Search Results (6,521)

Continuous monoculture alters rhizosphere soil conditions and microbial community structure, but the integrated soil biochemical, microbial, and metabolomic responses of pepper (Capsicum annuum L.) rhizosphere soils remain insufficiently characterized. Here, we compared uncropped/non-continuously cropped pepper soil (Y0) with soil under 10 years of pepper monoculture (Y10) using soil physicochemical assays, enzyme measurements, 16S rRNA and ITS amplicon sequencing, untargeted UHPLC-Q Exactive HFX metabolomics, and predictive functional profiling. Long-term monoculture markedly separated Y10 from Y0 in multivariate analyses. Y10 soils showed higher organic matter, available nitrogen, available phosphorus, available potassium, and electrical conductivity in soil-water extracts, whereas microbial biomass carbon and pH were lower. Soil enzyme profiles also differed between treatments. Microbial alpha diversity declined under Y10, and bacterial and fungal community structures were clearly separated between treatments. At the taxonomic level, Acidobacteriota and several oligotrophic bacterial taxa were relatively enriched in Y0, whereas Proteobacteria, Bacteroidota, Chloroflexi, Bacillota, Pseudomonas, Bacillus, and several fungal genus-level taxa increased in Y10. Untargeted metabolomics revealed extensive remodeling of rhizosphere metabolites, with 413 up-regulated and 21 down-regulated differential metabolites in Y10. Differential metabolites were mainly associated with carboxylic acids and derivatives, benzene and substituted derivatives, fatty acyls, aromatic-compound transformation, sulfur metabolism, alkaloid biosynthesis, and microbial metabolism. Correlation analyses further linked key microbial taxa with soil pH, microbial biomass carbon, available nutrients, electrical conductivity, and enzyme activities. These results indicate that long-term pepper monoculture is associated with coordinated shifts in soil chemical status, microbial community composition, and metabolite profiles. The study provides an integrated basis for understanding rhizosphere changes under pepper continuous-cropping systems while recognizing that functional predictions and metabolite annotations require experimental validation. Full article

Polysaccharides are major bioactive constituents and quality-related components of Anoectochilus roxburghii. However, how polysaccharide accumulation varies among cultivars and tissues remains poorly understood. Here, crude polysaccharide content was quantified in leaves and stems of three cultivars, Yuanye (YY), Hongxia (HX), and Jianye (JY), and the underlying molecular basis was investigated using transcriptomics, targeted sugar metabolomics, and integrated transcriptome–metabolome analysis. Stems accumulated significantly higher levels of crude polysaccharides than leaves, whereas cultivar-dependent differences were most pronounced in stems. JY stems showed the highest crude polysaccharide content, reaching 357.81 mg g⁻¹ dry weight. Transcriptomic and metabolomic profiles clearly differentiated the cultivars and tissues. Metabolic differences were concentrated at a limited number of sugar-metabolic nodes, whereas the transcriptome showed extensive transcriptional reprogramming. Integrative analyses consistently implicated starch and sucrose metabolism, precursor-sugar interconversion, nucleotide-sugar biosynthesis, and sugar transport, partitioning, and intracellular allocation in differential polysaccharide accumulation. Glucose and D-fructose emerged as key hub metabolites linking transcriptional variation to sugar-metabolic remodeling. These results suggest that tissue- and cultivar-dependent polysaccharide accumulation is associated with coordinated changes in sucrose turnover, precursor sugar supply, nucleotide-sugar formation, and sugar partitioning, particularly in stems. This study provides molecular evidence for the selection of high-polysaccharide germplasm and quality evaluation of A. roxburghii. Full article

