissions for strain 0912 and T2, dominated their volatiles profiles. The sulfur compounds could rep-resent 32.2% and 42.9% to the total volatile emissions for the context of the strain 0912 and T2, respectively, whereas only represented 1.4% for the stipes of the strain 0912 and 9.0% for the skin of strain T2. Proportions of the predominant C8 compounds (1-Octen-3-one, 1-Octen-3-ol and 3-Octanone) and sulfur compounds (Lenthionine, 1,2,4-Trithiolane, Di-methyl disulfide and Dimethyl trisurfide) changed depending on tissues and strains. We further reveal that the overall volatile flavor profiles varied greatly in different tissues and strains. With machine learning algorithm, we show that volatile profiles could 100% pre-dict strains 0912 and T2. The prediction accuracy for different tissues could also reach 100%. Our results highlight the tissue-specific volatile flavor variations of the L. edodes fruiting body.

As research into the relationship between the gut microbiome and health continues to evolve, probiotics are garnering increasing interest among consumers. Fermentation is rec-ognized as an efficacious biotechnology for augmenting the nutritional and functional at-tributes of foods. In this study, the ameliorative effects of Lycium barbarum L. lyophilized powder fermented with Lactobacillus plantarum NXU0011 (LP+Ly) on dextran sodium sul-fate (DSS)-induced ulcerative colitis (UC) in mice were investigated employing immuno-histochemistry, qRT-PCR, macrogenomics, and metabolomics. The results revealed that LP+Ly intervention significantly ameliorated histopathological inflammation in the ulcer-ated colon, diminished the expression of inflammatory markers such as IL-6, P-STAT3, and miR-214, and enhanced the diversity of intestinal flora in the mouse model group. Moreover, there was an increase in abundance of beneficial bacteria, including Lactobacillus, Prevotella, and Akkermansia. Metabolomic analysis indicated that 15 metabolites, including citrulline, D-xylose, and α-ketoisovaleric acid, exhibited significant variations following LP+Ly inter-vention. The metabolic pathways that displayed substantial differences included tryptophan biosynthesis, arginine biosynthesis, and amino sugar and nucleotide sugar metabolism. By modulating arginine biosynthesis, LP+Ly effectively improved the intestinal inflammatory state, thus mitigating the effects of UC.

Major depressive disorder (MDD) is a serious mental illness with a heavy social burden, but its underlying molecular mechanisms remain unclear. Mass spectrometry (MS)-based metabolomics is providing new insights into the heterogeneous pathophysiology, diagnosis, treatment, and prognosis of MDD by revealing multi-parametric biomarker signatures at the metabolite level. In this comprehensive review, recent developments of MS-based metabolomics in MDD research are summarized from the perspective of analytical platforms (liquid chromatography-MS, gas chromatography-MS, supercritical fluid chromatography-MS, etc.), strategies (untargeted, targeted, and pseudotargeted metabolomics), key metabolite changes (monoamine neurotransmitters, amino acids, lipids, etc.), and antidepressant treatments (both western and traditional Chinese medicines). Depression sub-phenotypes, comorbid depression, and multi-omics approaches are also highlighted to stimulate further advances in MS-based metabolomics in the field of MDD research.

Drought stress is a major abiotic factor affecting tomato production and fruit quality. However, the genes and metabolites associated with tomato responses to water deficiency and rehydration are poorly characterized. To identify the functional genes and key metabolic pathways underlying tomato responses to drought stress and recovery, drought-susceptible and drought-tolerant inbred lines underwent transcriptomic and metabolomic analyses. A total of 332 drought-responsive and 491 rehydration-responsive core genes were robustly differentially expressed in both genotypes. The drought-responsive and rehydration-responsive genes were mainly related to photosynthesis–antenna proteins, nitrogen metabolism, plant–pathogen interactions, and the MAPK signaling pathway. Various transcription factors, including homeobox-leucine zipper protein ATHB-12, NAC transcription factor 29, and heat stress transcription factor A-6b-like, may be vital for tomato responses to the water status. Moreover, 24,30-dihydroxy-12(13)-enolupinol, caffeoyl hawthorn acid, adenosine 5′-monophosphate, and guanosine were the key metabolites identified in both genotypes under drought and recovery conditions. The combined transcriptomic and metabolomic analysis highlighted the importance of 38 genes involved in metabolic pathways, biosynthesis of secondary metabolites, biosynthesis of amino acids, and ABC transporters for tomato responses to water stress. Our results provide valuable clues regarding the molecular basis of drought tolerance and rehydration. The data presented herein may be relevant for genetically improving tomato to enhance drought tolerance.

