Classification of grape seed residues from distillation industries in Europe according to the polyphenol composition highlights the influence of variety, geographical origin and color

Grape seed residues represent the raw material to produce several value-added products including polyphenol-rich extracts with nutritional and health attributes. Although the impact of variety and environmental conditions on the polyphenol composition in fresh berries is recognized, no data are available regarding grape seed residues. The chemical composition of grape seed residues from wine distilleries in France, Spain and Italy was characterized by mass spectrometry. Forty-two metabolites were identified belonging to non-galloylated and galloylated procyanidins as well as amino acids. Polyphenol concentrations in the red varieties originated from Champagne or Veneto were twice higher than in white varieties from the Loire Valley. The chemical profiles of grape seed residues were mainly classified according to the color variety with galloylated procyanidins as biomarkers of white varieties and non-galloylated procyanidins as biomarkers of red ones. The present approach might assist the selection of grape seed residues as quality raw materials for the production of polyphenol-rich extracts.

Effectiveness of modified atmosphere and vacuum packaging in preserving the volatilome of Stelvio PDO cheese over time

We aimed to assay the effectiveness of vacuum or modified atmosphere packaging in preserving the organoleptic characteristics of already ripened slices of Stelvio Protected Designation of Origin cheese during 3 months of storage. A multi-omics panel, including metagenomic and metabolomic analyses, was implemented together with physicochemical and sensory analyses. Among the 177 volatiles identified, 30 out of the 50 potent odorants were found to be prevalent, regardless of packaging. Isovaleric acid showed the highest relative intensity in all samples. Caproic and caprylic acids always increased during storage, while metabolites such as dodecane and 2,3-butanediol always decreased. Slow proteolysis occurred during storage, but did not differentiate cheese samples. The type of packaging differentiated the microbiota and volatile profile, with modified atmosphere packaging keeping the volatilome more stable. Out of the 50 potent odorants, 9 were relevant to sample discrimination, with 8-nonen-2-one, 2-nonanone, and caproic acid being more abundant in stored samples.

Impact of Saccharomyces cerevisiae yeast inoculation mode on wine composition

Inoculation modes are known to affect yeast behavior. Here, we characterized the impact of ADY and pre-culturing on the composition of the resulting wine, fermented by four commercial strains of Saccharomyces cerevisiae. Classical oenological parameters were not affected by the yeast inoculation mode. Using an untargeted metabolomic approach, a significant distinction in wine composition was noted regardless of the strain between the two inoculation modes, each associated with a specific metabolomic signature. 218 and 895 biomarkers were annotated, respectively, for ADYs associated with the preservation of wine polyphenols, and for pre-cultures related to the modulation of yeast nitrogen metabolism. Volatilome analysis revealed that the ester family was that most impacted by the inoculation mode whatever the strain. Ester production was enhanced in ADY condition. For the first time, the complete reprogramming of the yeast metabolism was revealed as a function of yeast preparation, which significantly impacts its volatilome and exometabolome.

Microbial mechanisms in nitrogen fertilization: Modulating the re-mobilization of clay mineral-bound cadmium in agricultural soils

Soil cadmium (Cd) can affect crop growth and food safety, and through the enrichment in the food chain, it ultimately poses a risk to human health. Reducing the re-mobilization of Cd caused by the release of protons and acids by crops and microorganisms after stabilization is one of the significant technical challenges in agricultural activities. This study aimed to investigate the re-mobilization of stabilized Cd within the clay mineral-bound fraction of soil and its subsequent accumulation in crops utilizing nitrogen ammonium nitrogen (NH4+-N) and nitrate nitrogen (NO3--N), at 60 and 120 mg kg-1. Furthermore, the study harvested root exudates at various growth stages to assess their direct influence on the re-mobilization of stabilized Cd and to evaluate the indirect effects mediated by soil microorganisms. The results revealed that, in contrast to the NO3--N treatment, the NH4+-N treatment significantly enhanced the conversion of clay mineral-bound Cd in the soil to NH4NO3-extractable Cd. It also amplified the accumulation of Cd in edible amaranth, with concentrations in roots and shoots rising from 1.7-6.0 mg kg-1 to 4.3-9.8 mg kg-1. The introduction of NH4+-N caused a decrease in the pH value of the rhizosphere soil and stimulated the production and secretion organic and amino acids, such as oxalic acid, lactic acid, stearic acid, succinic acid, and l-serine, from the crop roots. Furthermore, compared to NO3--N, the combined interaction of root exudates with NH4+-N has a more pronounced impact on the abundance of microbial genes associated with glycolysis pathway and tricarboxylic acid cycle, such as pkfA, pfkB, sucB, sucC, and sucD. The effects of NH4+-N on crops and microorganisms ultimately result in a significant increase in the re-mobilization of stabilized Cd. However, the simulated experiments showed that microorganisms only contribute to 3.8-6.6 % of the re-mobilization of clay mineral-bound Cd in soil. Therefore, the fundamental strategy to inhibit the re-mobilization of stabilized Cd in vegetable cultivation involves the regulation of proton and organic acid secretion by crops.

