Widely Targeted Metabolomics Analysis of Different Parts of Salsola collina Pall

Integrated Transcriptome and Metabolome Analysis of Salinity Tolerance in Response to Foliar Application of β-Alanine in Cotton Seedlings

Salinity is amongst the serious abiotic stresses cotton plants face, impairing crop productivity. Foliar application of β-alanine is employed to improve salt tolerance in various crops, but the exact mechanism behind it is not yet completely understood. An advanced line SDS-01 of upland cotton Gossypium hirsutum L. was utilized to determine its salt tolerance. Foliar treatment with the β-alanine solution at different concentrations was applied to the seedlings stressed with 0.8% NaCl solution. On the 10th day of treatment, samples were collected for transcriptome and metabolome analyses. β-alanine solution at a concentration of 25 mM was found to be the best treatment with the lowest mortality rate and highest plant height and above-ground biomass under salt stress. Both differentially expressed genes and accumulated metabolites analyses showed improved tolerance of treated seedlings. The photosynthetic efficiency improved in seedlings due to higher expression of photosynthesis-antenna proteins and activation of hormones signal transduction after treatment with β-alanine. Highly expressed transcription factors observed were MYB, HD-ZIP, ARF, MYC, EREB, DELLA, ABF, H2A, H4, WRKY, and HK involved in the positive regulation of salinity tolerance in β-alanine-treated seedlings. Furthermore, compared to the control, the high accumulation of polyamines, coumarins, organic acids, and phenolic compounds in the β-alanine-treated seedlings helped regulate cellular antioxidant (glutathione and L-Cysteine) production. Hence, to improve salt tolerance and productivity in cotton, foliar application of β-alanine at the seedling stage can be a valuable management practice.

Metabolome and transcriptome analyses identify the characteristics and expression of related saponins of the three genealogical plants of bead ginseng

Objective

The classification and clinical usage of the different species of bead ginseng are often confused. Therefore, we conducted an integrated metabolomics and transcriptome analysis of three main species of Panax, including Panax japonicas, Panax pseudoginseng, and Panax pseudo-ginseng var. elegantior.

Methods

A broad metabolome and transcriptome analysis for three origins of bead ginseng plants was performed using UPLC-ESI-MS/MS, RNA sequencing and annotation, and bioinformatic analysis of transcriptome data.

Results

The levels of 830 metabolites were determined. A total of 291 differentially accumulated metabolites (DAMs) between Panax pseudo-ginseng var. elegantior and Panax japonicas (Group A), with 73 upregulated and 218 downregulated. A total of 331 DAMs (110 upregulated and 221 downregulated) were found between Panax pseudoginseng and Panax japonicas (group B). There were 160 DAMs (102 up-regulated and 58 down-regulated) between Panax pseudoginseng and Panax pseudo-ginseng var. elegantior (group C). In addition, RNA sequencing was performed in the above three ways. A total of 16,074 differential expression genes (DEGs) were detected between Group A, in which 7,723 genes were upregulated and 8,351 genes were downregulated by RNA sequencing. Similarly, 15,705 genes were differentially expressed between group B, in which 7,436 genes were upregulated and 8,269 genes were downregulated. However, only 1,294 genes were differentially expressed between group C, in which 531 genes were upregulated and 763 genes were downregulated. We performed differential gene analysis on three groups of samples according to the Venn diagram and found that 181 differential genes were present. A total of 3,698 and 2,834 unique genes were in groups A and B, while 130 unique genes were in group C.

Conclusions

This study provides metabolome and transcriptome information for three bead ginseng plants. The analysis of the metabolite content showed differences in the attributes of the three bead ginseng, contained mainly flavonoids, phenolic acids as well as terpenes.

Insights into the nutritional properties and molecular basis of biosynthesis of amino acids and vitamins of Gastrodia elata offered by metabolomic and transcriptomic analysis