(1) Background: The typical transporter protein, P-glycoprotein (P-gp), has been proven to be associated with multidrug resistance (MDR). Pyxinol and 24S-Pyxinol amino acid ester derivatives had been demonstrated to be promising P-gp inhibitors for reversal of tumor MDR in KBV cells, however, their roles in MDR reversal in other tumor-resistant cells are still unclear. (2) Methods: In the present study, we synthesized 40 amino acid ester derivatives of Pyxinol and 24S-Pyxinol. The MDR reversal effects of these derivatives were evaluated in A549/Tax, MCF-7/ADR, and HCT-8/VCR cells using the CCK-8 assay. Subsequently, western blot assay, intracellular Rhodamine123 (Rh123) accumulation assay and P-gp ATPase activity assay were utilized to investigate the effects of active compound on P-gp. Molecular docking was used to predict the possible binding patterns of active compound to P-gp. Moreover, based on UPLC-Q/TOF-MS cellular metabolomics technology to identify endogenous differential metabolites and metabolic pathways associated with tumor MDR effects of the active compound. (3) Results: The results of the CCK-8 assay showed that compounds 8, 14, 16, 17, 18, 23, 25, 34, 36, 37 exhibited strong MDR reversal effect in A549/Tax, MCF-7/ADR and HCT-8/VCR cells, which were screened by reversal fold (RF) greater than 5. Among them, 10 μM of derivative 37 (new compound) showed the outstanding activity (RF: 15.31) in reversing MDR in A549/Tax cells. Compound 37 could act as a substrate for P-gp and inhibit the efflux function of P-gp by competitively binding to the binding site of antitumor drugs. Meanwhile, the molecular docking results confirmed that compound 37 was identified to under-go high-affinity binding to the drug binding site of P-gp. In addition, 14 endogenous differential metabolites and 6 metabolic pathways involved closely associated with the reversal of tumor MDR effects of compound 37 were identified. (4) Conclusions: Overall, a new candidate compound 37 (24S-3-L-threonyl-Pyxinol) could be provided for reversing tumor MDR by this study.

To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using the pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid content, as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes enrichment analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, a comprehensive regulatory network encompassing genes that contribute to metabolisms of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlies fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples.

Background: Atherosclerosis (AS) is a chronic progressive disease caused by lipometabolic disorder. However, the pathological characteristics and mechanism of AS have not been fully clarified. By high fat and cholesterol diet induction, Tibetan minipig could be developed to the AS model animal which had a very similar pathogenesis to human AS. Methods: Here, we built the AS model of Tibetan minipigs and identified the differential abundance metabolites in the development of AS based on untargeted metabolomics. Results: We found that the sphingolipid metabolism and glucose oxidation were enriched in the AS group and the phenylalanine metabolism was reduced in the AS group. Moreover, in the development of AS, gluconolactone was enriched in the late stage of AS whereas biopterin was enriched in the early stage of AS. Conclusion: Gluconolactone and biopterin could be potential biomarkers for indicating the development of AS. Our research provides novel clues for the metabolic mechanism of AS from the perspective of metabolomics.

Coptisine (Cop) exerts a neuroprotective effect in central nervous system disease, particularly ischemic stroke. However, its protective mechanism is still unclear. This study aimed to investigate the protective effect of Cop on cerebral ischemia-reperfusion (IR) rats with a middle cerebral artery occlusion model by integrating a gas chromatography-mass spectrometry (GC-MS) based metabolomics approach with biochemical assessment. Our results showed that Cop could improve neurobehavioral function and decrease the ischemia size in IR rats. In addition, Cop was found to decrease inflammatory mediators (e.g., prostaglandin D2 (PGD2) and tumor necrosis factor-α (TNF-α) and attenuate oxidative stress response (e.g., increase the superoxide dismutase (SOD) expression and decrease 8-iso-PGF2α level). Furthermore, GC-MS based cerebrospinal fluid (CSF) metabolomics analysis indicated that Cop influenced the level of glycine, 2,3,4-trihydroxybutyric acid, oleic acid, glycerol, and ribose during IR injury. Cop exhibited a good neuroprotective effect against cerebral IR injury and metabolic alterations which might be mediated through its antioxidant and anti-inflammatory property.

