OBJECTIVE: In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell\'s regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown.
METHODS: We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, Spirodela polyrhiza, to investigate how WGD affects metabolite abundances per cell and per biomass.
RESULTS: Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains.
CONCLUSIONS: The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.

Comparative metabolomics plays a crucial role in investigating gene function, exploring metabolite evolution, and accelerating crop genetic improvement. However, a systematic platform for comparing intra- and cross-species metabolites is currently lacking. Here, we report the Plant Comparative Metabolome Database (PCMD; http://yanglab.hzau.edu.cn/PCMD), a multilevel comparison database based on predicted metabolic profiles in 530 plant species. PCMD serves as a platform for comparing metabolite characteristics at various levels, including species, metabolites, pathways, and biological taxonomy. The database also provides a series of user-friendly online tools, such as Species-comparison, Metabolites-enrichment, and ID conversion, enabling users to perform comparisons and enrichment analyses of metabolites across different species. In addition, PCMD establishes a unified system based on existing metabolite-related databases by standardizing metabolite numbering. PCMD is the most species-rich comparative plant metabolomics database currently available, and a case study demonstrated its capability to provide new insights into understanding plant metabolic diversity.

Sojae semen praeparatum (SSP), a fermented product known for its distinctive flavor and medicinal properties, undergoes a complex fermentation process due to the action of various microorganisms. Despite its widespread use, the effect of these microorganisms on the flavor compounds and functional components of SSP remains poorly understood. This study aimed to shed light on this aspect by identifying 20 metabolites as potential key flavor substances in SSP. Moreover, glycine and lysine were identified as crucial flavor substances. Additionally, 24 metabolites were identified as key functional components. The dominant microorganisms involved in the fermentation process were examined, revealing six genera of fungi and 12 genera of bacteria. At the species level, 16 microorganisms were identified as dominant through metagenome sequencing. Spearman correlation analysis demonstrated a strong association between dominant microorganisms and both flavor substances and functional components. Furthermore, the study validated the significance of four core functional microorganisms in improving the flavor and quality of SSP. This comprehensive exploration of functional microorganisms of SSP on key flavor substances/functional components during SSP fermentation. The study findings serve as a valuable reference for enhancing the overall flavor and quality of SSP.

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

Citrus reticulata pericarpium (CRP), the peel of Citrus reticulata \'Dahongpao\' (DHP) is a medicinal herb with significant therapeutic value for treating ulcerative colitis (UC). However, the active therapeutic components of CRP are unclear. This study aims to reveal the metabolites potentially associated with the pharmacological properties of CRP. We performed flavonoid-targeting metabolomics to characterize the components of CRP (anti-UC part), tangerine pith and Citrus reticulata semen (no anti-UC effects parts) of DHP and further screened active components of CRP using network pharmacology and molecular docking. Lipopolysaccharide (LPS)-stimulated RAW 264.7 cells were used to study the anti-inflammatory effect of the selected biologically active components. The therapeutic effects of the selected components were further investigated in a mouse model of UC induced by DSS. Three compounds, namely nobiletin, sinensetin, and hispidulin had the lowest docking scores among all screened ingredients. IL-6 and NO concentrations were significantly decreased in the LPS-stimulated RAW264.7 cells compared with control cells treated with these compounds. Moreover, UC mice treated with these compounds showed a reversal in weight loss, inhibition of shortening of colon length, and amelioration of colon injury. Our results indicated that sinensetin, nobiletin, and hispidulin can be potentially used for the treatment of UC.

METHODS: Aged laying hen is recently suggested as a more attractive animal model than rodent for studying nonalcoholic fatty liver disease (NAFLD) of humans. This study aims to reveal effects and metabolic regulation mechanisms of taurine alleviating NAFLD by using the aged laying hen model.
RESULTS: Liver histomorphology and biochemical indices show 0.02% taurine effectively alleviated fat deposition and liver damage. Comparative liver lipidomics and gene expressions analyses reveal taurine promoted lipolysis, fatty acids oxidation, lipids transport, and reduced oxidative stress in liver. Furthermore, comparative serum metabolomics screen six core metabolites negatively correlated with NAFLD, including linoleic acid, gamma-linolenic acid, pantothenate, L-methionine, 2-methylbutyroylcarnitine, L-carnitine; and two core metabolites positively correlated with NAFLD, including lysophosphatidylcholine (14:0/0:0) and lysophosphatidylcholine (16:0/0:0). Metabolic pathway analysis reveals taurine mainly regulated linoleic acid metabolism, cysteine and methionine metabolism, carnitine metabolism, pantothenic acid and coenzyme A biosynthesis metabolism, and glycerophospholipid metabolism to up-adjust levels of six negatively correlated metabolites and down-adjust two positively correlated metabolites for alleviating NAFLD of aged hens.
CONCLUSIONS: This study firstly reveals underlying metabolic mechanisms of taurine alleviating NAFLD using the aged hen model, thereby laying the foundation for taurine\'s application in the prevention of NAFLD in both human and poultry.

