Search Results (2,883)

Background: This study aimed to investigate the effects of E. stephanianum-derived polyphenols on preventing the progression of collagen-induced arthritis (CIA) in mice and its associated metabolic alterations. Methods: The E. stephanianum plant was extracted, fractionated, and screened in vitro for anti-inflammatory, antibacterial, and antioxidant potential. Fraction 5 (identified as ellagic acid by nuclear magnetic resonance) exhibited the most potent activity and was selected for in vivo study. In the in vivo study, male DBA/1JGpt mice were randomized into five groups: control (CON), CIA (Model), low-dose extract (ES-L), high-dose extract (ES-H), and ellagic acid group. ES-L, ES-H, and ellagic acid were administered by daily oral gavage at 375, 750, and 250 mg/kg body weight, respectively, for 8 weeks. Arthritis severity was evaluated based on paw thickness, clinical score, ankle joint histopathology, and serum proinflammatory cytokine levels. To reveal the associated metabolic alterations, serum metabolites were characterized by ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. Results: Both the whole extract and ellagic acid revealed pronounced anti-inflammatory, antibacterial, and antioxidant properties. In vivo treatment with ES-L, ES-H, or ellagic acid similarly and significantly ameliorated CIA severity, showing smaller paw swelling, reduced clinical arthritis scores, milder joint histopathological injury, and lower serum tumor necrosis factor-α and interleukin-6 concentrations than the model group. Untargeted metabolomics identified 20 differential metabolites, mainly including triacylglycerols (containing n-3 fatty acids), pro-inflammatory phospholipids, and spermic acid 1. Moreover, the treatments significantly altered amino acid and purine metabolism. Conclusions:E. stephanianum derived polyphenols, like ellagic acid, significantly prevented the progress of CIA in mice. These effects were associated with the alteration of metabolic profiles. Full article

The characteristic red walnut germplasm ‘RW-1′ (Juglans regia L.) exhibits a stable red seed coat phenotype due to the abundant accumulation of anthocyanins and proanthocyanidins (PAs). The regulatory mechanisms underlying PA biosynthesis in red walnut remain poorly studied, which hinders the improvement of walnut color quality. Leucoanthocyanidin reductase (LAR) is a key enzyme in the PA metabolic pathway, while its function in red walnut remains unclear. Here, the leucoanthocyanidin reductase gene JrLAR1, whose expression pattern is consistent with the accumulation trend of PAs, was cloned from the seed coats of red walnut ‘RW-1′, and its function in PA biosynthesis was verified via heterologous overexpression in Arabidopsis thaliana, a well-recognized cross-species LAR functional validation system free of endogenous LAR interference due to absent native homologs. The results showed that the full-length coding sequence (CDS) of JrLAR1 gene is 1104 bp, encoding a 367-amino-acid protein belonging to the NADB_Rossmann superfamily, and the protein shares an extremely high sequence similarity with grape VvLAR2. Heterologous overexpression of JrLAR1 significantly increased total PA content in the leaves and seeds of A. thaliana. Integrated transcriptomic and metabolomic analyses further revealed that JrLAR1 overexpression markedly upregulated the core genes involved in PA metabolism and the transcription factor GL3 in A. thaliana, specifically induced (+)-catechin synthesis, and ultimately promoted the significant accumulation of procyanidin B3. In addition, a set of antioxidant enzyme-encoding genes were substantially upregulated in JrLAR1-overexpressing A. thaliana lines. Yeast one-hybrid and dual-luciferase reporter assays demonstrated that JrEGL1b, a homolog of A. thaliana GL3, can bind to the promoter region of JrLAR1 gene and significantly enhance its transcriptional activity. Transient overexpression of JrLAR1 or JrEGL1b in red walnut leaves significantly promoted PA accumulation, and JrEGL1b overexpression notably upregulated JrLAR1 expression. In conclusion, JrLAR1 plays a crucial role in PA biosynthesis in red walnut and is positively regulated by the transcription factor JrEGL1b. These findings improve the molecular regulatory network of pigment metabolism in red walnut and provide valuable molecular targets for the quality improvement and directional breeding of walnuts. Full article