Triploid fish have attracted considerable attention in aquaculture because of their sterility and rapid growth. In this study, a novel allotriploid fish (WA, 3n = 150) was obtained through distant hybridization of a female diploid hybrid fish (WR-II, 2n = 100) with a male allotetraploid fish (4nAT, 4n = 200). The measurable traits of WA exhibit significant differences from WR-II and its original parents (white crucian carp (WCC) and red crucian carp (RCC)). WA muscles exhibited higher protein, fat, and essential amino acid levels but lower moisture. Furthermore, WA enhanced growth performance and muscle hypertrophy compared to WCC and RCC. The transcriptomes and metabolomics of the muscle tissues of WA, WCC, and RCC were analyzed. In total, 3889 and 1863 differential expressed genes (DEGs) were identified in WA vs. WCC and WA vs. RCC, respectively. These DEGs were mainly enriched in pathways related to amino acid biosynthesis and oxidative phosphorylation. In total, 421 and 304 differential metabolites (DMs) were identified in WA vs. WCC and WA vs. RCC, respectively. These DMs were mainly enriched in the pathways related to glycerophospholipid and fatty acid metabolism. Integrated transcriptomic and metabolomic analyses revealed that the expression patterns of acta1, myh, myog, and aldoa were associated with changes in the abundance of oleoyl ethanolamide, betaine, inosine, docosahexaenoic acid (DHA), and PC (38:6), suggesting their potential involvement in the enhanced growth performance of WA. This study provides a potential genetic resource for aquaculture and identifies molecular features associated with enhanced growth performance in this allotriploid fish. Full article

Gastrodia elata Bl. (GE), a representative medicine–food homology material, requires appropriate processing prior to food application to meet established medicinal quality standards. However, the effects of different traditional processing methods on its quality attributes remain insufficiently elucidated. In this study, three representative processing methods, steaming, moistening, and bran-frying, were systematically compared to evaluate their impact on the structural, compositional, and flavor characteristics of GE. The results demonstrated that processing markedly altered both the physical structure and chemical composition of GE. Moistening caused minimal disruption to the native tissue architecture and largely preserved the free-water distribution pattern. Notably, gastrodin and p-hydroxybenzyl alcohol contents reached 0.38% and 4.16%, respectively, the highest among all treatments, while the overall flavor profile remained closest to that of fresh GE. In contrast, bran-frying induced pronounced dehydration and structural densification, with volatile compounds and differential metabolites accounting for 72.83% and 41.01%, respectively. This treatment also exhibited elevated levels of total phenolics, flavonoids, and protein. Steaming, by comparison, promoted starch gelatinization and water redistribution, shifting the flavor profile from a delicate herbal note toward enhanced umami, floral, and mildly roasted characteristics. Overall, these findings reveal that processing-induced structural remodeling and changes in water state play critical roles in regulating the quality attributes of GE. By integrating structural characterization, water-state analysis, and multi-omics data, this study provides a systematic understanding of the formation of GE quality attributes under different processing methods, offering a theoretical basis for quality control and process optimization. Full article

Examining the relationship between an animal’s diet and physiology is crucial to understanding their responses to environmental change. Dietary-induced physiological variation can influence key life history processes, including growth and reproduction, ultimately affecting individual fitness. Reported here are the plasma biochemical parameters related to energy storage, use and nutritional condition in juvenile white sharks (Carcharodon carcharias) in Eastern Australia. Specifically, we used plasma metabolites (triglyceride, cholesterol and β-hydroxybutyrate), thyroid hormone thyroxine and fatty acid profiles from 50 juvenile white sharks (152–340 cm total length) captured on SMART drumlines in Eastern Australia to examine blood biochemistry and nutritional ecology. Concentrations of triglycerides and β-hydroxybutyrate indicated high energy expenditure likely associated with the broad-scale migration of white sharks along the Australian coast, highlighting the importance of β-hydroxybutyrate as an energy source. Seasonal variation in the triglyceride/cholesterol and ω3/ω6 fatty acid ratio, in conjunction with lower docosahexaenoic acid, suggests that lower-quality prey is consumed during winter months, thereby influencing the nutritional condition of these sharks. Additionally, the positive correlation between thyroxine concentrations and water temperature suggests reduced metabolic activity during cooler months. Such fluxes in food quality and nutritional condition may affect juvenile white sharks’ growth and development rate and future reproductive success. Full article