Metabolic disturbance of short- and medium-chain chlorinated paraffins to zebrafish larva

Chlorinated paraffins (CPs) are widely produced chemicals. Short-chain CPs (SCCPs) and medium-chain CPs (MCCPs) were listed as Persistent Organic Pollutants (POPs) and candidate POPs under the Stockholm Convention, respectively. The present study explored the developmental toxicity and metabolic disruption caused by SCCPs and MCCPs in zebrafish (Danio rerio) larvae. CPs exposure at environmentally relevant levels caused no obvious phenotypic changes with zebrafish larvae except that the body length shortening was observed after exposure to CPs at 1-200 μg/L for 7 day post fertilization. A further metabolomic approach was conducted to explore the early biological responses of developmental toxicity induced by CPs at low dose (1, 5, and 10 μg/L). The results of metabolic disorder, pathway analysis and chronic values indicated that, compared with SCCPs, MCCPs exhibited more risks to zebrafish larvae at low doses. Lipid metabolism was markedly affected in SCCPs exposure group, whereas MCCPs primarily disturbed lipid metabolism, amino acid, and nucleotide metabolisms. Compare with SCCPs, the relatively higher lipid solubility, protein affinity and metabolic rate of MCCPs can probably explain why MCCP-mediated metabolic disruption was significantly higher than that of SCCP. Notably, SCCPs and MCCPs have the same potential to cause cancer, but no evidence indicates the mutagenicity. In summary, our study provides insight into the potential adverse outcome for SCCP and MCCP at low doses.

Enteric coronavirus PDCoV evokes a non-Warburg effect by hijacking pyruvic acid as a metabolic hub

The Warburg effect, also referred as aerobic glycolysis, is a common metabolic program during viral infection. Through targeted metabolomics combined with biochemical experiments and various cell models, we investigated the central carbon metabolism (CCM) profiles of cells infected with porcine deltacoronavirus (PDCoV), an emerging enteropathogenic coronavirus with zoonotic potential. We found that PDCoV infection required glycolysis but decreased glycolytic flux, exhibiting a non-Warburg effect characterized by pyruvic acid accumulation. Mechanistically, PDCoV enhanced pyruvate kinase activity to promote pyruvic acid anabolism, a process that generates pyruvic acid with concomitant ATP production. PDCoV also hijacked pyruvic acid catabolism to increase biosynthesis of non-essential amino acids (NEAAs), suggesting that pyruvic acid is an essential hub for PDCoV to scavenge host energy and metabolites. Furthermore, PDCoV facilitated glutaminolysis to promote the synthesis of NEAA and pyrimidines for optimal proliferation. Our work supports a novel CCM model after viral infection and provides potential anti-PDCoV drug targets.

Abnormal energy metabolism, oxidative stress, and polyunsaturated fatty acid metabolism in depressed adolescents associated with childhood maltreatment: A targeted metabolite analysis

The purpose of this study was to explore the metabolomic differences between Major depressive disorder (MDD) and healthy individuals among adolescents and the association between childhood maltreatment (CM) and differentially abundant metabolites. The exploratory study included 40 first-episode drug-naïve adolescents with MDD and 20 healthy volunteers. We used the Beck Depression Inventory (BDI-13) to assess the severity of depression and the Childhood Trauma Questionnaire (CTQ) to assess the presence of childhood maltreatment. The plasma samples from all participants were collected for targeted metabolomics analysis using ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC‒MS/MS) methods. Spearman correlation was applied to analyse the correlations between clinical variables and metabolites. We found 11 increased metabolites and 37 decreased metabolites that differed between adolescents with MDD and healthy individuals. Pathway enrichment analysis of differentially abundant metabolites showed abnormalities in energy metabolism and oxidative stress in MDD. Importantly, we found that creatine, valine, isoleucine, glutamic acid and pyroglutamic acid were negatively correlated with the BDI-13, while isocitric acid, fatty acid and acylcarnitine were negatively associated with CTQ, and 4-hydroxyproline was positively related to CTQ in adolescents with MDD. These studies provide new ideas for the pathogenesis and potential treatment of adolescents with MDD.

Methionine inducing carbohydrate esterase secretion of Trichoderma harzianum enhances the accessibility of substrate glycosidic bonds

BACKGROUND

The conversion of plant biomass into biochemicals is a promising way to alleviate energy shortage, which depends on efficient microbial saccharification and cellular metabolism. Trichoderma spp. have plentiful CAZymes systems that can utilize all-components of lignocellulose. Acetylation of polysaccharides causes nanostructure densification and hydrophobicity enhancement, which is an obstacle for glycoside hydrolases to hydrolyze glycosidic bonds. The improvement of deacetylation ability can effectively release the potential for polysaccharide degradation.

RESULTS

Ammonium sulfate addition facilitated the deacetylation of xylan by inducing the up-regulation of multiple carbohydrate esterases (CE3/CE4/CE15/CE16) of Trichoderma harzianum. Mainly, the pathway of ammonium-sulfate's cellular assimilates inducing up-regulation of the deacetylase gene (Thce3) was revealed. The intracellular metabolite changes were revealed through metabonomic analysis. Whole genome bisulfite sequencing identified a novel differentially methylated region (DMR) that existed in the ThgsfR2 promoter, and the DMR was closely related to lignocellulolytic response. ThGsfR2 was identified as a negative regulatory factor of Thce3, and methylation in ThgsfR2 promoter released the expression of Thce3. The up-regulation of CEs facilitated the substrate deacetylation.