Gastrodia elata Blume (GE), a traditional and precious Chinese medicinal material, has been approved as a functional food. However, understanding GE's nutritional properties and its molecular basis remains limited. Here, metabolomic and transcriptomic analyses were performed on young and mature tubers of G. elata.f.elata (GEEy and GEEm) and G. elata.f.glauca (GEGy and GEGm). A total of 345 metabolites were detected, including 76 different amino acids and their derivatives containing all human essential amino acids (e.g., l-(+)-lysine, l-leucine), 13 vitamins (e.g., nicotinamide, thiamine), and 34 alkaloids (e.g., spermine, choline). GEGm has higher amino acid accumulation than GEEy, GEEm and GEGy, and vitamin contents were also slightly different in all four samples. Implying that GE, especially GEGm, is a kind of excellent complementary food as amino acid nutrition provider. From assembled 21,513 transcripts (genes) based on the transcriptome, we identified many genes that encode enzymes (e.g., pfkA, bglX, tyrAa, lysA, his B, aroA), which are responsible for the biosynthesis of amino acids and enzymes (e.g., nadA, URH1, NAPRT1, punA, rsgA) that related to vitamins metabolism. A total of 16 pairs of the differentially expressed genes (DEG) and differentially accumulated metabolites (DAM) (e.g., gene-tia006709 coding GAPDH and l-(+)-arginine, and gene-tia010180 coding tyrA and l-(+)-arginine) and three DEG-DAM pairs (e.g., gene-tia015379 coding NadA and nicotinate d-ribonucleoside) show significant similar positive or negative correlation based on three, and two comparisons of GEEy vs. GEGy, GEGy vs. GEGm, GEEy vs. GEGy and GEEm vs. GEGm, which involved into amino acid biosynthesis, and nicotinate nicotinamide metabolism, respectively. These results prove that the enzyme coded by these DEG promotes (positive correlation) or inhibits (negative correlation) the biosynthesis of parallel DAM in GE. Overall, the data and corresponding analysis in this study provide new insights into the nutritional properties of GE and the related molecular basis.

Analysis of Metabolites and Metabolic Pathways of Three Chinese Jujube Cultivar

Most studies on metabolites in jujube fruits focus on specific types of metabolites, but there are only a few comprehensive reports on the metabolites in jujube fruits. In order to understand the variance of metabolites in fruits of different jujube varieties. The objective of this study was to explore the metabolic components of jujube fruit by comparing three cultivars, namely Linyi LiZao (LZ), Jiaocheng SuantianZao (STZ), and Xianxian Muzao (MZ). The metabolites present in the fruits of these three cultivars were evaluated and compared. The results revealed the detection of 1059 metabolites across the three jujube varieties, with each cultivar exhibiting distinct metabolic characteristics. Notably, MZ exhibited a higher abundance of six metabolite classes, namely amino acids and derivatives, flavonoids, lipids, organic acids, phenolic acids, and terpenoids, compared to LZ. Conversely, LZ exhibited higher concentrations of alkaloids, lignans, coumarins, nucleotides, and their derivatives compared to the other two cultivars. In terms of STZ, its content of amino acids and derivatives, lignans and coumarins, organic acids, and phenolic acids was largely similar to that of LZ. However, the content of alkaloids, nucleotides, and their derivatives, and terpenoids was significantly higher in STZ compared to LZ. Additionally, STZ exhibited lower levels of flavonoids and lipids compared to LZ. Moreover, MZ was found to be less nutritionally rich than STZ, except for lignans and coumarins, as it displayed lower levels of all the metabolites. KEGG pathway enrichment analysis revealed six significantly different metabolic pathways (p < 0.05) between LZ and MZ, including arginine and proline metabolism, sphingolipid metabolism, flavonoid biosynthesis, glutathione metabolism, glycerophospholipid metabolism, and cysteine and methionine metabolism. The metabolites in STZ and MZ exhibited three significantly different pathways (p < 0.05), primarily associated with flavonoid biosynthesis, arginine and proline metabolism, and sphingolipid metabolism. The significantly differential metabolites between LZ and STZ were observed in the phenylpropionic acid biosynthesis pathway and the ubiquinone and other terpenoid-quinone biosynthesis pathways. LZ showed a closer relationship with STZ than with MZ. STZ and LZ exhibited higher medicinal values, while LZ had lower acidity and MZ displayed better antioxidant activity. This study presents the first thorough analysis of metabolites in LZ, STZ, and MZ cultivars, which can serve as a theoretical basis for quality analysis, functional research, and classification processing of jujube fruit.