Over the last several decades, China has continuously introduced Duroc boars and used them as breeding boars. Although this crossbreeding method has increased pork production, it has affected pork quality. Nowadays, one of the primary goals of industrial breeding and production systems is to enhance the quality of meat. This research adds to our understanding of the molecular mechanisms that control the quality of pork and may be used as a guide for future efforts to enhance meat quality. We investigated the genetic mechanisms of cross-breeding for meat quality improvement by combining transcriptome and metabolome analysis, using Chinese native Jiaxing black (JXB) pigs and crossbred Duroc × Duroc × Berkshire × JXB (DDBJ) pigs. In the longissimus Dorsi muscle, the content of inosinic acid, polyunsaturated fatty acid, and amino acids was considerably higher in JXB pigs in contrast with that of DDBJ pigs, whereas DDBJ pigs have remarkably greater levels of polyunsaturated fatty acids than JXB pigs. Differentially expressed genes (DEGs) and differential metabolites were identified using transcriptomic and metabolomic KEGG enrichment analyses. Differential metabolites mainly include amino acids, fatty acids, phospholipids. In addition, we found several DEGs that may explain differences in meat quality between the two pig types, including genes associated with lipid metabolism (e.g., DGKA, LIPG, and LPINI), fatty acid metabolism (e.g., ELOVL5, ELOVL4, and ACAT2), and amino acid metabolism (e.g., SLC7A2, SLC7A4). Combined with the DEGS-enriched signaling pathways, the regulatory mechanisms related to amino acids, fatty acids, and phospholipids were mapped. The abundant metabolic pathways and DEGs may provide insight into the specific molecular mechanism that regulates meat quality. Optimizing the composition of fatty acids, phospholipids, amino acids, and other compounds in pork is conducive to improving meat quality. Overall, these findings will give useful information and further groundwork for enhancing the meat quality that may be achieved via hybrid breeding.

Embryo quality evaluation during in vitro development is vital for the success of assisted reproductive technologies (ART). However, the subjective morphological assessment by embryologists may result in inconsistencies that affect the selection of the best embryo for transfer. To provide a more comprehensive evaluation of embryo quality, we performed the integration of embryo metabolomics with standardized morphokinetic classification. The culture medium of 55 embryos (from 21 couples undergoing ICSI) was collected at two timepoints (day 3 and 5). Samples were split into Good (n=29), Lagging (n=19) and Bad (n=10) according to embryo morphokinetic evaluation. Embryo metabolic performance was assessed by 1H-NMR, monitoring the variation of specific metabolites (pyruvate, lactate, alanine, glutamine, acetate, formate). Adjusted metabolite differentials were observed during the first three days of culture and found to be discriminative of embryo quality at the end of day 5. Pyruvate, alanine, glutamine, and acetate were major contributors to this discrimination. Good and Lagging embryos were found to export and accumulate pyruvate and glutamine in the 3 first days of culture, while Bad embryos consumed them. This suggests that Bad embryos have a less active metabolism than Good and Lagging embryos and these two metabolites as putative biomarkers for embryo quality. This study provides a more comprehensive evaluation of embryo quality and can lead to improvements in ART by enabling the selection of the best embryos. By combining morphological assessment and metabolomics, the selection of high-quality embryos with the potential to result in successful pregnancies may become more accurate and consistent.