CONCLUSION

Ammonium sulfate increased the polysaccharide deacetylation capacity by inducing the up-regulation of multiple carbohydrate esterases of T. harzianum, which removed the spatial barrier of the glycosidic bond and improved hydrophilicity, and ultimately increased the accessibility of glycosidic bond to glycoside hydrolases.

Comparative physiological, biochemical, metabolomic, and transcriptomic analyses reveal the formation mechanism of heartwood for Acacia melanoxylon

Acacia melanoxylon is well known as a valuable commercial tree species owing to its high-quality heartwood (HW) products. However, the metabolism and regulatory mechanism of heartwood during wood development remain largely unclear. In this study, both microscopic observation and content determination proved that total amount of starches decreased and phenolics and flavonoids increased gradually from sapwood (SW) to HW. We also obtained the metabolite profiles of 10 metabolites related to phenolics and flavonoids during HW formation by metabolomics. Additionally, we collected a comprehensive overview of genes associated with the biosynthesis of sugars, terpenoids, phenolics, and flavonoids using RNA-seq. A total of ninety-one genes related to HW formation were identified. The transcripts related to plant hormones, programmed cell death (PCD), and dehydration were increased in transition zone (TZ) than in SW. The results of RT-PCR showed that the relative expression level of genes and transcription factors was also high in the TZ, regardless of the horizontal or vertical direction of the trunk. Therefore, the HW formation took place in the TZ for A. melanoxylon from molecular level, and potentially connected to plant hormones, PCD, and cell dehydration. Besides, the increased expression of sugar and terpenoid biosynthesis-related genes in TZ further confirmed the close connection between terpenoid biosynthesis and carbohydrate metabolites of A. melanoxylon. Furthermore, the integrated analysis of metabolism data and RNA-seq data showed the key transcription factors (TFs) regulating flavonoids and phenolics accumulation in HW, including negative correlation TFs (WRKY, MYB) and positive correlation TFs (AP2, bZIP, CBF, PB1, and TCP). And, the genes and metabolites from phenylpropanoid and flavonoid metabolism and biosynthesis were up-regulated and largely accumulated in TZ and HW, respectively. The findings of this research provide a basis for comprehending the buildup of metabolites and the molecular regulatory processes of HW formation in A. melanoxylon.

Variation in pigments in pecan testa during kernel development and storage

The pecan (Carya illinoinensis) is an important tree nut worldwide. Browning of the testa during storage considerably reduces its quality. However, the pigments that cause browning and their accumulation patterns are poorly understood. We analyzed the color changes in the testa during the five developmental stages of the kernel after storage at room temperature to compare differences in their color and identify the pigments. Samples exhibiting different colors along with their corresponding -80 °C storage samples were selected for metabolomic analysis. A total of 591 phenolic compounds were detected, 52 phenolics showed regulatory effects on testa discoloration, and 59 metabolites were identified as possible precursors of the pigments. This study revealed the most thorough phenolic composition of pecan to date. Further, the findings provide new insights into the mechanisms of testa browning, deepens our understanding of the bioactive value of pecans, and contributes to the breeding of less browning-susceptible varieties.

Untargeted Metabolomic to Access Chemical Differences Induced by Dual Endophyte Cultures Isolated from Euphorbia umbellata

Endophytic fungi live asymptomatically inside vegetal tissues, and such uncommon habitat contributes to their exceptional chemical diversity. Isolating natural products from endophytic fungi could fail due to silent biosynthetic gene clusters under ordinary in vitro culture conditions, and co-culturing has been assayed to trigger their metabolism. We carried out single and dual cultures with 13 endophyte strains isolated from Euphorbia umbellata leaves. Multivariate statistics applied to untargeted metabolomics compared the chemical profiles of all endophyte cultures. PCA analysis guided the selection of the Aspergillus pseudonomiae J1 - Porogramme brasiliensis J9 dual culture for its most significant chemical differentiation: Five compounds were putatively annotated in the J1-J9 culture according to UHPLC-HRMS data, kojic acid, haliclonol and its diastereoisomer, caffeic acid, and 2-(3,4-dihydroxyphenyl)acetaldehyde. Analysis by PLS-DA using VIP score showed that kojic acid displayed the most significative importance in discriminating single and dual J1-J9 cultures.

Metabolomic reveals the responses of sludge properties and microbial communities to high nitrite stress in denitrifying phosphorus removal systems

Nitrite, as an electron acceptor, plays a good role in denitrifying phosphorus removal (DPR); however, high nitrite concentration has adverse affects on sludge performance. We investigated the precise mechanisms of responses of sludge to high nitrite stress, including surface characteristics, intracellular and extracellular components, microbial and metabolic responses. When the nitrite stress reached 90 mg/L, the sludge settling performance was improved, but the activated sludge was aging. FTIR and XPS analysis revealed a significant increase in the hydrophobicity of the sludge, resulting in improve settling performance. However, the intracellular carbon sources synthesis was inhibited. In addition, the components in the tightly bound extracellular polymeric substances (TB-EPS) of sludge were significantly reduced and indicated the disturb of metabolism. Notably, Exiguobacterium emerged as a new genus when face high nitrite stress that could maintaining survival in hostile environments. Moreover, metabolomic analysis demonstrated strong biological response to nitrite stress further supported above results that include the inhibited of carbohydrate and amino acid metabolism. More importantly, some lipids (PS, PA, LysoPA, LysoPC and LysoPE) were significantly upregulated that related enhanced membrane lipid remodeling. The comprehensive analyses provide novel insights into the high nitrite stress responses mechanisms in activated sludge systems.

