Search Results (1,608)

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

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

Plant–microbe interactions can modulate the production of bioactive compounds involved in plant growth-promoting activity. This study investigates the metabolic reprogramming of the actinomycete model strain Streptomyces coelicolor M145 during co-cultivation with Citrus aurantium and Citrus limon seeds, used as defined plant-derived chemical inputs, under contrasting nutritional conditions with or without L-tryptophan (Trp) supplementation. Untargeted metabolome profiling revealed medium- and Citrus seed-dependent metabolic shifts in co-cultures compared with corresponding Citrus seed and S. coelicolor single cultures used as controls. Under R2YE production conditions, co-cultivation with C. limon resulted in 27 extracellular metabolites, compared with 11 detected in the TSB vegetative medium; similar trends were observed for C. aurantium. Multivariate analyses confirmed that growth medium, Citrus species, and Trp significantly shaped S. coelicolor extracellular metabolic profiles, mainly in quantitative terms. Production conditions, particularly with Trp supplementation, promoted metabolites associated with antimicrobial activity and iron acquisition, whereas vegetative conditions promoted primary metabolism and biotransformation of Citrus-derived compounds. Spent medium bioassays on Solanum lycopersicum showed that these metabolic differences were correlated with distinct biological responses. Overall, these findings demonstrate that defined plant-derived inputs modulate S. coelicolor specialized metabolism in a context-dependent manner, generating metabolomic signatures associated with differential plant growth responses compared to single cultures. Full article

Anhua Qianliang tea, a traditionally crafted dark tea, is highly prized for its unique sensory properties that develop and improve during long-term aging. To elucidate the material basis driving the quality transformation of Anhua Qianliang tea during prolonged storage, samples aged for 2 to 25 years were investigated using physicochemical analysis, untargeted metabolomics, and sensory evaluation. Prolonged storage reduced total polyphenols, free amino acids, and most catechins, whereas alkaloids remained relatively stable. Phenylpropanoids and polyketides, organic acids and derivatives, and lipids and lipid-like molecules were the main metabolite classes contributing to storage-stage discrimination, accompanied by extensive remodeling of flavonoid, phenylpropanoid, amino acid-related, and central carbon metabolism. Sensory evolution was closely associated with coordinated changes in catechins, polyphenols, phenolic acids, amino acid-related compounds, and storage-responsive metabolites. These insights significantly deepen the understanding of dark tea maturation and offer new perspectives for scientific evaluation and industrial standardization. Full article

Production system may affect meat quality and muscle metabolic characteristics in Tibetan sheep. In this study, the biceps femoris muscles of twelve 3-year-old Tibetan sheep with similar body weights were used as experimental materials during a 6-month experimental period. The housed group (n = 6) was defined as the control group (C group), whereas the grazing group (n = 6) was defined as the L group. Meat quality measurement, nutritional composition analysis, untargeted lipidomics, and amino acid metabolomics (AAM) were integrated to investigate the effects of contrasting grazing and house-feeding production systems on meat quality and metabolic characteristics in Tibetan sheep. The results showed that cooking loss and drip loss were significantly decreased, whereas water-holding capacity (WHC) was significantly increased in the L group. However, shear force was also increased, indicating that grazing and house-feeding systems were associated with differences in muscle WHC and shear force. The L group exhibited significant alterations in lipid composition and increased concentrations of several n-3 polyunsaturated fatty acids and increased levels of omega-3 polyunsaturated fatty acids (n-3 PUFAs), including α-linolenic acid (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), suggesting that grazing and house-feeding systems were associated with differences in the lipid nutritional profile of muscle. Lipidomic analysis showed that the differential lipids were mainly enriched in triacylglycerols (TGs), phosphatidylethanolamines (PEs), and phosphatidylcholines (PCs), and several PUFA-containing TGs and membrane lipid molecules were closely associated with meat quality traits. AAM analysis showed that branched-chain amino acids (BCAAs), including L-leucine and L-valine, as well as N,N-dimethylglycine, were upregulated in the L group, whereas kynurenine and 1-methyl-L-histidine were downregulated. These findings suggest that BCAA metabolism and tryptophan–kynurenine metabolism were associated with metabolic differences observed between production systems in muscle metabolic adaptation. However, amino acid metabolomics analysis revealed that no amino acid metabolites remained significant after FDR correction, and thus the observed pathway-level changes (e.g., BCAA metabolism and tryptophan–kynurenine pathway) should be interpreted as nominal and exploratory findings. Overall, the results indicate that feeding systems were associated with alterations in the lipid and amino acid metabolic profiles of the biceps femoris muscle in Tibetan sheep, which were further associated with differences in muscle WHC, shear force, lipid nutritional composition, and the profile of flavor precursors. This study provides a theoretical basis for optimizing plateau meat sheep production systems and developing high-quality Tibetan sheep meat products. Full article