Vitamin E, a potent antioxidant, is a necessary and complex micronutrient for cows. During the transition period, vitamin E deficiency (VED) is among the highest prevalent micronutrient deficits in dairy cows. It may eventually result in oxidative stress and immunological malfunction, and it increases the risk of peripartum disorders. At present, detailed data on blood metabolites in VED cows are limited. Consequently, the purpose of this research was to examine the alterations in the serum metabolic profile of VED cows throughout the early postpartum period. Using comprehensive 1H nuclear magnetic resonance (1H NMR), the alterations in serum metabolic activities of VED cows were analyzed. In total, 28 multiparous Holstein cows were assigned according to serum α-tocopherol (α-Toc) concentrations into a normal (α-Toc ≥ 4 μg/mL, n = 14) and VED (α-Toc &lt; 3 μg/mL, n = 14) groups at 21 days postpartum, and their blood samples were collected for biochemical and 1H NMR analyses. A t-test on independent samples as well as multivariate statistics were used to assess the findings. In comparison with normal cows, VED cows showed significantly worse body condition scores, milk yield, and dry matter intake (p &lt; 0.05). Significantly higher levels of serum non-esterified fatty acids, aspartate aminotransferase, low-density lipoprotein, and malonaldehyde were found in VED-affected cows, as well as lesser concentrations of serum albumin, high-density lipoprotein, and total antioxidant capacity in comparison with normal cows (p &lt; 0.01), while other vitamins and minerals concentrations showed no distinction between the groups (p &gt; 0.05). Furthermore, 24 upregulated serum metabolites were identified under VED conditions. The metabolomics pathway analysis of these metabolites demonstrated that a global metabolic response to VED in cows was represented by changes in 11 metabolic pathways, comprising energy, carbohydrate, and amino acid metabolism. These outcomes suggest that VED cows were more likely to experience a negative energy balance characterized by alterations of common systemic metabolic processes and develop oxidative stress, inflammation, and ultimately liver injury. This study provides the first evidence of metabolic changes in cows with VED.

The COVID-19 pandemic has raised questions about indirect impact in pregnant women on the development of their future children. Investigating the characteristics of lipid metabolism in the "mother-placenta-fetus" system can give information about the pathophysiology of COVID-19 infection during pregnancy. 234 women were included in study. Maternal plasma, cord blood, amniotic fluid lipidome were analyzed using HPLC-MS/MS. Differences in lipid profile were searched by Manna-Whitney and Kruskall-Wallis test, diagnostic model based on logistic regres-sion were bilt by AIC. Elevation levels of lysophospholipids, triglycerides, sphingomyelins, and oxidized lipids was registered in patients’ after COVID-19 maternal and cord plasma. An increase in maternal plasma sphingomyelins and oxidized lipids was observed in cases of infection during the second trimester. In amniotic fluid, compared to the control group, nine lipids are reduced, six lipids are elevated. Levels of phosphoglycerides, lysophosphoglycerides, and phosphatidylinosi-tols decreased during infection in the second and third trimesters of pregnancy. Newborn’s health diagnostic model based on maternal plasma were developed for each group and exhibit good di-agnostic value (AUC> 0.85). Maternal and cord plasma’s lipidome changes during delivery, asso-ciated with Covid-19 infection during pregnancy, are synergistic. The most significant disturbances occur with infections in the second trimester of pregnancy.

Background: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex and debilitating disease with a significant global prevalence of over 65 million individuals. It affects various systems, including the immune, neurological, gastrointestinal, and circulatory systems. Studies have shown abnormalities in immune cell types, increased inflammatory cytokines, and brain abnormalities. Further research is needed to identify consistent biomarkers and develop targeted therapies. A multidisciplinary approach is essential for diagnosing, treating, and managing this complex disease. The current study aims at employing explainable artificial intelligence (XAI) and machine learning (ML) techniques to identify discriminative metabolites for ME/CFS. Material and Methods: The present study used a metabolomics dataset of CFS patients and healthy controls, including 26 healthy controls and 26 ME/CFS patients aged 22-72. The dataset encapsulated 768 metabolites, classified into nine metabolic super-pathways: amino acids, carbohydrates, cofactors, vitamins, energy, lipids, nucleotides, peptides, and xenobiotics. Random forest-based feature selection and Bayesian Approach based-hyperparameter optimization were implemented on the target data. Four different ML algorithms [Gaussian Naive Bayes (GNB), Gradient Boosting Classifier (GBC), Logistic regression (LR) and Random Forest Classifier (RFC)] were used to classify individuals as ME/CFS patients and healthy individuals. XAI approaches were applied to clinically explain the prediction decisions of the optimum model. Performance evaluation was performed using the indices of accuracy, precision, recall, F1 score, Brier score, and AUC. Results: The metabolomics of C-glycosyltryptophan, oleoylcholine, cortisone, and 3-hydroxydecanoate were determined to be crucial for ME/CFS diagnosis. The RFC learning model outperformed GNB, GBC, and LR in ME/CFS prediction using the 1000 iteration bootstrapping method, achieving 98% accuracy, precision, recall, F1 score, 0.01 Brier score, and 99% AUC. Conclusion: RFC model proposed in this study correctly classified and evaluated ME/CFS patients through the selected biomarker candidate metabolites. The methodology combining ML and XAI can provide a clear interpretation of risk estimation for ME/CFS, helping physicians intuitively understand the impact of key metabolomics features in the model.