Untargeted metabolomics to discriminate liver and lung hydatid cysts: Importance of metabolites involved in the immune response

The Echinococcus granulosus sensu lato species complex is responsible for the neglected zoonotic disease known as cystic echinococcosis (CE). Humans and livestock are infected via fecal-oral transmission. CE remains prevalent in Western China, Central Asia, South America, Eastern Africa, and the Mediterranean. Approximately one million individuals worldwide are affected, influencing veterinary and public health, as well as social and economic matters. The infection causes slow-growing cysts, predominantly in the liver and lungs, but can also develop in other organs. The exact progression of these cysts is uncertain. This study aimed to understand the survival mechanisms of liver and lung CE cysts from cattle by determining their metabolite profiles through metabolomics and multivariate statistical analyses. Non-targeted metabolomic approaches were conducted using quadrupole-time-of-flight liquid chromatography/mass spectrometry (LC-QTOF-MS) to distinguish between liver and lung CE cysts. Data processing to extract the peaks on complex chromatograms was performed using XCMS. PCA and OPLS-DA plots obtained through multiple statistical analyses showed interactions of metabolites within and between groups. Metabolites such as glutathione, prostaglandin, folic acid, and cortisol that cause different immunological reactions have been identified both in liver and lung hydatid cysts, but in different ratios. Considering the differences in the metabolomic profiles of the liver and lung cysts determined in the present study will contribute research to enlighten the nature of the cyst and develop specific therapeutic strategies.

Impact of Bariatric Surgery on Circulating Metabolites and Cognitive Performance

INTRODUCTION

Bariatric surgery is an effective intervention to reduce obesity and improve associated comorbidities. However, its effects on cognitive function are still the subject of debate. Given that the bioavailability of circulating metabolites can influence brain metabolism and cognitive performance, we aimed to assess the effects of bariatric surgery on plasma metabolic profiles and cognitive performance.

METHODS

We recruited 26 women undergoing gastric bypass surgery. We conducted anthropometric assessments and collected plasma samples for metabolomic analysis. A set of 4 cognitive tests were used to evaluate cognitive performance. Participants were reevaluated 1 year post-surgery.

RESULTS

After surgery, attention capacity and executive function were improved, while immediate memory had deteriorated. Regarding metabolic profile, reduction of beta-tocopherol and increase of serine, glutamic acid, butanoic acid, and glycolic acid were observed. To better understand the relationship between cognitive function and metabolites, a cluster analysis was conducted to identify more homogeneous subgroups based on the cognitive performance. We identified cluster 1, which did not show changes in cognitive performance after surgery, and cluster 2, which showed improved attention and executive function, but reduced performance in the immediate memory test. Thus, cluster 2 was more homogeneous group that replicated the results of non-clustered subjects. Analysis of the metabolic profile of cluster 2 confirmed serine, glutamic acid, and glycolic acid as potential metabolites associated with cognitive performance.

CONCLUSIONS

Metabolites identified in this study have potential for biomarkers and alternative therapeutic target to prevent obesity-related cognitive decline.

KEY POINTS

• Attention capacity and executive function were improved 12 months post bariatric surgery. • Immediate memory was worsened 12 months post bariatric surgery. • Serine, glutamic acid, and glycolic acid are potential metabolites linked to the alteration of cognitive performance.

Enhanced delignification and production of bioactive compounds in wheat straw by optimizing sterilization methods for Irpex lacteus fermentation

This study aimed to examine the effects of sterilization methods on the degradation ability and bioactive compound production of Irpex lacteus in wheat straw. Following 28 days of fermentation, the lignin content of samples autoclaved and pasteurized at pH 4.5 was reduced by 16.0 % - 21.7 % compared to pasteurized samples without pH adjustment, accompanied by a significant increase in sugar yield ranging from 83.30 % - 96.35 %. Autoclaved samples exhibited the lowest total phenol content and antioxidant activity (P < 0.05). Bacillus occupied an absolute advantage (89.1 %) in samples pasteurized at pH 4.5, whereas 10 bacterial genera exhibited abundances above 1 % in pasteurized samples without pH adjustment. Furthermore, 45.1 % - 47.2 % of the metabolites comprised lipids and lipid-like molecules, and some of them were improved by pasteurization at pH 4.5. Overall, pasteurization at acidic conditions is an effective sterilization method for the fungal conversion of wheat straw.

Multi-omics approaches for drug-response characterization in primary biliary cholangitis and autoimmune hepatitis variant syndrome

BACKGROUND

Primary biliary cholangitis (PBC) and autoimmune hepatitis (AIH) variant syndrome (VS) exhibit a complex overlap of AIH features with PBC, leading to poorer prognoses than those with PBC or AIH alone. The biomarkers associated with drug response and potential molecular mechanisms in this syndrome have not been fully elucidated.