Hawthorn (Crataegus pinnatifida) pulp is characterized by high levels of organic acids and polyphenols, yet its strong acidity limits sensory acceptance. In this study, Streptococcus thermophilus 540, Lactobacillus brevis 647, and their mixed culture (1:1) were applied to ferment hawthorn pulp. Changes in organic acids, individual phenolics, free amino acids, volatile compounds, antioxidant capacity, and global metabolic profiles were systematically investigated using targeted analysis combined with untargeted metabolomics. Fermentation markedly reshaped the metabolic composition of hawthorn pulp, with mixed fermentation exhibiting the most pronounced metabolic reprogramming. Co-fermentation significantly enhanced phenolic derivatives and aromatic amino acid-related metabolites, while promoting a more balanced distribution of organic acids and esters, contributing to improved antioxidant potential and flavor coordination. Multivariate analyses confirmed that mixed fermentation formed a distinct metabolic pattern rather than a simple additive effect of single strains, characterized by expanded metabolic diversity and pathway complementarity. These findings provide mechanistic insight into strain-dependent and synergistic metabolic modulation during fruit fermentation and support mixed lactic acid bacteria fermentation as a promising strategy for improving the functional and sensory quality of hawthorn-based products. Full article

Toxoptera aurantii is a globally distributed piercing-sucking pest that severely threatens tea production. While the direct damage caused by aphid feeding is well documented, the systemic effects of infestation on plant-associated and soil microbial communities remain poorly understood. Here, we employed full-length 16S rRNA gene sequencing and untargeted metabolomics to investigate the influence of T. aurantii infestation on the microbiota of tea plants (Camellia sinensis) and rhizosphere soil across four sample compartments: aphid bodies, healthy leaves, aphid-infested leaves, and root-zone soil. Our results revealed pronounced niche-specific microbial assembly patterns. The aphid microbiome exhibited the lowest diversity and was dominated by obligate endosymbionts, including Buchnera aphidicola and the secondary symbiont Serratia symbiotica. Soil harbored the highest microbial diversity with a balanced phylum-level structure. Aphid infestation significantly reduced phyllosphere microbial diversity (Shannon index) and shifted community composition, with a decline in a sequence putatively assigned to Methylobacterium brachiatum and a modest increase in a taxon assigned to the opportunistic plant pathogen OTU assigned to Dickeya chrysanthemi. This pattern suggests a hypothesis that aphid infestation may create conditions permissive for such opportunistic pathogens, although experimental validation is required. Concurrently, infestation was associated with profound metabolic reprograming in tea leaves, including upregulation of defense-related flavonoids and terpenoids and downregulation of several primary metabolites. Notably, the phyllosphere of infested leaves showed reduced microbial diversity and an increased relative abundance of a 16S rRNA sequence assigned to Dickeya chrysanthemi, while certain plant-derived antimicrobial metabolites were decreased. These patterns suggest a possible association between aphid infestation, altered antimicrobial metabolite profiles and increased relative abundance of Dickeya-assigned sequences. These findings demonstrate that T. aurantii infestation triggers a systemic response in the aboveground compartments (aphid and leaf), while the soil compartment maintains a distinct and highly diverse microbial community that serves as a potential reservoir. The study characterizes microbial communities across these three compartments without inferring infestation-driven soil remodeling. This study advances our understanding of tripartite interactions in tea ecosystems and provides a basis for developing microbiome-based strategies for sustainable pest management. Full article

This study investigated the effects of starter feed supplementation on growth performance, immune-related parameters, intestinal microbiota, and metabolite profiles in preweaning yak calves. Twenty healthy 30-day-old male yak calves with similar body weight were randomly assigned to either a control group (A), receiving milk replacer and alfalfa hay, or a starter-supplemented group (AS), receiving milk replacer, alfalfa hay, and a concentrate-based starter feed. Growth traits, nutrient digestibility, serum immune indices, intestinal microbial communities, and metabolomic characteristics were evaluated. Compared with the A group, calves in the AS group exhibited greater total dry matter intake, final body weight, heart girth, cannon circumference, and apparent digestibility of calcium and phosphorus (p < 0.05). Average daily gain tended to increase but did not differ significantly between treatments (p > 0.05). Starter supplementation also increased serum concentrations of IgA, IL-6, TNF-α, M-CSF, and IFN-γ (p < 0.05). In contrast, jejunal TNF-α concentration was lower in the AS group than in the A group (p < 0.05). Microbial analysis demonstrated that starter supplementation modified intestinal bacterial community composition. In the jejunum, the relative abundances of Family_XIII_AD3011_group and Acetitomaculum were increased, whereas Bacteroidota and Bacteroides were enriched in the colon. Untargeted metabolomic analysis further revealed distinct metabolic profiles between groups, with differential metabolites mainly associated with amino acid metabolism, vitamin metabolism, and energy-related pathways. Overall, starter feed supplementation was associated with changes in nutrient utilization, immune-related indicators, intestinal microbial composition, and metabolic characteristics. These findings suggest that starter supplementation may facilitate dietary adaptation and support gastrointestinal function in preweaning yak calves. Full article