Acidifiers are functional feed additives that may improve egg quality by modulating intestinal microbiota and host metabolism. This study investigated the effects of dietary acidifier supplementation on laying performance, yolk fatty acid composition, eggshell ultrastructure, intestinal function, cecal microbiota, serum metabolome, and antioxidant status in laying hens. Sixty 52-week-old Jingfen No. 6 laying hens were randomly assigned to either a control group or an acidifier-supplemented group for 6 weeks. Acidifier supplementation increased laying rate and egg mass while reducing the feed-to-egg ratio. It also increased the concentrations of seven yolk fatty acids, including tetradecanoic acid, myristoleic acid, palmitic acid, palmitoleic acid, stearic acid, cis-vaccenic acid, and arachidic acid. In addition, acidifier supplementation resulted in a denser eggshell microstructure, improved cecal mucosal morphology, and enhanced the activities of lipase, chymotrypsin, amylase, and trypsin. Although cecal microbial alpha diversity remained unchanged, acidifier supplementation altered the overall microbial community structure and enriched several genera, including Slackia_A, Megasphaera_A, Veillonella_A, Merdimonas, and Caccocola. Serum metabolomic analysis identified 395 differential metabolites, primarily associated with lipid, amino acid, energy, and bile acid metabolism. Representative altered metabolites included taurodeoxycholic acid 3-glucuronide, LysoPE (0:0/20:0), 15-HETE, cholic acid, malic acid, and succinic acid. Acidifier supplementation also favorably affected serum HDL-C, LDL-C, and calcium concentrations and enhanced antioxidant capacity. Collectively, these findings indicate that dietary acidifier supplementation improves laying performance, yolk fatty acid deposition, eggshell structure, intestinal function, and antioxidant status, accompanied by alterations in cecal microbiota and serum metabolism. These coordinated changes may contribute to the observed improvements in egg quality. Full article

Sugar starvation during seed germination requires coordinated regulation of reserve mobilization, redox homeostasis, and intracellular recycling. In lupin seeds, asparagine is a major nitrogen-rich metabolite, but its role in starvation-induced autophagy and redox regulation remains unclear. Here, isolated embryonic axes of white lupin (Lupinus albus L.) and Andean lupin (Lupinus mutabilis Sweet) were cultured in vitro under sucrose-fed or sugar-starved conditions, with or without asparagine supplementation. Using transcriptomic, proteomic, immunoblot, enzymatic, antioxidant activity, and confocal microscopy analyses, we show that sugar starvation induced redox- and autophagy-related reprogramming, including changes in reactive oxygen species (ROS)-related proteins, catalase accumulation, autophagy-related (ATG) gene expression, vacuolar hydrolase-related responses, and proteolytic activity. Peroxisome-associated components, including glycolate oxidase, acyl-CoA oxidase, and catalase, were strongly affected, indicating dynamic remodeling of peroxisome-related metabolism during starvation. Asparagine modified this response by increasing antioxidant capacity and catalase accumulation under sugar starvation, while reducing detectable autophagosome number, many ATG and vacuolar hydrolase transcripts, and proteolytic activity. Together with previous evidence for asparagine-induced accumulation of autophagic bodies in vacuoles, these results are consistent with asparagine-dependent modulation of several autophagy-related processes rather than with an effect restricted to a single autophagic step. White and Andean lupin shared the same general regulatory framework but differed in response intensity. Thus, asparagine links nitrogen status with redox stabilization, vacuolar catabolism, and autophagy-related dynamics in sugar-starved lupin embryonic axes. Full article