METHODS

Whole-transcriptome sequencing was employed to discern differentially expressed (DE) RNAs within good responders (GR) and poor responders (PR) among patients with PBC/AIH VS. Subsequent gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted for the identified DE RNAs. Plasma metabolomics was employed to delineate the metabolic profiles distinguishing PR and GR groups. The quantification of immune cell profiles and associated cytokines was achieved through flow cytometry and immunoassay technology. Uni- and multivariable logistic regression analyses were conducted to construct a predictive model for insufficient biochemical response. The performance of the model was assessed by computing the area under the receiver operating characteristic (AUC) curve, sensitivity, and specificity.

FINDINGS

The analysis identified 224 differentially expressed (DE) mRNAs, 189 DE long non-coding RNAs, 39 DE circular RNAs, and 63 DE microRNAs. Functional pathway analysis revealed enrichment in lipid metabolic pathways and immune response. Metabolomics disclosed dysregulated lipid metabolism and identified PC (18:2/18:2) and PC (16:0/20:3) as predictors. CD4+ T helper (Th) cells, including Th2 cells and regulatory T cells (Tregs), were upregulated in the GR group. Pro-inflammatory cytokines (IFN-γ, TNF-α, IL-9, and IL-17) were downregulated in the GR group, while anti-inflammatory cytokines (IL-10, IL-4, IL-5, and IL-22) were elevated. Regulatory networks were constructed, identifying CACNA1H and ACAA1 as target genes. A predictive model based on these indicators demonstrated an AUC of 0.986 in the primary cohort and an AUC of 0.940 in the validation cohort for predicting complete biochemical response.

CONCLUSION

A combined model integrating genomic, metabolic, and cytokinomic features demonstrated high accuracy in predicting insufficient biochemical response in patients with PBC/AIH VS. Early recognition of individuals at elevated risk for insufficient response allows for the prompt initiation of additional treatments.

Parkinson's disease-derived α-synuclein assemblies combined with chronic-type inflammatory cues promote a neurotoxic microglial phenotype

Parkinson's disease (PD) is a common age-related neurodegenerative disorder characterized by the aggregation of α-Synuclein (αSYN) building up intraneuronal inclusions termed Lewy pathology. Mounting evidence suggests that neuron-released αSYN aggregates could be central to microglial activation, which in turn mounts and orchestrates neuroinflammatory processes potentially harmful to neurons. Therefore, understanding the mechanisms that drive microglial cell activation, polarization and function in PD might have important therapeutic implications. Here, using primary microglia, we investigated the inflammatory potential of pure αSYN fibrils derived from PD patients. We further explored and characterized microglial cell responses to a chronic-type inflammatory stimulation combining PD patient-derived αSYN fibrils (FPD), Tumor necrosis factor-α (TNFα) and prostaglandin E2 (PGE2) (TPFPD). We showed that FPD hold stronger inflammatory potency than pure αSYN fibrils generated de novo. When combined with TNFα and PGE2, FPD polarizes microglia toward a particular functional phenotype departing from FPD-treated cells and featuring lower inflammatory cytokine and higher glutamate release. Whereas metabolomic studies showed that TPFPD-exposed microglia were closely related to classically activated M1 proinflammatory cells, notably with similar tricarboxylic acid cycle disruption, transcriptomic analysis revealed that TPFPD-activated microglia assume a unique molecular signature highlighting upregulation of genes involved in glutathione and iron metabolisms. In particular, TPFPD-specific upregulation of Slc7a11 (which encodes the cystine-glutamate antiporter xCT) was consistent with the increased glutamate response and cytotoxic activity of these cells toward midbrain dopaminergic neurons in vitro. Together, these data further extend the structure-pathological relationship of αSYN fibrillar polymorphs to their innate immune properties and demonstrate that PD-derived αSYN fibrils, TNFα and PGE2 act in concert to drive microglial cell activation toward a specific and highly neurotoxic chronic-type inflammatory phenotype characterized by robust glutamate release and iron retention.

Analysis of heterologous expression of phaCBA promotes the acetoin stress response mechanism in Bacillus subtilis using transcriptomics and metabolomics approaches

Acetoin, a versatile platform chemical and popular food additive, poses a challenge to the biosafety strain Bacillus subtilis when produced in high concentrations due to its intrinsic toxicity. Incorporating the PHB synthesis pathway into Bacillus subtilis 168 has been shown to significantly enhance the strain's acetoin tolerance. This study aims to elucidate the molecular mechanisms underlying the response of B. subtilis 168-phaCBA to acetoin stress, employing transcriptomic and metabolomic analyses. Acetoin stress induces fatty acid degradation and disrupts amino acid synthesis. In response, B. subtilis 168-phaCBA down-regulates genes associated with flagellum assembly and bacterial chemotaxis, while up-regulating genes related to the ABC transport system encoding amino acid transport proteins. Notably, genes coding for cysteine and D-methionine transport proteins (tcyB, tcyC and metQ) and the biotin transporter protein bioY, are up-regulated, enhancing cellular tolerance. Our findings highlight that the expression of phaCBA significantly increases the ratio of long-chain unsaturated fatty acids and modulates intracellular concentrations of amino acids, including L-tryptophan, L-tyrosine, L-leucine, L-threonine, L-methionine, L-glutamic acid, L-proline, D-phenylalanine, L-arginine, and membrane fatty acids, thereby imparting acetoin tolerance. Furthermore, the supplementation with specific exogenous amino acids (L-alanine, L-proline, L-cysteine, L-arginine, L-glutamic acid, and L-isoleucine) alleviates acetoin's detrimental effects on the bacterium. Simultaneously, the introduction of phaCBA into the acetoin-producing strain BS03 addressed the issue of insufficient intracellular cofactors in the fermentation strain, resulting in the successful production of 70.14 g/L of acetoin through fed-batch fermentation. This study enhances our understanding of Bacillus's cellular response to acetoin-induced stress and provides valuable insights for the development of acetoin-resistant Bacillus strains.