Background: This study aimed to assess the relationship between age-related changes in Neuro-filament Light Chain (NFL), a marker of neuronal function, and various factors including muscle function, body composition, and metabolomic markers. Methods: The study included 40 partici-pants, aged 20 to 85 years. NFL levels were measured, and muscle function, body composition, and metabolomic markers were assessed. Results: NFL levels increased significantly with age, particularly in men. Negative correlations were found between NFL levels and measures of mus-cle function, such as grip strength, walking speed, and chair test performance, indicating a decline in muscle performance with increasing NFL. These associations were more pronounced in men. NFL levels also negatively correlated with muscle quality in men, as measured by 50 kHz phase angle. In terms of body composition, NFL was positively correlated with markers of fat mass and negatively correlated with markers of muscle mass, predominantly in men. Metabolomic analy-sis revealed significant associations between NFL levels and specific metabolites, with gen-der-dependent relationships observed. Conclusions: This study provides insights into the rela-tionship between circulating serum NFL, muscle function, and aging. The findings highlight gen-der differences and contribute to our understanding of age-related changes in neuronal function and their impact on muscle health.

Breast cancer (BC) is the most common malignancy and the second cause of cancer specific death in women from high-income countries. More than 70% of all breast cancer are hormone receptor-positive BC, and elevated estrogen circulating in blood has been proved to be a strong risk for BC development. This is due to its contribution to enhance proliferation of cancerous cells, angiogenesis and metastasis stimulation and therapy resistance. The estrogen (E) metabolism–gut microbiome axis is functional with underlying individual variations in E levels. It is reasonable that the estrobolome (bacterial genes whose products are capable of metabolizing E) could contribute to the risk of hormone-driven malignancies including BC and may serve as a potential biomarker and target. Gut microbial β -glucuronidase (GUS) enzymes have been suggested to be involved in the estrobolome. Furthermore, bacterial GUS enzymes within the gastrointestinal tract have been postulated to contribute to hormone breast cancer. In this review, we discuss the recent knowledge about the role of GUS enzyme in the pathogenesis of breast cancer. We focus on the role of GUS in (i)-the microbioma and estrogen metabolism, (ii) diet, estrobolome, and the BC development, (iii) other activities of the bacterial β-glucuronidase, and (iv) the new molecular target for BC therapeutic application.

The global prevalence of insulin resistance (IR) is increasing continuously, influencing metabolic parameters and fertility as well. The metabolic changes due to IR can alter the molecular composition of plasma and other body fluids. Follicular fluid (FF) is derived mainly from plasma, and it is a critical microenvironment for the developing oocytes. It contains various metabolites and amino acids, and the quality of the oocytes is linked at least partially to amino acid metabolism. Our goal was to determine quantitatively the amino acid (AA) profile of FF in IVF patients and to compare IR and non-insulin resistance (NIR) groups to investigate the AA changes in their FF. By UHPLC-based method we quantified the main 20 amino acids from human FF samples in the IR and NIR groups. Several amino acids (aspartate, glycine, glutamate, and cysteine) differed significantly (p&lt;0.05 or less) between the two groups. The most significant alterations between the IR and NIR groups were related to the glutathione metabolic pathway involving glycine, serine, and threonine. Since insulin resistance alters the amino acid composition of the FF, the oocytes may undergo metabolism-induced changes resulting in poor oocyte quality and less fertility in the insulin resistance groups.