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating multisystem illness characterised by post-exertional malaise, non-restorative sleep, and cognitive impairment, yet no objective diagnostic biomarkers have been established. Untargeted plasma metabolomics provides a broad view of the biochemical disturbances underlying ME/CFS; however, the high dimensionality of omics datasets and the limited interpretability of conventional classifiers nevertheless hinder translation into clinical practice. This study evaluates three ensemble classifiers—Explainable Boosting Machine (EBM), XGBoost, and LightGBM—for binary ME/CFS classification using plasma metabolomic and lipidomic profiles from 197 participants (106 ME/CFS; 91 healthy controls; 888 features). Feature dimensionality was reduced using a Pareto-Guided Recursive Neural Network (PRNN) pipeline. Model performance was assessed via 50-repeat stratified hold-out validation. EBM achieved the highest accuracy (0.909; 95% CI: 0.868–0.949) and area under the receiver operating characteristic curve (AUC: 0.940; 95% CI: 0.909–0.983), with XGBoost and LightGBM performing comparably. Interpretability analyses revealed that pairwise metabolite interaction terms—particularly proline & indole-3-lactate, tyrosine & N-acetylornithine, and maleic acid & arachidic acid—contributed the greatest discriminative signal. An ablation analysis comparing the full interaction-augmented EBM (AUC = 0.940) with a main-effects-only EBM (AUC = 0.882) confirmed that pairwise metabolite co-variation contributes additional discriminative value beyond individual metabolite levels, implicating amino acid catabolism, tryptophan–kynurenine pathway dysregulation, mitochondrial energy impairment, and lipid remodelling as central pathophysiological features. Global and instance-level explanations jointly demonstrated population-level metabolic signatures alongside individual heterogeneity, highlighting the added clinical value of explainable artificial intelligence (XAI) in metabolomics. These findings support EBM-based metabolomic profiling as an internally validated approach for ME/CFS classification, subject to external validation, calibration assessment, and prospective testing. Full article

Tea breeding increasingly requires a continuous evidence chain from germplasm identity to molecular variation and progeny performance, but cultivar passports, genome resources, transcriptome profiles, metabolite data and breeding records are often managed separately. Here, we present Ningbo TeaBase (NB-TeaBase), an open, cultivar-centered database for robust-bud tea (Camellia sinensis) breeding. The platform uses named cultivars as the organizing unit and integrates germplasm passport information for eight elite cultivars with 23 chromosome-level genomes, whole-genome resequencing variants, RNA-seq expression profiles, untargeted LC-MS/MS metabolite features, annotations and downloadable records. Shared cultivar, gene, variant, pathway and metabolite identifiers allow users to characterize a cultivar across genomic, transcriptomic and metabolic layers and to connect these profiles with breeding records. A parental-prediction module incorporates genome-wide markers and phenotypes from 122 progeny assigned to seven observed parental combinations; it reports genomic estimated breeding values (GEBVs) for candidate crosses and observed-family general and specific combining-ability summaries for seven traits. By combining germplasm documentation, multi-omics evidence and progeny-informed cross ranking, NB-TeaBase supports cultivar evaluation, parent selection, cross prioritization and breeding strategy formulation. Current prediction outputs remain exploratory because the phenotypic training data cover only seven parental combinations and require broader validation. Full article

Fermented foods are chemically complex systems in which substrate composition, microbial community dynamics, and physicochemical conditions interact to generate thousands of metabolites across diverse chemical classes. Conventional targeted analytical approaches quantify predefined compounds with high precision but operate within a restricted chemical space, systematically excluding emergent features central to product identity, safety, and sensory character. Untargeted metabolomics addresses this limitation by capturing global chemical fingerprints of fermented matrices, enabling discovery-driven investigation across a broad fraction of the metabolome. This review examines the application of untargeted metabolomics across key research areas in fermented food science, including fermentation monitoring, microbial interactions, flavour development, process optimisation, post-fermentation stability, and safety assessment. Across these domains, untargeted approaches reveal system-level metabolic relationships beyond the reach of targeted analyses, while also presenting interpretive challenges. A central limitation is the annotation bottleneck: despite high feature detection rates, only a small fraction of signals are structurally identified, constraining mechanistic interpretation and cross-study comparability. Additional challenges in data processing, statistical validation, and interlaboratory reproducibility further limit data interpretation. Addressing these constraints through improved spectral libraries, standardised workflows, and integration with complementary omics is essential for advancing untargeted metabolomics towards robust knowledge generation in fermented food systems. Full article