Metabolomic Analysis in Saliva and Different Brain Regions of Older Mice with Postoperative Delirium Behaviors

Objective

Postoperative delirium (POD) has become a critical challenge with severe consequences and increased incidences as the global population ages. However, the underlying mechanism is yet unknown. Our study aimed to explore the changes in metabolites in three specific brain regions and saliva of older mice with postoperative delirium behavior and to identify potential non-invasive biomarkers.

Methods

Eighteen-month-old male C57/BL6 mice were randomly assigned to the anesthesia/surgery or control group. Behavioral tests were conducted 24 h before surgery and 6, 9, and 24 h after surgery. Complement C3 (C3) and S100 calcium-binding protein B protein (S100beta) levels were measured in the hippocampus, and a metabolomics analysis was performed on saliva, hippocampus, cortex, and amygdala samples.

Results

In total, 43, 33, 38, and 14 differential metabolites were detected in the saliva, hippocampus, cortex, and amygdala, respectively. "Pyruvate" "alpha-linolenic acid" and "2-oleoyl-1-palmitoy-sn-glycero-3-phosphocholine" are enriched in one common pathway and may be potential non-invasive biomarkers for POD. Common changes were observed in the three brain regions, with the upregulation of 1-methylhistidine and downregulation of D-glutamine.

Conclusion

Dysfunctions in energy metabolism, oxidative stress, and neurotransmitter dysregulation are implicated in the development of POD. The identification of changes in the level of salivary metabolite biomarkers could aid in the development of noninvasive diagnostic methods for POD.

TON1 recruiting motif 21 positively regulates the flavonoid metabolic pathway at the translational level in Arabidopsis thaliana

MAIN CONCLUSION

This study reveals that TRM21 acts as a positive regulator of flavonoid biosynthesis at the translational level in Arabidopsis, impacting both secondary metabolites and genes associated with root hair growth. TRM (TONNEAU1-recruiting motif) superfamily proteins are reported to be involved in microtubule assembly. However, the functions of this protein family are just beginning to be uncovered. Here, we provide metabolomic and genetic evidence that 1 of the 34 TRM members, TRM21, positively regulates the biosynthesis of flavonoids at the translational level in Arabidopsis thaliana. A loss-of-function mutation in TRM21 led to root hair growth defects and stunted plant growth, accompanied by significant alterations in secondary metabolites, particularly a marked reduction in flavonoid content. Interestingly, our study revealed that the transcription levels of genes involved in the flavonoid biosynthesis pathway remained unchanged in the trm21 mutants, but there was a significant downregulation in the translation levels of certain genes [flavanone 3-hydroxylase (F3H), dihydroflavonol-4-reductase (DFR), anthocyanidin reductase (ANR), flavanone 3'-hydroxylase (F3'H), flavonol synthase (FLS), chalcone synthase (CHS)]. Additionally, the translation levels of some genes related to root hair growth [RHO-related GTPases of plant 2 (ROP2), root hair defective 6 (RHD6), root hair defective 2 (RHD2)] were also reduced in the trm21 mutants. Taken together, these results indicate that TRM21 functions as a positive regulator of flavonoid biosynthesis at the translational level in Arabidopsis.

Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets

BACKGROUND

The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear. Herein, we investigated the potential correlation between the gut microbiota of piglets and their disease resistance using single-cell transcriptomics, 16S amplicon sequencing, metagenomics, and untargeted metabolomics.

RESULTS

Porcine epidemic diarrhea virus (PEDV) infection leads to significant changes in the gut microbiota of piglets. Notably, Landrace pigs lose their resistance quickly after being infected with PEDV, but transplanting the fecal microbiota of Min pigs to Landrace pigs alleviated the infection status. Macrogenomic and animal protection models identified Lactobacillus reuteri and Lactobacillus amylovorus in the gut microbiota as playing an anti-infective role. Moreover, metabolomic screening of the secondary bile acids' deoxycholic acid (DCA) and lithocholic acid (LCA) correlated significantly with Lactobacillus reuteri and Lactobacillus amylovorus, but only LCA exerted a protective function in the animal model. In addition, LCA supplementation altered the distribution of intestinal T-cell populations and resulted in significantly enriched CD8+ CTLs, and in vivo and in vitro experiments showed that LCA increased SLA-I expression in porcine intestinal epithelial cells via FXR receptors, thereby recruiting CD8+ CTLs to exert antiviral effects.