Although numerous citrus varieties have recently been developed to enhance their quality, information on their quality characteristics is limited. We assessed the quality characteristics of Yellowball, a novel citrus variety, by evaluating its appearance, storability, sensory properties, functionality, and metabolite profiles and comparing these characteristics with those of its parent varieties: Haruka and Kiyomi. The metabolite profiles between the citrus varieties differed significantly, resulting in distinct physicochemical and functional qualities. The storability of Yellowball was significantly increased compared with that of its parent varieties owing to its strong antifungal activity and unique peel morphology, including the stoma and albedo layers. While we did not investigate the volatile compounds, overall functional activities, and detailed characteristics of each metabolite, our data provide valuable insights into the relationship between citrus metabolites, peel morphology, physicochemical properties, and storability and demonstrate the potential of Yellowball as a promising variety in the citrus industry.

The advancement of mass spectrometry technologies has revolutionised plant metabolomics research by enabling the acquisition of raw metabolomics data. However, the identification, analysis, and visualisation of these data require specialised tools. Existing solutions lack a dedicated plant-specific metabolite database and pose usability challenges. To address these limitations, we developed PlantMetSuite, a web-based tool for comprehensive metabolomics analysis and visualisation. PlantMetSuite encompasses interactive bioinformatics tools and databases specifically tailored for plant metabolomics data, facilitating upstream-to-downstream analysis in metabolomics and supporting integrative multi-omics investigations. PlantMetSuite can be accessed directly through a user's browser without the need for installation or programming skills. The tool is freely available at https://plantmetsuite.verygenome.com/ and will undergo regular updates and expansions to incorporate additional libraries and newly published metabolomics analysis methods. The tool's significance lies in empowering researchers with an accessible and customisable platform for unlocking plant metabolomics insights.

Plasma-activated water (PAW) is an emerging and promising green technology in the agriculture sector during recent years. The aim of this study was to examine the influence of the spraying of PAW and amino acid fertilizer concentrations on the physiological, biochemical and phytochemical characteristics of German chamomile varieties under field conditions. Method: The experiment was performed during 2020–2021 as a factorial using a randomized complete block design with three replications, in an arid and warm region. The factors contained five fertilizer levels (0 (control), 1, 2, 3 ml·L−1 amino acid and PAW) and three German chamomile cultivars Bona, Bodegold, Lianka). Physiological, biochemical and phytochemical traits such as plant height, fresh and dried flower weight, chlorophyll a, b, carotenoids, CHN elements, C:N ratio, total protein, amino acid profile, essential oil yield, apigenin content and major secondary metabolites were examined. Results: The ANOVA indicated that the impact of the cultivar and fertilizer was significant on all physiological, biochemical and phytochemical studied parameters. The amino acid fertilizer and PAW enhanced physiological features, hydrogen, C:N ratio, essential oil yield, apigenin content and main phytochemical compositions like chamazulene and α-bisabolol, but it had no incremental effect on the carbon, nitrogen, and total protein percentage. Conclusion: Findings revealed that the application of foliar amino acid fertilizer and PAW treatments improves physiological, biochemical and phytochemical parameters in German chamomile cultivars under field conditions.

The seasonal variation in fatty acids and minerals concentrations was investigated through the analysis of Pecorino Romano cheese samples collected in January, April, and June. A fraction of samples contained missing values in their fatty acid profile. Probabilistic Principal component analysis coupled with Linear Discriminant Analysis was employed to classify cheese samples on a production season basis while accounting for missing data and quantifying the missing Fatty acids concentration for the sample in which they were absent. The levels of rumenic acid, vac-cenic acid and omega-3 compounds were positively correlated with the spring season, while the length of the saturated fatty acids increased throughout the production seasons. Concerning the classification performances, the optimal number of principal components (i.e., 5) achieved an ac-curacy in cross-validation equal to 98 %. Then, when the model was tasked to impute the lacking Fatty acid concentration values, the optimal number of principal components resulted in an R2 value in cross-validation of 99.53%