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

Good canine gastrointestinal health depends on the suppression of enteric pathogens and maintenance of epithelial barrier integrity. Limosilactobacillus reuteri ATCC PTA 6127 (Lr6127) is a dog-derived probiotic, but evidence supporting its functional properties remains limited. Here, we evaluated the antimicrobial and epithelial-supportive effects of Lr6127 using a canine epithelial cell model. Cell-free supernatant (CFS) from Lr6127 significantly inhibited the growth of canine-relevant pathogens, including Enterotoxigenic Escherichia coli (52.0 ± 1.3%), Clostridium perfringens (54.0 ± 2.7%), and Salmonella enterica subsp. enterica serovar Typhimurium (48.6 ± 1.2%), compared with the medium control (p < 0.0001). Pathogen inhibition increased in a dose-dependent manner with increasing CFS concentration. Untargeted metabolomic analysis revealed enrichment of multiple antimicrobial-associated metabolites, indicating a multi-component profile consistent with pathogen suppression, with genomic analysis supporting the aromatic amino acid-derived metabolite findings. In addition, viable Lr6127 significantly reduced the epithelial adhesion of all the tested pathogens (p < 0.01). Beyond direct antimicrobial effects, Lr6127 CFS promoted epithelial wound healing at later time points, accompanied by the coordinated modulation of proteins associated with cytoskeletal remodeling and barrier repair. Collectively, these findings support the idea that Lr6127 is associated with antimicrobial and epithelial-related effects, highlighting its potential to contribute to epithelial function under controlled in vitro conditions. Full article

Citrus aurantium L. is a citrus-derived functional food rich in various phenolic compounds, including flavonoids. However, the bioavailability of its phytochemicals and sensory quality remain limited. This study investigated the effects of ultrasound-assisted fermentation by Lactiplantibacillus plantarum on microbial growth, phytochemical transformation, antioxidant activity, and metabolic profiles of C. aurantium. Ultrasound treatments were applied at different fermentation stages and power levels, among which treatment at 100 W during the exponential growth phase (ULP4) exhibited the best overall performance. Compared with conventional fermentation by L. plantarum (LP), ULP4 significantly promoted microbial growth, accelerated acidification, enhanced carbohydrate utilization, and stimulated β-glucosidase activity compared with conventional fermentation. Consequently, total phenolic content, total flavonoid content, and antioxidant capacities were markedly improved. Untargeted full-MS/MS metabolomic analysis revealed extensive metabolic alterations following ultrasound treatment, with 335 metabolites significantly altered between LP and ULP4. Differential metabolites were mainly associated with flavone and flavonol biosynthesis, secondary metabolite biosynthesis, amino acid metabolism, and lipid metabolism. These metabolic changes were closely associated with improved antioxidant properties and functional quality. Overall, ultrasound treatment during the exponential growth phase effectively enhanced microbial metabolism and phytochemical transformation, offering a promising strategy to improve the functional value of fermented C. aurantium products. Full article

Training induces sweat morphology changes in horses from muddy sweat (MS) to foamy sweat (FS) and clear sweat (CS), reflecting physiological adaptation. However, the metabolic mechanisms linking sweat phenotypes to systemic amino acid dynamics remain unclear. This study integrated sweat untargeted metabolomics and plasma amino acid targeted metabolomics to reveal coordinated metabolic remodeling. Six 2-year-old Yili horse stallions underwent 10-week training. Plasma and sweat were sampled pre- and post-race at each stage. LC-MS/MS and UHPLC-MS/MS were used for sweat metabolome and plasma amino acid analysis, followed by multivariate statistics, KEGG enrichment, and correlation network (CNet) analysis. Differential sweat metabolites decreased across stages (45, 127, and 38 for MS vs. FS, MS vs. CS, and FS vs. CS). Pre-race BCAA concentrations were higher in MS than in FS and CS, while glycine was lower. Post-race valine, histidine, and aspartate were elevated only in MS. Pre-race plasma amino acids positively correlated with sweat lipids and organic acids, shifting to negative post-race. ABC transporters, mTOR signaling, and BCAA metabolic pathways were key co-regulators. The MS-to-CS transition reflects metabolic remodeling from acute stress to homeostatic adaptation. Plasma BCAAs and sweat cortisol are potential biomarkers, with ABC transporters and mTOR pathways mediating sweat-plasma metabolic coordination. Full article