CONCLUSIONS

Overall, our findings indicate that the diversity of gut microbiota influences the development of the disease, and manipulating Lactobacillus reuteri and Lactobacillus amylovorus, as well as LCA, represents a promising strategy to improve PEDV infection in piglets. Video Abstract.

Photocatalytic inactivation mechanism of nano-BiPO4 against Vibrio parahaemolyticus and its application in abalone

Vibrio parahaemolyticus (V. parahaemolyticus) is the main pathogenic bacteria in seafood that can cause serious food-borne illness. The annual incidence of V. parahaemolyticus infection in the United States exceeds 45,000 cases, indicating there are potential shortcomings in seafood sterilization techniques. Meanwhile, the ongoing emergence of antibiotic-resistant strains highlights the urgent need for novel bacteriostatic strategies to eliminate V. parahaemolyticus. Nano-BiPO4 is a semiconductor with high H2O2 production efficiency and has potential for photocatalytic bacterial inactivation. But the effectiveness and mechanism of BiPO4 photocatalytic inactivation of V. parahaemolyticus has not been reported. In this study, nano-BiPO4 synthesized in pure water (P1) was found to exhibit optimal H2O2 production efficiency (1203 μmol h-1g-1) and antibacterial activity (in 0.8 g/L). Under UV light irradiation, P1 induced alterations in bacterial cell morphology, elevation in intracellular levels of ROS, H2O2, O2-, GSSG and MDA, and reduction in GSH level. Meanwhile, metabolomic analysis revealed that P1 stimulates the arginine biosynthesis, TCA cycle and alanine, aspartate and glutamate metabolism. These abnormal changes in the oxidative stress indicators and metabolic pathways proved that the bacterial damage was related to the H2O2 produced by nano-BiPO4 photocatalysis. Moreover, sliced abalone and hemolysis assay were used to demonstrate the applicability and biosafety of P1. This study provides theoretical support for exploring nano-BiPO4 as a bacterial inhibitor against V. parahaemolyticus.

Transcriptomic and metabolomic analysis of the mechanisms underlying stress responses of the freshwater snail, Pomacea canaliculata, exposed to different levels of arsenic

Arsenic (As) pollution poses an important problem, but limited information is available about the physiological effects of As on freshwater invertebrates. Here, we investigated the physiological effects of chronic As exposure on Pomacea canaliculata, a freshwater invertebrate. High level of As (Ⅲ, 5 mg/L) inhibited the growth of P. canaliculata, whereas low level of As (Ⅲ, 2 mg/L) promoted growth. Pathological changes in shell and cellular ultrastructure due to As accumulation likely explain the growth inhibition at high As level. Low level of As simulated the expression of genes related to DNA replication and chitosan biosynthesis, potentially accounting for the growth promotion observed. High level of As enrichment pathways primarily involved cytochrome P450, glutathione, and arachidonic acid-mediated metabolism of xenobiotics. ATP-binding cassette (ABC) transporters, specifically the ABCB and ABCC subfamilies, were involved in As transport. Differential metabolites were mainly associated with the metabolism and biosynthesis of amino acids. These findings elucidate the dose-dependent effects of As stress on P. canaliculata growth, with low levels promoting and high levels inhibiting. Additionally, our findings also provide insights into As metabolism and transport in P. canaliculata.

A multi-omics analysis of viral nucleic acid poly(I:C) responses to mammalian testicular stimulation

The male reproductive system has a standard immune response regulatory mechanism, However, a variety of external stimuli, including viruses, bacteria, heat, and medications can damage the testicles and cause orchitis and epididymitis. It has been shown that various RNA viruses are more likely to infect the testis than DNA viruses, inducing orchitis and impairing testicular function. It was found that local injection of the viral RNA analog poly(I:C) into the testes markedly disrupted the structure of the seminiferous tubules, accompanied by apoptosis and inflammation. Poly(I:C) mainly inhibited the expression of testosterone synthesis-associated proteins, STAR and MGARP, and affected the synthesis and metabolism of amino acids and lipids in the testis. This led to the disruption of the metabolite levels in the testis of mice, thus affecting the normal spermatogenesis process. The present study analyzed the acute inflammatory response of the testis to viral infection using a multi-omics approach. It provides insights into how RNA virus infection impairs testicular function and offers a theoretical basis for future studies on immune homeostasis and responses under stress conditions in male reproduction.

Chronic lactate exposure promotes cardiomyocyte cytoskeleton remodelling

We investigated the effect of growing on lactate instead of glucose in human cardiomyocyte assessing their viability, cell cycle activity, oxidative stress and metabolism by a proteomic and metabolomic approach. In previous studies performed on elite players, we found that adaptation to exercise is characterized by a chronic high plasma level of lactate. Lactate is considered not only an energy source but also a signalling molecule and is referred as "lactormone"; heart is one of the major recipients of exogenous lactate. With this in mind, we used a cardiac cell line AC16 to characterize the lactate metabolic profile and investigate the metabolic flexibility of the heart. Interestingly, our data indicated that cardiomyocytes grown on lactate (72 h) show change in several proteins and metabolites linked to cell hypertrophy and cytoskeleton remodelling. The obtained results could help to understand the effect of this metabolite on heart of high-performance athletes.