To investigate the differences in pulp metabolites among four varieties of Pouteria caimito fruit (JZL1, JZL3, JZL5, and JZL6), ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) was employed for the separation and identification of metabolites. A total of 1285 metabolites were identified, including 648 in positive ion mode and 637 in negative ion mode. At the class level, carboxylic acids and derivatives (14.32%) and organooxygen compounds (11.83%) accounted for the highest proportions; at the subclass level, amino acids, peptides, and analogues (12.53%) as well as carbohydrates and carbohydrate conjugates (9.49%) were the main categories. PLS-DA analysis revealed significant differences in metabolite profiles among the four varieties, with numerous up-regulated and down-regulated metabolites in each comparison group, and some metabolites showed fold changes > 10 or <0.1. KEGG pathway enrichment analysis further indicated that differential metabolites were primarily enriched in pathways such as ABC transporters, citrate cycle (TCA cycle), starch and sucrose metabolism, and linoleic acid metabolism. This study provides an important metabolomic basis for variety identification, nutritional quality evaluation, and functional component development of Pouteria caimito fruit. Full article

Elevated ammonia nitrogen significantly reduces the survival rate of Litopenaeus vannamei under low-salinity conditions. Low-salinity culture is widely adopted in shrimp farming but susceptible to ammonia accumulation; however, relevant studies mainly focus on juvenile shrimp under single stress or normal salinity. With the aim of exploring how L. vannamei responds physiologically and molecularly to elevated ammonia nitrogen after low-salinity adaptation, shrimp were gradually acclimated to 5‰ salinity. They were reared at 5‰ for one week before being exposed to high levels of ammonia nitrogen for 96 h. Under these conditions, the shrimp’s hepatopancreas showed antioxidant imbalance and oxidative damage. Elevated blood ammonia, urea nitrogen and uric acid reflected activated synthesis pathways that clear excess ammonia. Transcriptomic and metabolomic profiling at 12, 48, and 96 h revealed 112 DEGs and pronounced alterations in lipids and amino acid derivatives. Integrated gene-metabolite correlation analysis uncovered three core pathways, along with 11 key DEGs and 17 associated metabolites. In the secretion pathway, solute carrier family 4 (anion exchanger),member 2 (slc4a3) was strongly correlated with saquinavir and carnitine. In the metabolism pathway, nicotinamide/nicotinate riboside kinase (nmrk1), chitinase (chia), Gamma-glutamyltranspeptidase (ggt1), UDP-glucose 4-epimerase (gale), and spermine oxidase (smox) were linked to L-pyroglutamic acid, betaine, etc. In the immune pathway, mitogen-activated protein kinase 8/9/10 (bsk) and integrin beta 1 (cd29) were associated with leukotriene E4 and niacin. This study reveals that ammonia stress after low-salinity acclimation induces oxidative stress damage, elevated physiological changes in L. vannamei, and further elucidates the regulatory pathways underlying its response to ammonia nitrogen stress. Full article

Background: Sarcopenia, the age-related loss of muscle mass and strength, affects over 20% of older adults in Taiwan and contributes to frailty and functional decline. Nutritional supplementation offers a promising strategy for those unable to engage in structured exercise, yet multi-ingredient MCT–leucine–creatine-based interventions remain understudied in clinically defined sarcopenic populations. Methods: We conducted an 8-week randomized, double-blind, placebo-controlled trial at National Taiwan University Hospital (ClinicalTrials.gov NCT06376266). Seventy-three older adults (mean age 77.3 ± 7.7 years) meeting AWGS 2019 sarcopenia criteria were randomized to TLN-01 (a multi-ingredient supplement containing whey protein, branched-chain amino acids, medium-chain triglycerides, creatine, resveratrol, and vitamin D₃, n = 34) or isocaloric placebo (n = 39). Primary outcomes were changes in appendicular skeletal muscle mass (ASM) assessed by DXA and handgrip strength. Targeted plasma amino acid metabolomics (LC-MS) was performed as an exploratory endpoint. Results: ASM increased significantly in the TLN-01 group (+0.42 kg, +3.2%; p < 0.001) but remained unchanged in controls (p = 0.785), with a significant between-group difference (ANCOVA p < 0.01); this absolute change was below the commonly cited minimal clinically important difference. Handgrip strength did not differ significantly between groups (p = 0.32); within-group analysis showed a significant decline in the placebo group (−7.0%; p < 0.001) that was not observed in the intervention group (p = 0.537). Metabolomic analysis revealed reductions in plasma taurine and 1-methylhistidine and an increase in kynurenine; given the absence of clear separation on PCA/PLS-DA, these findings are considered exploratory and hypothesis-generating rather than confirmatory evidence of altered amino acid utilization or proteolysis. No clinically significant adverse metabolic or renal events occurred. Conclusions: Eight weeks of this multi-ingredient MCT–leucine–creatine-based supplement induced a modest increase in muscle mass and attenuated the decline in handgrip strength observed in the placebo group among sarcopenic older adults without a structured exercise program, supporting further investigation as a safe and practical nutritional adjunct in geriatric care. Full article