Ngueak Pla Mo is a Thai medicinal crude drug derived from the pharmacopoeial Acanthus species A. ebracteatus Vahl and A. ilicifolius L.; however, morphological similarity and the occurrence of non-pharmacopoeial substitutes such as A. montanus (Nees) T. Anderson may complicate authentication and quality control. This study aimed to develop an integrated molecular–chemical approach for differentiating pharmacopoeial Ngueak Pla Mo species from A. montanus. Twenty authenticated Acanthus samples were analyzed using ITS2 DNA barcoding, including nucleotide variation, pairwise genetic distance, barcode gap, haplotype network, phylogenetic analysis, and predicted ITS2 secondary structure. Representative samples were further examined by untargeted LC–QTOF/MS metabolite profiling combined with hierarchical clustering, PCA, PLS-DA, VIP analyses, fold-change evaluation, and specificity scoring. ITS2 analyses clearly separated A. montanus from A. ebracteatus and A. ilicifolius, supported by diagnostic sequence variation, positive barcode gaps, distinct haplotypes, phylogenetic clustering, and secondary-structure differences, whereas A. ebracteatus and A. ilicifolius could not be reliably differentiated from each other at the species level using ITS2. LC–QTOF/MS profiling revealed species-consistent metabolite patterns and prioritized gallic acid, catechol, 3,4-dihydroxybenzoic acid, trigonelline, and ursolic acid as preliminary candidate markers for A. montanus discrimination. These results indicate that combining ITS2 barcoding with metabolite profiling provides complementary evidence for Ngueak Pla Mo authentication and supports future quality-control development. Full article

Bacteria are constantly exposed to stress, which intensifies as cells age, nutrients are depleted, and metabolite levels change. As metabolic activity increases, the cytoplasm transitions from a glass-like to a more fluid state, supporting the stochastic (spontaneous) and chaotic (nonlinear and unpredictable) movement of particles. The rate at which suspended particles or those in vacuole-like “cages” move depends on the cytoplasm’s energized and fluidic state. Cells respond to stochastic and chaotic behavior by regulating gene transcription, translation, and post-translational modifications. These stochastic and chaotic reactions generate a liquid–liquid phase separation (LLPS), causing particles to separate. This produces a dynamic force that drives cytoplasmic “turnover”. Internal and external physicochemical changes are monitored by chemoreceptors on the cell surface and embedded in the cell membrane, which activate transcriptional regulators to control gene expression, modulate enzymatic fluctuations, and regulate post-translational modifications. Sentience may also arise from the quantum-like behavior of ions, electrons, neutrons, and protons (tunneling and entanglement) and from hyperstructures that drive complex enzymatic reactions. This is, however, a highly debated topic. We argue that bacteria are conscious and do not rely solely on phosphorylation states, as in two-component systems (TCSs), but also on other cytoplasmic dynamics. We provide several examples to support the argument. It is, however, important to note that bacterial consciousness cannot be compared to that of higher life forms with a central nervous system. We refer to bacteria’s awareness of their environment as sentience and define bacterial sentience as the ability to respond to external stimuli and to reactions within a dynamic cytoplasm, thereby transferring signals either directly or via signal transduction pathways to turn gene expression on or off. We also point out that stochastic/chaotic randomness keeps the cytoplasm in a permanently dynamic, flexible, and stochastic state, safeguarding the cell against sudden, unpredictable environmental changes. Full article

Mitochondrial quality control (QC) comprises interconnected pathways that preserve organelle function by detecting damage and mediating repair, remodelling, or elimination of defective components. Although many sub-organellar QC mechanisms are well characterised, stress is often sensed first at the level of mitochondrial function rather than at individual molecular targets. Functional domains such as oxidative folding, bioenergetics, redox balance, pH, and thermogenesis act as sensory portals that detect perturbations and trigger adaptive reprogramming of mitochondrial activity. In this perspective, we provide a conceptual perspective for mitochondrial QC as a mechanistically integrated network, emphasising how changes in these functional states couple diverse QC modules—including proteases, antioxidant systems, mitochondrial dynamics, mitophagy, and mitochondrial-derived vesicles—into a unified surveillance system. We propose that primary stressors, such as redox imbalance, are progressively converted into secondary stress signals, including reactive oxygen species accumulation, membrane depolarisation, metabolite redistribution, and altered lipid or nucleic-acid structure. These secondary signals propagate across mitochondrial and cytosolic compartments, amplifying QC by coordinating the engagement of repair, remodelling, and organelle-elimination pathways. This cascading transformation of stress signals not only limits the impact of the initial insult but also enhances adaptive capacity by driving synergistic deployment of QC processes across multiple mechanistic layers. Full article