Bibliometric studies on inherited metabolic diseases(IMDs) didn't exist in the literature.Our research aims to conduct a bibliometric study to determine the current status,trending topics,and missing points of publications on IMDs.Between 1968-2023, we conducted a literature search with keyword "inherited metabolic disease" in the SCOPUS-database.We included research articles in medicine written in English,published in the final section.We created our data pool using VoSviewer, SciMAT, and Rstudio software programs for bibliometric parameters of the articles that met the inclusion criteria.We performed bibliometric analysis of the data with R-package "bibliometrix" and BibExcel programs.We included 2702 research articles published on IMDs.Top three countries that have written the most articles in this field are; USA(n= 501), United Kingdom(n=182), and China(n= 172).The most preferred keywords by the authors were;newborn screening(n=54), mutation(n=43), phenylketonuria(n=42), children(n=35), genetics(n= 34) and maple syrup urine disease(n=32).Trending topics were osteoporosis, computed tomography, bone marrow transplantation in the early years of the study, chronic kidney disease, urea cycle disorders, next-generation sequencing, newborn screening, and familial hypercholesterolemia in the final years of the study. This study provides clinicians with a new perspective showing that molecular and genetic studies in inherited metabolic diseases will play an essential role in diagnosis and treatment in the future.

Turmeric, Curcuma longa L., is a type of medicinal plant characterized by its perennial nature and rhizomatous growth. It is a member of the Zingiberaceae family and is distributed across the world’s tropical and subtropical climates, especially in South Asia. Its rhizomes are highly valued for food supplements, spices, flavoring agents, and yellow dye in South Asia since ancient times. It exhibits a diverse array of therapeutic qualities that encompass its ability to combat diabetes, reduce inflammation, act as an antioxidant, exhibit anticancer properties, and promote anti-aging effects. In this study, organic extracts of C. longa rhizomes were subjected to HPLC separation followed by mass spectrometry analysis. The Global Natural Product Social Molecular Networking (GNPS) approach was utilized for the first time in this ethnobotanically important species to conduct an in-depth analysis of its metabolomes based on their fragments. A total of 30 metabolites including 16 diarylheptanoids, 1 diarylpentanoid, 3 bisabolocurcumin ethers, 4 sesquiterpenoids, 4 cinnamic acid derivatives, and 2 fatty acid derivatives were identified. Among 16 diarylheptanoids identified in this study, five of them are reported for the first time in this species.

Metabolomics is an advanced technology, still under development, with multiple research applications, especially in the field of health. Individual metabolic profiles, the functionality of the body, as well as its interaction with the environment can be established using this technology. The body's response to various external factors, including the food consumed and the nutrients it contains, has increased researchers' interest in nutrimetabolomics. Establishing correlations between diet and the occurrence of various diseases or even the development of personalized nutrition plans, could contribute to advances in precision medicine. The interdependence between humans, animals and the environment are of particular importance today, with the dramatic emergence and spread of zoonotic diseases, food, water and soil contamination, and the degradation of resources and habitats. All these events have led to an increase of risk factors for functional diseases, burdening global health. Thus, this study aimed to highlight the importance of metabolomics, in particular of nutrimetabolomics, as a technical solution for a holistic, collaborative, and precise approach for the advancement of the One Health strategy.

Panax ginseng C. A. Meyer (P. ginseng), has been widely used in traditional Chinese medicine (TCM). It contains a number of chemical components and possesses a variety of pharmacological activities. Alzheimer's disease (AD) is neurodegenerative disease that creates a huge burden on the lives and health of individuals. In recent years, studies have indicated that the chemical components of P. ginseng, especially ginsenosides, play a pronounced positive role in the prevention and treatment of neurological diseases. This review aimed to summarize currently studies on chemical components and the mechanisms action in AD intervention treatment of P. ginseng, especially ginsenosides. In this review, the components of P. ginseng and their respective active effects were first introduced. Then the key molecular mechanisms and signaling pathways of P. ginseng were introduced, and its different active ingredients in the prevention and treatment of Alzheimer's disease-related pathogenesis were also summarized from the pathogenesis of AD Aβ generation and aggregation, hyperphosphorylation of tau protein，oxidant stress，neuroinflammation，mitochondrial damage，disorder of neurotransmitter and gut microbiota. Signaling pathway networks related to the action of ginseng active ingredients was constructed, which could serve as a therapeutic target for Alzheimer's disease. In addition to a detailed report on P. ginseng in improving Alzheimer's disease-related pathogenesis, the application of the current technology, spatial metabonomics in AD therapeutics and diagnostics were later discussed. Spatial metabonomics could be applied to investigate the multi-target intervention of P. ginseng on Alzheimer's disease. Research perspectives for the study of P. ginseng in the treatment of Alzheimer's disease were provided for further studies.