Mianning ham is a traditional dry-cured ham from southwestern China, but the coordinated relationships among quality changes, microbial succession, and nonvolatile metabolite remodeling during long-term ripening remain poorly understood. Therefore, samples of Mianning ham aged for one, two, three, and four years were comparatively analyzed. High-throughput sequencing was used to characterize microbial community composition, and untargeted metabolomics was applied to analyze differential metabolite changes and their associations with dominant microorganisms. The results showed that the physicochemical and sensory characteristics of Mianning ham exhibited stage-dependent changes during ripening, with moisture content and pH generally decreasing, while color, texture, and mature flavor characteristics gradually developed. Multivariate statistical analysis identified 99 differential metabolites, which were mainly involved in peptide accumulation, amino acid metabolism, and nitrogen-containing compound transformation. The bacterial communities were mainly composed of Bacillota and Pseudomonadota, while Ascomycota was the predominant fungal phylum. Distinct successional patterns of dominant microbial taxa were observed at different ripening stages. Furthermore, microorganism–metabolite correlation analysis revealed distinct association patterns between internal and surface samples of the ham. Internal microbial communities were mainly associated with nucleotide-related metabolism- and umami-related characteristics, whereas surface microbial communities were more closely associated with the transformation of protein-derived nitrogen-containing compounds and the accumulation of flavor precursors. This study provides insights into the quality formation patterns of Mianning ham during ripening and offers a theoretical basis for ripening-stage evaluation and quality regulation. Full article

Precision nutrigenomics requires a diet–microbiome–host perspective because microorganisms can transform feed substrates, generate bioactive metabolites, compete with pathogens, and modify intestinal and systemic gene regulation. This structured narrative review synthesizes representative controlled feeding trials, transcriptomic and targeted gene-expression studies, microbiome analyses, and complementary multi-omic evidence concerning dietary regulations in cultured finfish. The available evidence is concentrated particularly on soybean-derived proteins, lipid-source replacements, selected amino acids and micronutrients, functional additives, probiotics, and fermented ingredients in a limited range of cultured finfish species; therefore, the synthesis is not intended to provide exhaustive coverage of every dietary intervention or finfish taxon. Recurrent host responses involve intestinal inflammation and barrier integrity, nutrient transport, lipid and bile-acid metabolism, long-chain polyunsaturated fatty-acid biosynthesis, targets of rapamycin/insulin-like growth factor (TOR/IGF) signaling, and nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) antioxidant defense. The expanded microorganism-centered synthesis shows that dietary effects depend on microbial niche, substrate availability, community succession, metabolite production, and strain-specific probiotic or pathobiont activity. Lactic-acid bacteria, Bacillus-associated interventions, butyrate-generating strategies, fermented ingredients, and microbial biomass may support digestion, immune balance, and disease resistance, but taxonomic shifts alone do not demonstrate functional benefit. Current evidence is limited by extensive reliance on 16S ribosomal RNA (16S rRNA) relative-abundance data, inconsistent digesta-versus-mucosa sampling, inadequate feed and water controls, and weak causal validation. Future precision aquafeed studies should combine host transcriptomics with absolute microbial quantification, shotgun metagenomics, metatranscriptomics, metabolomics, culturomics, histology, and pathogen challenge. Integrating microbial function with host phenotype can improve sustainable feed design, intestinal health, and resilience. Full article