Poplar, a woody tree species, is widely used for industrial production and as a protective forest belt. Different clones of poplar exhibit clear variation in terms of morphological and physiological features, however, the impact of the genetic variation on the composition and abundance of wood metabolite have not been fully determined. In this study, ultra-high pressure liquid chromatography-triple time of flight-mass spectrometer (UPLC-Triple-TOF-MS) was used to explore the metabolite changes in poplar wood from three clones, including Populus deltoides CL. \'55/65\', P. deltoides CL. \'Danhong\', and P. nigra CL. \'N179\'. A total of 699 metabolites were identified. Clustering analysis and principal component analysis display that the metabolic differences of wood have allowed distinguishing different species of poplar. Meanwhile, eight significantly different metabolites were screened between P. deltoides and P. nigra, which may be considered as valuable markers for chemotaxonomy. In addition, the highly discriminant 352 metabolites were obtained among the three clones, and those may be closely related to the distinction in unique properties (e.g., growth, rigidity and tolerance) of the poplar wood cultivars. This study provides a foundation for further studies on wood metabolomics in poplar, and offers chemotaxonomic markers that will stimulate the early screening of potentially superior trees.

Yaks are tough animals living in Tibet\'s hypoxic stress environment. However, the metabolite composition of yak milk and its role in hypoxic stress tolerance remains largely unexplored. The similarities and differences between yak and human milk in hypoxic stress tolerance are also unclear. This study explored yak colostrum (YC) and yak mature milk (YMM) using GC-MS, and 354 metabolites were identified in yak milk. A comparative metabolomic analysis of yak and human milk metabolites showed that over 70% of metabolites were species-specific. Yak milk relies mainly on essential amino acids- arginine and essential branched-chain amino acids (BCAAs): L-isoleucine, L-leucine, and L-valine tolerate hypoxic stress. To slow hypoxic stress, human breast milk relies primarily on the neuroprotective effects of non-essential amino acids or derivates, such as citrulline, sarcosine, and creatine. In addition, metabolites related to hypoxic stress were significantly enriched in YC than in YMM. These results reveal the unique metabolite composition of yak and human milk and provide practical information for applying yak and human milk to hypoxic stress tolerance.

GuangChenpi (GCP), the dried pericarps of Citrus reticulata \'Chachi\', has been consumed daily as a food and dietary supplement in China for centuries. Its health benefits are generally recognized to be dependent on storage time. However, the specific roles of microorganisms and metabolites during long-term storage are still unclear. In this study, comparative metabolomics and high-throughput sequencing techniques were used to investigate the effects of co-existing microorganisms on the metabolites in GCP stored from 1 to 30 years. In total, 386 metabolites were identified and characterized. Most compounds were flavonoids (37%), followed by phenolic acids (20%). Seventeen differentially upregulated metabolites were identified as potential key metabolites in GCP, and 8 of them were screened out as key active ingredients by Venn diagram comparative analyses and verified by network pharmacology and molecular docking. In addition, long-term storage could promote the accumulation of secondary metabolites. Regarding the GCP microbiota, Xeromyces dominated the whole 30-year aging process.Moreover, Spearman correlation analysis indicated that Bacillus thuringiensis and Xeromyces bisporus, the dominant bacterial and fungal species, were strongly associated with the key active metabolites. Our results suggested that the change of active ingredients caused by the dominant microbial is one of the mechanisms affecting the GCP aging process. Our study provides novel functional insights and research perspectives on microorganism-associated metabolite changes that may improve the GCP aging process.

Insect metabolites play vital roles in regulating the physiology, behavior, and numerous adaptations of insects, which has contributed to them becoming the largest class of Animalia. However, systematic metabolomics within the insects is still unclear. The present study performed a widely targeted metabolomics analysis based on the HPLC-MS/MS technology to construct a novel integrated metabolic database presenting comprehensive multimetabolite profiles from nine insect species across three metamorphosis types. A total of 1442 metabolites were identified, including amino acids and their metabolites, organic acids and their derivatives, fatty acids (FAs), glycerophospholipids (GPs), nucleotides and their metabolites, and benzene and its substituted derivatives. Among them, 622 metabolites were used to generate a 0 and 1 matrix based on their presence or absence, and these metabolites were enriched in arachidonic acid metabolism, tyrosine metabolism, phenylalanine metabolism, and insect hormone biosynthesis pathways. Our study revealed that there is a high coincidence between the evolutionary relationships of the species and the hierarchical cluster based on the types of metabolites, while the quantities of the metabolites show a high diversity among species. The metabolome of the nine representative insects provides an important platform for implementing the analysis of insect systemic metabolites and biological events at the metabolic level.