Comparative analysis of the metabolites in Pinellia ternata from two producing regions using ultra-high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry

The rhizomes of Pinellia ternata have a long history of being used as a traditional Chinese herb. To determine the chemical constituents of Pinelliae rhizome, Xi banxia and Jing banxia were collected from two different producing regions and subjected to analysis using ultra-high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry. A total of 573 metabolites were identified in 12 different categories. Next, cluster analysis and principal component analysis were performed, which revealed a distinct separation between the two species. The analysis of the differential metabolites revealed that among the 155 metabolites in Xi banxia, 68 metabolites were upregulated, and 87 metabolites were downregulated. The relative concentration of flavonoids in Xi banxia was higher than that in Jing banxia, while the relative concentrations of alkaloids, phenolic acids, and terpenoids were higher in Jing banxia. These results would provide a theoretical basis for the pharmacological activity analysis and functional study of P. ternata.

Metabolomics Analysis of Different Tissues of Lonicera japonica Thunb. Based on Liquid Chromatography with Mass Spectrometry

Lonicera japonica Thunb. (LJT) has been widely used as medicines or food additives in Asian countries for thousands of years. The flower buds are often medicinally used, and the other tissues are ignored. However, flowers, leaves and stems have also been reported to have antimicrobial, anti-inflammatory and antioxidant effects. In the current study, un-targeted metabolomics analysis was performed to investigate the metabolic difference among different tissues (flowers, flower buds, stems and leaves) of LJT based on liquid chromatography with mass spectrometry. A total of 171 metabolites were identified, including 28 flavonoids, 35 phenolic acids, 43 iridoids, 9 amino acids, 6 nucleotides, 16 fatty acids, 22 lipids and 12 others. Four new secondary metabolites were discovered. Some flavonoids and iridoids were not detected in leaves and stems. Principal component analysis showed significant differences among four different tissues. Some 27, 81, 113 differential metabolites were found between flowers/flower buds, leaves/flower buds, stems/flower buds, respectively. Primary metabolites showed a higher content in the flowers and flower buds. For the flavonoids, flavones were mainly accumulated in the leaves, flavonols were mainly accumulated in the flower buds, and acylated flavonol glucosides were mainly accumulated in the flowers. Most phenolic acids showed a higher content in the flowers or flower buds, while phenolic acid-glucosides showed significantly higher content in the flower buds. The most abundant iridoids in the LJT also showed a higher content in the flowers and flower buds. These results can provide new insights into the understanding of the metabolites changes in different tissues, and lay a theoretical foundation for the comprehensive utilization of LJT.

Identification of nutritional components in unripe and ripe Docynia delavayi (Franch.) Schneid fruit by widely targeted metabolomics

Docynia delavayi (Franch.) Schneid is an evergreen tree with multiple benefits and high development and utilization value. The fruit is consumed as fresh and dry fruit, juices, and other products. However, it is unknown the chemical changes that occur upon fruit maturation. The metabolite content of unripe and ripe fruit was examined using UPLC-MS/MS technology based on a broadly targeted metabolome. We identified 477 metabolites, of which 130 differed between ripe and unripe fruit. These compounds are primarily involved in the biosynthesis of secondary metabolites, such as pantothenic acid, flavonoids, and amino acids. Moreover, in ripe fruit, there are 94 metabolites that are upregulated, particularly flavonoids and terpenoids. In comparison, compounds associated with sour flavors (amino acids, phenolic acids, organic acids) are down-regulated. Remarkably, these metabolites have a strong relationship with the medicinal properties of D. delavayi. This study provides a global perspective of the D. delavayi fruit metabolome and a comprehensive analysis of metabolomic variations during fruit development, thereby increasing the knowledge of the metabolic basis of important fruit quality traits in D. delavayi fruit.

Phytochemical analysis of Ziziphus jujube leaf at different foliar ages based on widely targeted metabolomics

Based on metabolomics, the metabolites of Jujube leaves LS1 (one bud and two leaves), LS2 (one bud and three leaves), and LS3 (one bud and four leaves) were taken and examined by ultra-high performance liquid chromatography-mass spectrometry technique. There were 22 substance categories that were identified. Principal component analysis was also utilized to distinguish the metabolomics at the three different foliar ages, and the results suggested that the samples at different foliar ages were clearly separated, demonstrating that the metabolites in the three foliar ages were significantly different. Through the screening of differential metabolites and hierarchical clustering analysis, our results suggested that the composition and the content distribution of the differential metabolites at three different foliar ages were significantly different. In the LS1, delphinidin, N-hydroxy tryptamine, serotonin, methylquercetin O-hexoside, tricin 7-O-hexoside, and eriodictyol C-hexoside were identified as the distinctive compounds. In the LS2, N-caffeoyl agmatine, lysoPC 18:3 (2n isomer), N-(4′-O-glycosyl)-p-coumaroyl-agmatine, dihydromyricetin, and hydroxy-methoxycinnamate were identified as the distinctive compounds. Similarly, the 3-O-p-coumaroyl-quinic acid, O-feruloyl 4-hydroxylcoumarin, isorhamnetin 3-O-neohesperidoside, cyanidin 3-O-galactoside, quercetin O-acetylhexoside, and DIMBOA glucoside were identified as the distinctive compounds in LS3. These characteristic compounds could provide a strong theoretical basis for rapid identification of jujube leaves at different foliar ages.