Background: Flower color is a well-defined trait in Platycodon grandiflorus, whereas little is known about the effects of flower color variation on the metabolic profiles of reproductive organs. Triterpenoid saponins and flavonoids have common precursors upstream, suggesting a potential carbon flux trade-off. Methods: Untargeted UPLC-MS/MS metabolomics was performed on the reproductive organs of purple- and white-flowered P. grandiflorus at six stages of flower development. Mfuzz time-series clustering, PCA, and metabolite correlation networks were used for data analysis. Results: Six clusters were assigned to 25 metabolites (17 triterpenoid saponins and 8 flavonoids). Flavonoid glycosides were found to possess a conserved inverted V-shaped accumulation pattern in both germplasms. By contrast, saponins derived from triterpenoids showed strong germplasm-dependent accumulation patterns. White-flowered plants showed sustained accumulation, with a peak at the young fruit stage. In purple-flowered plants, accumulation peaked transiently at the withering stage, followed by a decline. PCA validated that metabolic divergence increased with developmental progression. Conclusions: Based on the metabolomic profiles, we hypothesize a putative trade-off model in which floral color divergence may change upstream carbon flux allocation between the triterpenoid saponin and flavonoid pathways. The young fruit stage of white-flowered plants is a candidate harvesting period for bioactive saponins. These conclusions are based only on the pattern of metabolite accumulation and need to be validated by multi-omics. Full article

Superovulation and embryo transfer techniques are effective strategies for improving reproductive efficiency in sheep flocks. To characterize changes in plasma metabolites and reproductive hormones following HMG or FSH superovulatory treatment, and to screen for biomarkers closely associated with embryo quality, we employed liquid chromatography-based untargeted metabolomics and enzyme-linked immunosorbent assay (ELISA) to analyze plasma samples from donor ewes on day 6 after hormone administration. This study aimed to identify small-molecule biomarkers affecting embryo quality under different hormonal regimens. A total of 46 Kazakh ewes were allocated into two groups: the HMG group received HMG treatment, while the FSH group received FSH treatment; both groups were superovulated using a tapering dose regimen administered via intramuscular injection. Our results show that the average number of viable embryos in the HMG group (5.36 ± 3.29, n = 11) was significantly higher than that in the FSH group (2.91 ± 2.60, n = 35) (p < 0.05). Plasma progesterone concentrations differed significantly between the two groups (p = 0.01). Metabolomic analysis identified three key differential metabolites: 5-fluorouridine, ADP, and hexadecanoic acid. Functional enrichment analysis revealed 45 significantly enriched metabolic pathways. In conclusion, HMG effectively improves sheep embryo quality by modulating the levels of small-molecule metabolites associated with embryonic development. Full article

Interactions among the gut, brain, and skin are increasingly understood as a systemic regulatory network connecting intestinal activity, neuroimmune communication, and cutaneous homeostasis. Microbiota-derived metabolites, immune mediators, and neuroendocrine pathways can influence central nervous system activity and subsequently regulate skin homeostasis. This review summarizes current evidence on how functional ingredients modulate the gut–brain–skin axis in the context of aging and skin health. Polyphenols, probiotics, and omega-3 fatty acids appear to act through overlapping biological routes, including reshaping microbial communities, supporting epithelial barrier function, regulating immune activity, and limiting oxidative stress. These gut-derived signals may affect the brain through neural, endocrine, and immune pathways, thereby modulating neuroinflammation, hypothalamic–pituitary–adrenal (HPA) axis activity, and neurotransmitter balance. Through brain–skin communication, these changes may influence inflammation, epidermal barrier integrity, collagen remodeling, and skin aging processes. Emerging clinical evidence suggests potential improvements in skin-related outcomes and systemic inflammatory markers; however, studies remain heterogeneous, and integrated assessments of gut, brain, and skin endpoints are limited. Further studies that integrate multi-omics profiling with carefully designed clinical trials will be required to define causal pathways and support the development of evidence-based nutritional approaches targeting this axis. Full article