Yeast hydrolysate (YH) is a yeast-derived functional feed ingredient containing bioactive peptides, amino acids, nucleotides, β-glucans, and mannan oligosaccharides, which may exert prebiotic-like effects by regulating nutrient metabolism, host health, and intestinal microbial homeostasis. However, its effects on lactating Dezhou jennies remain largely unclear. This study investigated the effects of dietary YH supplementation on body weight change, serum biochemical parameters, serum metabolomic profiles, and fecal microbiota composition in lactating Dezhou jennies. Sixteen healthy lactating Dezhou jennies were randomly assigned to a control group fed a basal diet (MCON, n = 8) or a YH supplementation group fed the basal diet supplemented with YH (MYE, n = 8) for 60 days. Compared with the MCON group, the MYE group showed numerically higher final body weight and body weight change. Serum biochemical analysis showed that YH supplementation significantly decreased alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities and increased triglyceride (TG) concentrations, while all measured biochemical parameters remained within physiological reference ranges. Serum metabolomic profiling identified 193 differential metabolites between the two groups, including 55 upregulated and 138 downregulated metabolites in the MYE group. These metabolites were mainly associated with amino acid metabolism, lipid metabolism, bile acid metabolism, steroid hormone biosynthesis, mineral absorption, ABC transporters, and protein digestion and absorption, indicating that YH supplementation reshaped nutrient-related metabolic pathways in lactating Dezhou jennies. Fecal microbiota analysis showed no significant changes in α-diversity or overall community structure; however, the MYE group displayed numerically higher microbial richness indices, more unique ASVs and genera, a lower relative abundance of Bacteroidota, and a higher relative abundance of Bacillota. LEfSe analysis further revealed enrichment of specific bacterial taxa in the MYE group, including Christensenellaceae_R-7_group, Anaerovorax, and UCG-related taxa. Collectively, these preliminary findings suggest that dietary YH supplementation may alter selected serum biochemical indices and circulating metabolites and may selectively affect the relative abundance of certain fecal bacterial taxa in lactating Dezhou jennies. However, given the limited sample size, these results should be interpreted cautiously, and larger-scale studies are needed to confirm their reproducibility and practical significance. Full article

Kaposi’s Sarcoma Herpesvirus (KSHV) is the etiological agent of Kaposi’s Sarcoma (KS), which induces metabolic stress in infected host cells. KSHV reprograms host metabolic pathways for efficient viral replication and infectious virion production. Here, we report a time-course global metabolomics study conducted in iSLK.BAC16 cells to compare latent and lytic KSHV infection. Our data show that amino acid, central carbon, and nucleotide metabolic pathways are highly dysregulated upon reactivation. During lytic KSHV infection, pathway enrichment analysis identifies purine and pyrimidine metabolism as the top two most significantly impacted and dysregulated pathways. Further experiments have shown that nucleotide metabolism is required during lytic KSHV infection to produce maximal infectious virus. Treatment with the FDA-approved drug, methotrexate (MTX), a folate antagonist that decreases nucleotide metabolism by reducing tetrahydrofolate cofactors, significantly reduced KSHV copy number and late lytic viral gene expression upon reactivation compared to controls. Additionally, titers of cell-free supernatants from MTX-treated lytic samples showed a significant reduction in infectious virion production. Furthermore, MTX significantly decreased the viral titer of murine herpesvirus 68 (MHV-68), a model virus to study gammaherpesvirus. Overall, our study demonstrates that metabolic inhibition during lytic gammaherpesvirus infection decreases productive infection and hence serves as a potential therapeutic antiviral target. Full article

Background/Objectives: Water deficit during the pod filling stage severely limits the productivity of common beans (Phaseolus vulgaris). Although the effects of water scarcity have been extensively studied in leaves and roots, the contribution of xylem sap to systemic metabolic adaptation remains poorly understood. This study investigated genotype-specific metabolic changes in xylem sap exudates in response to water deficit in two common bean genotypes with contrasting growth rates. The OTI genotype has a growth cycle of 120 days, while Rosa La Bufa (RB) completes its cycle in 80 days under both well-watered and water deficit conditions. Methods: Physiological responses were evaluated, and xylem sap exudate metabolites were profiled using untargeted UPLC–ESI–QTOF–MS. Protein–metabolite interaction networks were reconstructed using STITCH v5 to identify genotype-specific metabolic organization under stress. Results: Water deficit reduced the abundance of multiple xylem metabolites, including flavonoids, isoflavones, phenolic acids, sugars, amino acids, and oxylipin-related compounds, indicating systemic metabolic contraction. OTI exhibited extensive metabolic changes characterized by enrichment of citrate, aromatic amino acids, glycolytic intermediates, flavonoid glycosides, and detoxification-associated metabolites, consistent with active carbon remobilization and oxidative stress responses. In contrast, RB accumulated isoflavones, including genistein, biochanin A, and baicalein, together with glycosylated triterpenoid saponins. Network analysis revealed that OTI developed a broad stress-responsive interactome that integrated phenylpropanoid metabolism, carbon remobilization, and detoxification pathways, whereas RB maintained a compact interactome reinforced by oxylipin-, jasmonate-, and isoflavone-associated modules. Conclusions: Xylem sap undergoes genotype-dependent metabolic adjustment under water deficit, suggesting contrasting drought adaptation strategies. Long growth cycle genotypes activate extensive metabolic plasticity, whereas reduced growth cycle genotypes rely on more specialized defense networks. These findings highlight xylem metabolomics as a valuable approach for understanding systemic drought adaptation and identifying putative metabolic biomarkers associated with drought resilience in common beans. Full article