Optimization of the extraction process and metabonomics analysis of uric acid-reducing active substances from Gymnadenia R.Br. and its protective effect on hyperuricemia zebrafish

Background

As Gymnadenia R.Br. (Gym) has an obvious uric acid-lowering effect, but its specific bioactive substances and mechanism are still unclear. The key metabolites and pathways used by Gym to reduce uric acid (UA) were identify.

Methods

An optimized extraction process for urate-lowering active substances from Gym was firstly been carried out based on the xanthine oxidase (XOD) inhibition model in vitro; then, the Ultra-high-performance liquid chromatography and Q-Exactive mass spectrometry (UHPLC-QE-MS) based on non-targeted metabolomics analysis of Traditional Chinese Medicine were performed for comparison of Gym with ethanol concentration of 95% (low extraction rate but high XOD inhibition rate) and 75% (high extraction rate but low XOD inhibition rate), respectively; finally, the protective effect of ethanolic extract of Gym on zebrafish with Hyperuricemia (referred to as HUA zebrafish) was explored.

Results

We found that the inhibition rate of Gym extract with 95% ethanol concentration on XOD was 84.02%, and the extraction rate was 4.32%. Interestingly, when the other conditions were the same, the XOD inhibition rate of the Gym extract with 75% ethanol concentration was 76.84%, and the extraction rate was 14.68%. A total of 539 metabolites were identified, among them, 162 different metabolites were screened, of which 123 were up-regulated and 39 were down-regulated. Besides significantly reducing the contents of UA, BUN, CRE, ROS, MDA, and XOD activity in HUA zebrafish by Gym and acutely reduce the activity of SOD.

Conclusion

Along with the flavonoids, polyphenols, alkaloids, terpenoids, and phenylpropanoids, the ethanolic extract of Gym may be related to reduce the UA level of Gym.

Combined transcriptome and metabolome analysis revealed pathways involved in improved salt tolerance of Gossypium hirsutum L. seedlings in response to exogenous melatonin application

BACKGROUND

Salinization is major abiotic stress limiting cotton production. Melatonin (MT) has been implicated in salt stress tolerance in multiple crops including upland cotton. Here, we explored the transcriptomic and metabolomic response of a salt-tolerant self-bred high-yielding cotton line SDS-01, which was exogenously sprayed with four MT concentrations (50, 100, 200, and 500 μM).

RESULTS

Here we found that MT improves plant biomass and growth under salt stress. The combined transcriptome sequencing and metabolome profiling approach revealed that photosynthetic efficiency is improved by increasing the expressions of chlorophyll metabolism and antenna proteins in MT-treated seedlings. Additionally, linoleic acid and flavonoid biosynthesis were improved after MT treatment. The Na+/K+ homeostasis-related genes were increasingly expressed in salt-stressed seedlings treated with MT as compared to the ones experiencing only salt stress. Melatonin treatment activated a cascade of plant-hormone signal transduction and reactive oxygen scavenging genes to alleviate the detrimental effects of salt stress. The global metabolome profile revealed an increased accumulation of flavonoids, organic acids, amino acids and derivatives, saccharides, and phenolic acids in MT-treated seedlings. Interestingly, N, N'-Diferuloylputrescine a known antioxidative compound was highly accumulated after MT treatment.

CONCLUSION

Collectively, our study concludes that MT is a salt stress regulator in upland cotton and alleviates salt-stress effects by modulating the expressions of photosynthesis (and related pathways), flavonoid, ROS scavenging, hormone signaling, linoleic acid metabolism, and ion homeostasis-related genes.