(1) Background: Inflammatory bowel diseases (IBD) involve complex interactions between genetic factors, aberrant immune activation, and gut microbial dysbiosis. While metabolomic studies have focused on feces and serum, fewer investigations have examined the intestinal mucosa despite its crucial role in metabolite absorption and transport. The current study aimed to identify novel mucosal metabolic pathways that are altered during chronic colitis and to determine microbial contributions to such changes. (2) Methods: The chronic Dextran sulfate sodium (DSS) colitis was induced for five weeks in 7-9-week-old wild-type C57BL/6J male mice followed by microbial profiling with targeted 16srRNA sequencing service. Mucosal metabolite measurements were performed by Metabolon (Morrisville, NC). The data were analyzed using the bioinformatic tools Pathview, MetOrigin, and Metaboanalyst. (3) Results: Our novel findings demonstrated increases in several host- and mi-crobe-derived purine, pyrimidine, endocannabinoid, and ceramide metabolites in colitis. Origin analysis revealed microbial-related tryptophan metabolites kynurenine, anthranilate, 5-hydroxyindoleacetate, and C-glycosyltryptophan were significantly increased in colon mucosa during chronic inflammation and strongly correlated with disease activity. (4) Conclusions: These findings offer new insights into the pathophysiology of IBD and provide novel potential targets for microbial-based therapeutics.

Graviera is a very popular yellow hard cheese produced in mainland Greece and the Aegean islands, and in three PDO (Protected Denomination of Origin) locations. Apart from geographic location, milk type and production practices are also factors that affect cheese composition, and make this dairy product unique in taste and aroma. In this work, 1H NMR spectroscopy in combination with chemometrics has been used to determine the metabolite profile (40 compounds) of graviera cheese produced in different geographic locations, with emphasis on cheeses produced on the island of Crete. Organic acids and amino acids were the main components quantified in the polar cheese fraction, while the fatty acid composition of the lipid fraction was also obtained. Analysis of Variance (Anova) of the dataset showed that γ-aminobutyric acid (GABA), conjugated linoleic acids (CLA) and linoleic acid differentiate gravieras produced in different areas of Crete, and that total amino acid content was higher in cheeses produced in eastern Crete. Targeted Discriminant Analysis models classified gravieras produced in mainland Greece, Cyclades and Crete based on differences in 1,2-diglycerides, sterols, GABA and fatty acid composition. Targeted and untargeted OPLS-DA models were capable of differentiating between gravieras produced in the island of Crete and hold promise as the basis for the authentication of PDO graviera products.

Cathodic protection is widely used to protect metal structures from corrosion and is commonly applied on marine structures in seaports using sacrificial galvanic anodes. These anodes, either in Zinc, or preferen-tially nowadays in Al-Zn-In alloys, are expected to corrode instead of the metal to be protected. This leads to the release of specific dissolved species, Zn2+, Al3+, In3+ and solid phases like Al(OH)3. Few studies were conducted on the effects of anodes on marine organisms and concluded that further detailed investiga-tions are needed in controlled environments. We therefore propose an experimental approach to evaluate the effects of Zn and Al-Zn-In anodes on oysters stabulated in tanks, under conditions approaching those used in the ports. We chose a non-targeted metabolomic approach, using UHPLC coupled to HRMS, to study the effects on the entire metabolome, without any a priori. A modelling study of the chemical species, corresponding to the deg-radation products of the anodes, likely to be present near the exposed oysters, was also included. We identified 16 and 2 metabolites modulated by Zn- and Al-Zn-In-anodes respectively, involved in bi-ological functions, such as energy metabolism, osmoregulation, oxidative stress, lipid, nucleotide nucle-oside and amino acid metabolisms, defense and signaling pathways.