Liriomyza trifolii is a global pest of vegetables and ornamental plants and a major invasive species in China. Long-term irrational use of chemical insecticides has reduced control efficacy, driving interest in plant-derived alternatives. Bitter gourd, Momordica charantia, extracts show potential against various pests, but their effects on L. trifolii are unknown. To address this, host suitability tests were first conducted and revealed that L. trifolii exhibited significantly higher adaptability to kidney bean than to bitter gourd in terms of both oviposition and feeding, and failed to complete its life cycle on bitter gourd. Further treatment with ethanol extracts of bitter gourd leaves demonstrated dose-dependent adulticidal activity; at the LC₅₀ concentration, the extract not only reduced feeding punctures and oviposition, but also significantly decreased egg hatching and larval survival, while showing no significant impact on pupation or emergence. To elucidate the underlying molecular mechanisms, integrative transcriptomic and metabolomic analyses were subsequently performed. Transcriptomics identified 254 differentially expressed genes (DEGs) enriched in ribosome, oxidative phosphorylation, and peroxisome pathways, and upregulated DEGs included a vitellin-degrading protease and cytochrome P450. Meanwhile, metabolomics detected 272 differential metabolites (DEMs): upregulated metabolites were linked to purine metabolism, while downregulated ones were associated with cysteine/methionine and arginine/proline metabolism. Integrated analysis revealed “Biosynthesis of amino acids” as the sole common pathway, with S-adenosyl-L-homocysteine, N-succinyl-LL-2,6-diaminoheptanedioate, and glutamine synthetase (Ltr05G008090) showing significant correlations. These findings suggest that reprogramming of amino acid and nitrogen metabolism may participate in the response and could serve as a candidate response pathway. Accordingly, this study may offer a theoretical basis for the future development of botanical insecticides based on bitter gourd leaf extract against L. trifolii. Full article

Date palm (Phoenix dactylifera L.) plays a vital agronomic and nutritional role in arid regions of the Gulf Cooperation Council (GCC), where sustainable crop improvement is essential. Among the many cultivars, Sukkary, Mejhoul, and Khlass stand out for their commercial importance, adaptability, and distinctive fruit characteristics. This study investigated their metabolomic profiles during fruit development, focusing on sugars, amino acids, polyphenols, and organic acids. Distinct biochemical signatures were identified among cultivars. Mejhoul exhibited the highest Brix (~79), reflecting elevated glucose and fructose, while Sukkary and Khlass (~72) showed sucrose predominance. Sugar profiles revealed cultivar-specific patterns: Sukkary accumulated more sucrose, whereas Mejhoul and Khlass had higher invert sugars, with inositol uniquely abundant in Khlass. Amino acid analysis showed Sukkary enriched in glutamine, valine, and GABA—metabolites linked to nitrogen metabolism and stress tolerance. Mejhoul contained more tyrosine and glutamine, and Khlass was rich in methionine and urea. Organic acid profiling highlighted Sukkary’s dominance in TCA intermediates (fumaric, succinic, and malic acids), Khlass in citric and citraconic acids, and lower organic acid levels in Mejhoul. Sukkary also exhibited the highest polyphenol content, consistent with elevated phenylalanine and activation of the phenylpropanoid pathway. These metabolomic distinctions reflect cultivar-specific physiological and nutritional traits: Mejhoul suits fresh consumption and fermentation, Sukkary favors functional food and storage potential, and Khlass offers balanced sugar-acid and inositol profiles. The findings provide a biochemical basis for cultivar-specific breeding, postharvest optimization, and enhanced nutritional value under climate stress. Full article