Non-Targeted Analytical Technology in Herbal Medicines: Applications, Challenges, and Perspectives

Herbal medicines (HMs) have been utilized to prevent and treat human ailments for thousands of years. Especially, HMs have recently played a crucial role in the treatment of COVID-19 in China. However, HMs are susceptible to various factors during harvesting, processing, and marketing, affecting their clinical efficacy. Therefore, it is necessary to conclude a rapid and effective method to study HMs so that they can be used in the clinical setting with maximum medicinal value. Non-targeted analytical technology is a reliable analytical method for studying HMs because of its unique advantages in analyzing unknown components. Based on the extensive literature, the paper summarizes the benefits, limitations, and applicability of non-targeted analytical technology. Moreover, the article describes the application of non-targeted analytical technology in HMs from four aspects: structure analysis, authentication, real-time monitoring, and quality assessment. Finally, the review has prospected the development trend and challenges of non-targeted analytical technology. It can assist HMs industry researchers and engineers select non-targeted analytical technology to analyze HMs' quality and authenticity.

Widely targeted metabolomics reveals stamen petaloid tissue of Paeonia lactiflora Pall. being a potential pharmacological resource

Paeonia lactiflflora Pall. has a long edible and medicinal history because of the very high content of biologically active compounds. However, little information is available about the metabolic basis of pharmacological values of P. lactiflora flowers. In this study, we investigated metabolites in the different parts of P. lactiflora flowers, including petal, stamen petaloid tissue and stamen, by widely targeted metabolomics approach. A total of 1102 metabolites were identified, among which 313 and 410 metabolites showed differential accumulation in comparison groups of petal vs. stamen petaloid tissue and stamen vs. stamen petaloid tissue. Differential accumulated metabolites analysis and KEGG pathway analysis showed that the flavonoids were the most critical differential metabolites. Furthermore, difference accumulation of flavonoids, phenolic acids, tannins and alkaloids might lead to the differences in antioxidant activities and tyrosinase inhibition effects. Indeed, stamen petaloid tissue displayed better antioxidant and anti-melanin production activities than petal and stamen through experimental verification. These results not only expand our understanding of metabolites in P. lactiflora flowers, but also reveal that the stamen petaloid tissues of P. lactiflora hold the great potential as promising ingredients for pharmaceuticals, functional foods and skincare products.

Microbial community roles and chemical mechanisms in the parasitic development of Orobanche cumana

Orobanche cumana Wallr. is a holoparasite weed that extracts water and nutrients from its host the sunflower, thereby causing yield reductions and quality losses. However, the number of O. cumana parasites in the same farmland is distinctly different. The roots of some hosts have been heavily parasitized, while others have not been parasitized. What are the factors contributing to this phenomenon? Is it possible that sunflower interroot microorganisms are playing a regulatory role in this phenomenon? The role of the microbial community in this remains unclear. In this study, we investigated the rhizosphere soil microbiome for sunflowers with different degrees of O. cumana parasitism, that is, healthy, light infection, moderate infection, and severe infection on the sunflower roots. The microbial structures differed significantly according to the degree of parasitism, where Xanthomonadaceae was enriched in severe infections. Metagenomic analyses revealed that amino acid, carbohydrate, energy, and lipid metabolism were increased in the rhizosphere soils of severely infected sunflowers, which were attributed to the proliferation of Lysobacter. Lysobacter antibioticus (HX79) was isolated and its capacity to promote O. cumana seed germination and increase the germ tube length was confirmed by germination and pot experiments. Cyclo(Pro-Val), an active metabolite of strain HX79, was identified and metabolomic and molecular docking approaches confirmed it was responsible for promoting O. cumana seed germination and growth. And we found that Pseudomonas mandelii HX1 inhibited the growth of O. cumana in the host rhizosphere soil. Our findings clarify the role of rhizosphere microbiota in regulating the parasite O. cumana to possibly facilitate the development of a new weed suppression strategy.