Background: Imidacloprid, a widely used neonicotinoid insecticide, is routinely applied to control pests in Astragalus membranaceus var. mongholicus, a crucial medicinal herb producing Astragali Radix. However, the early short-term transcriptional and metabolic responses of its seedlings under imidacloprid gradient stress remain poorly characterized. Methods: In this study, 80-day seedlings were subjected to three foliar spray treatments: blank control (CK), the recommended imidacloprid concentration (2000-fold dilution, 475 mg·L⁻¹), and an excessively high concentration (500-fold dilution, 1900 mg·L⁻¹). Leaf samples were harvested 24 h post-treatment for untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC–MS/MS) metabolomics (6 biological replicates) and RNA-seq transcriptome sequencing (3 biological replicates). Results: The low- and high-dose treatments induced 1076 and 860 differential metabolites and 6818 and 7283 differentially expressed genes, respectively. Flavonoids, saponins, terpenoids, amino acid metabolites, and energy-related pathways were prominently affected. KEGG enrichment indicated activation of flavone/flavonol biosynthesis, phenylpropanoid metabolism, amino acid metabolism, MAPK signaling, cutin/suberin/wax biosynthesis, and ABC transporter pathways, whereas high-dose exposure was associated with stronger changes in genes related to DNA replication and cell wall remodeling. Integrated network analysis highlighted CHS, PAL, MYC2, KCS, and ABCG40 as candidate regulators linking stress signaling, secondary metabolism, and metabolite transport. Conclusions: Seedlings of A. membranaceus var. mongholicus exhibit dose-dependent acute responses to imidacloprid. Moderate pesticide exposure primarily activates defensive secondary metabolism, whereas excessive dosage triggers genome-wide transcriptional reprogramming. This work identifies key metabolic pathways and hub genes, offering candidate molecular markers for investigating pesticide stress adaptation in medicinal Astragalus and guiding standardized pesticide application in cultivation. Full article

Background/Objectives: Major depressive disorder (MDD) is a highly prevalent and disabling psychiatric condition for which current therapies remain inadequate. Probiotics acting on the microbiota–gut–brain axis are a promising preventive strategy, but their benefits are strain-specific. Here we examined whether Lacticaseibacillus paracasei LP36 alleviates lipopolysaccharide (LPS)-induced depression-like behavior in mice, and we characterized its metabolic actions using serum untargeted metabolomics. Methods: Sixty male C57BL/6J mice were randomized into eight groups (58 completed the study and were analyzed) and received saline or LP36 (1 × 10⁸, 1 × 10⁹, or 1 × 10¹⁰ colony-forming units (CFU)/mL) by gavage for 28 days, with LPS (0.5 mg/kg, i.p.) or saline given during the last 10 days. Results: LP36 pretreatment alleviated LPS-induced depression-like behavior in the sucrose preference, forced swimming, and tail suspension tests. Of 2867 annotated serum metabolites, 404 differed between the LPS and control groups, and 601 between the LP36 (10¹⁰)-treated and LPS groups. Among 180 shared differential metabolites, 172 (95.6%) changed in opposite directions, indicating that LP36 mainly reverses LPS-induced metabolic perturbations. KEGG enrichment localized these effects to lipid-related pathways, with lower relative signal intensities of polyunsaturated fatty acids and sphingolipids under LPS and higher relative signal intensities after LP36. In addition, the relative signal intensities of several microbiota-derived metabolites, including indoles, kynurenines, and secondary bile acids, shifted toward control-group values after LP36 intervention, which might reflect a contribution of the gut microbiota. Conclusions: LP36 is thus a candidate psychobiotic that may alleviate depression by reshaping gut microbiota-related metabolism and the associated lipid remodeling. Full article