Meat quality is an important economic trait in beef cattle and is influenced by breed-related metabolic characteristics. Yanbian cattle (YB) are valued for desirable meat quality, whereas Yanhuang cattle (YH), developed using Limousin cattle as the paternal line and Yanbian cattle as the maternal line, exhibit improved growth performance and carcass yield. However, the molecular basis underlying metabolic variation between these two genetically related cattle populations remains unclear. In this study, longissimus thoracis muscle samples from six animals per breed were analyzed using LC-MS/MS-based metabolomics and GC×GC-TOF/MS-based volatile compound profiling, and a subset of three samples per breed from the same cohort was selected for transcriptomic sequencing. A total of 1697 metabolites were detected. Based on the screening criteria of VIP > 1 and p < 0.05, 202 candidate metabolites were identified, among which 11 remained statistically significant after false discovery rate (FDR) correction. Volatile compound profiling detected 1333 and 1516 compounds in YB and YH, respectively, of which 809 were shared. Based on the same screening criteria, 39 candidate volatile compounds were identified, although none remained significant after FDR correction. Transcriptomic analysis identified 360 differentially expressed genes using |log₂FC| > 1 and adjusted p < 0.05, with enrichment mainly observed in pathways associated with carbohydrate metabolism, lipid turnover, and energy utilization. Integrative analyses indicated that amino acid-related metabolites, including phenylpyruvate, 2-aminobenzoic acid, and asparagine, were more closely associated with candidate volatile compounds than metabolites involved in central carbon metabolism. Several genes involved in lipid metabolism, energy metabolism, and muscle structure, including DGAT2, MGLL, CRYAB, CSRP3, AGPAT2, PHKA1, AMPD1, and PGM2L1, were associated with distinct metabolic modules. These findings provide an exploratory view of breed-related metabolic variation and identify candidate molecular features for future validation. Full article

Background/Objectives: Clematis huchouensis Tamura, a genuine medicinal herb endemic to Huzhou, Zhejiang Province. However, its secondary metabolic profile and organ-specific distribution of bioactive constituents remain largely uncharacterized. This study aims to systematically characterize the metabolic profile of its roots, stems, and leaves, and to elucidate organ-specific accumulation patterns of pharmacologically relevant constituents, thereby providing a scientific basis for resource evaluation and quality control of this regional germplasm. Methods: A widely targeted metabolomics approach was employed to profile metabolites in the roots, stems, and leaves of C. huchouensis. Comprehensive annotation and relative quantification were performed using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) combined with database matching. Cluster analysis and pathway enrichment were conducted to compare metabolic profiles across organs. Results: A total of 1561 metabolites were identified, exhibiting distinct organ-specific accumulation patterns. Flavonoids, alkaloids, and most phenolic acids were predominantly enriched in the aerial parts, whereas the roots accumulated high levels of glutathione and its related peptides, reflecting their significant antioxidant activity. Amino acids displayed complementary tissue-specific distribution, with peptides enriched in leaves and sulfur-containing amino acids such as L-methionine in stems. Organ-specific metabolic differences were significantly associated with pathways including flavonoid biosynthesis and linoleic acid metabolism. Notably, numerous pharmacologically active compounds, such as hispidulin, diosmetin, trigonelline, colchicoside, and oleanolic acid-3-O-xylosyl(1→3)glucuronide—exhibited marked tissue-selective accumulation. Conclusions: This first metabolomic study of C. huchouensis reveals organ-specific accumulation of bioactive compounds, providing a metabolic foundation for its quality control and rational utilization. Full article

Global climate change-driven drought aggravation seriously threatens the survival and distribution of desert shrubs. Nitraria sibirica Pall. has outstanding drought tolerance, yet its growth adaptation strategies and internal regulatory mechanisms under different soil moisture conditions lack systematic research. This study combined physiological determination with transcriptome and metabolome analyses to investigate its physiological responses and molecular regulation mechanisms at different growth stages and habitats. Nitraria sibirica from riparian habitats exhibited lower leaf organic carbon and higher total nitrogen. Desert-grown N. sibirica possessed far more drought-responsive differentially expressed genes and metabolites than riparian ones. Hormone signal transduction and lipid metabolism dominated regulation in riparian habitats, whereas secondary metabolite biosynthesis and amino acid metabolism—especially flavonoid biosynthesis and tryptophan metabolism—were core in desert habitats. Its drought response displayed distinct stage-specificity, with hormone signal transduction most enriched in drought-responsive genes across growth periods. This study clarifies the stress adaptation mechanisms of desert shrubs and provides theoretical support for germplasm evaluation and vegetation restoration in arid regions. Full article