Widely Targeted Metabolomics Analysis of Soybean and Chickpea and Their Different Advantages and New Functional Compounds for Diabetes

Soybean is widely used as a kind of bean for daily consumption. Chickpea is increasingly utilised because of its good healthcare function. At present, using chickpeas could have better results than soybeans in some areas. Previous studies of the two legumes focused on certain components and failed to fully reveal the differences between the two legumes. Thus, understanding the comprehensive similarities and differences between the two legumes is necessary to apply and develop these legumes effectively. In this study, we performed a UPLC-ESI-MS/MS-based widely targeted metabolomics analysis on two legumes. A total of 776 metabolites (including primary metabolites and secondary metabolites) were detected, which were divided into more than a dozen broad categories. The differential analysis of these metabolites showed that there were 480 metabolites with significant differences in relative contents between the two legumes. Compared with soybean, the expression of 374 metabolites of chickpea was down-regulated and that of 106 metabolites was up-regulated. The metabolic pathway analysis showed significant differences in the flavonoids biosynthesis, phenylpropanoid biosynthesis, linoleic acid metabolism and alkaloid biosynthesis between the two legumes. The advantages and applicability of the two kinds of legumes were confirmed through the analysis of anti-diabetic components. Moreover, some novel compounds (with contents higher than that of soybean) with hypoglycaemic activity were found in chickpea. This study provides an important reference for the in-depth study and comparative application of soybean and chickpea.

Widely Targeted Metabolic Profiling Reveals Differences in Polyphenolic Metabolites during Rosa xanthina f. spontanea Fruit Development and Ripening

Rose hips are rich in various nutrients and have long been used for food and medicinal purposes. Owing to the high phenolic content, rose hips can be used as natural antioxidants. In this study, ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to conduct a widely targeted metabolomics analysis on the polyphenolic components of Rosa xanthina f. spontanea in three ripening stages: unripe, half-ripe and fully ripe fruit. A total of 531 polyphenol metabolites were detected, including 220 phenolic acids, 219 flavonoids, 50 tannins and 42 lignans and coumarins. There were 160 differential metabolites between unripe and half-ripe rose hips (61 downregulated and 99 upregulated) and 157 differential metabolites between half-ripe and fully ripe rose hips (107 downregulated and 50 upregulated). The results of our study not only greatly enrich the chemical composition database of rose hips but also provide metabolomics information on the changes in polyphenolic metabolism during fruit development for the first time, which will help select the optimal harvest time of rose hips to achieve better quality.

Profiling alkaloids in Aconitum pendulum N. Busch collected from different elevations of Qinghai province using widely targeted metabolomics

Aconitum pendulum N. Busch (Ranunculaceae) is rich in alkaloids with anti-inflammatory and analgesic activities. Many studies have focused on the identification or quantification of alkaloid components using low-throughput tests. However, the metabolic differences of plants from environmentally distinct regions remain unclear. The present study profiled alkaloid chemical compounds in the rhizomes of A. pendulum from different regions. A total of 80 chemical compounds were identified using a widely targeted ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) approach. Principal component, hierarchical clustering, and orthogonal partial least squares-discriminant analyses of the chemical compounds indicated that the plants from 6 regions clearly separated into distinct groups. A total of 19 compounds contributed the most to the metabolite differences between collection areas and were identified as potential metabolic markers. The anti-inflammatory activities of the A. pendulum extracts were also evaluated and the potential environmental effects on the regulation of metabolite composition and bioactivity were explored. These results improve our understanding of the variation in chemical composition of plants from different regions and will serve as a reference for evaluating the medicinal value of A. pendulum in different environments.

Profiling of Widely Targeted Metabolomics for the Identification of chemical composition in epidermis, xylem and pith of Gleditsiae spina

Gleditsiae spina, the thorn of Gleditsia sinensis Lam., has a long history of being used as a traditional medicine in East Asian countries. However, only a few biologically active substances have been identified from Gleditsiae spina. In this study, the epidermis, xylem and pith of Gleditsiae spina, respectively, namely Gs-E, Gs-X and Gs-P, were studied. We used a widely targeted metabolomics method to investigate the chemical composition in Gs-E, Gs-X and Gs-P. A total of 728 putative metabolites were identified from Gleditsiae spina, including 211 primary metabolites and 517 secondary metabolites. These primary and secondary metabolites could be categorized into more than 10 different classes. Flavonoids, phenolic acids, lipids, and amino acids and derivatives, and organic acids constituted the main metabolite groups. Multivariate statistical analysis showed that the Gs-E, Gs-X and Gs-P samples could be clearly separated. Differential accumulated metabolite (DAM) analysis revealed that more than half of the DAMs exhibited the highest relative concentrations in Gs-E, and most of the DAMs showed the lowest relative concentrations in Gs-X. Moreover, 11 common differential primary metabolites and 79 common differential secondary metabolites were detected in all comparison groups. These results further our understanding of chemical composition and metabolite accumulation of Gleditsiae spina.