Integrated analysis of metabolomic and transcriptomic profiling reveals the effect of Atractylodes oil on Spleen Yang Deficiency Syndrome in rats

ETHNOPHARMACOLOGICAL RELEVANCE

Spleen Yang Deficiency Syndrome (SYDS), which is a syndrome commonly treated with Traditional Chinese Medicine (TCM), manifests as overall metabolic dysfunction caused mainly by digestive system disorders. Atractylodes lancea (Thunb.) DC. (AL) is a widely used traditional herb with the efficacy of eliminate dampness and strengthen the spleen, Atractylodes oil (AO) is a medicinal component of AL and can be used to treat various gastrointestinal disorders. However, its effects on SYDS and underlying mechanisms have not been clarified to date.

AIM OF THE STUDY

The present study aimed to investigate the efficacy of AO in the improvement of the symptoms of SYDS in rat and the underlying mechanism by integrating transcriptomics, and metabolomics.

MATERIALS AND METHODS

The SYDS rats induced by reserpine were treated with AO. The protective effect of AO on SYDS rats was evaluated by serum biochemical detection, histopathological analyses. Enzyme-linked immunosorbent assay (ELISA), colorimetric assay and immunofluorescence (IF) were performed to determine the levels of relevant indicators of mitochondrial function and energy metabolism in the liver. Liver metabolites and transcript levels were assessed by non-targeted metabolomics and transcriptomics to analyze potential molecular mechanisms and targets. The expression of the corresponding proteins was verified using Western blotting.

RESULTS

AO not only regulated the digestion, absorption function and oxidative stress status of SYDS rats, but also improved mitochondrial function and alleviated energy metabolism disorders in SYDS rats. Metabolomic and transcriptomic analyses demonstrated that AO regulation is mainly exerted in amino acid metabolism, unsaturated fatty acid metabolism, TCA cycle as well as PPAR and AMPK signaling pathways. In addition, The AMPK signaling pathway was verified and AO promoted AMPK phosphorylation and the expression of SIRT1, PGC-1α, and PPARα in SYDS rats.

CONCLUSIONS

The therapeutic effect of AO on SYDS is potentially attributable to activation of the AMPK/SIRT1/PGC-1α signaling pathway, which enhances transport and regulation of energy metabolism.

Exercise Alleviates Fluoride-Induced Learning and Memory Impairment in Mice: Role of miR-206-3p and PREG

Fluorosis decreases the learning and memory ability in humans and animals, while exercise can reduce the risk of cognitive decline. However, the effect of exercise on learning and memory in fluoride-exposed mice is unclear. For this purpose, in this study, mice were randomly allotted into four groups (16 mice per group, half male and half female): control group (group C), fluoride group (group F, 100 mg/L sodium fluoride (NaF)), exercise group (group E, treadmill exercise), and E plus F group (group EF, treadmill exercise, and 100 mg/L NaF). During 6 months of exposure, exercise alleviated the NaF-induced decline in memory and learning. In addition, NaF induced injuries in mitochondria and myelin sheath ultrastructure and reduced the neurons number, while exercise restored them. Metabolomics results showed that phosphatidylethanolamine, pregnenolone (PREG), and lysophosphatidic acid (LysoPA) were altered among groups C, F, and EF. Combined with previous studies, it can be suggested that PREG might be a biomarker in response to exercise-relieving fluorine neurotoxicity. The miRNA sequencing results indicated that in the differently expressed miRNAs (DEmiRNAs), miR-206-3p, miR-96-5p, and miR-144-3p were shared in groups C, F, and EF. After the QRT-PCR validation and in vitro experiments, it was proved that miR-206-3p could reduce cell death and regulate AP-1 transcription factor subunit (JunD) and histone deacetylase 4 (HDAC4) to alleviate fluoride neurotoxicity. To sum up, the current study reveals that exercise could alleviate NaF-induced neurotoxicity by targeting miR-206-3p or PREG, which will contribute to revealing the pathogenesis and therapeutic method of fluoride neurotoxicity.

Serum multi-omics analysis in hindlimb unloading mice model: Insights into systemic molecular changes and potential diagnostic and therapeutic biomarkers

Microgravity, in space travel and prolonged bed rest conditions, induces cardiovascular deconditioning along with skeletal muscle mass loss and weakness. The findings of microgravity research may also aid in the understanding and treatment of human health conditions on Earth such as muscle atrophy, and cardiovascular diseases. Due to the paucity of biomarkers and the unknown underlying mechanisms of cardiovascular and skeletal muscle deconditioning in these environments, there are insufficient diagnostic and preventative measures. In this study, we employed hindlimb unloading (HU) mouse model, which mimics astronauts in space and bedridden patients, to first evaluate cardiovascular and skeletal muscle function, followed by proteomics and metabolomics LC-MS/MS-based analysis using serum samples. Three weeks of unloading caused changes in the function of the cardiovascular system in c57/Bl6 mice, as seen by a decrease in mean arterial pressure and heart weight. Unloading for three weeks also changed skeletal muscle function, causing a loss in grip strength in HU mice and atrophy of skeletal muscle indicated by a reduction in muscle mass. These modifications were partially reversed by a two-week recovery period of reloading condition, emphasizing the significance of the recovery process. Proteomics analysis revealed 12 dysregulated proteins among the groups, such as phospholipid transfer protein, Carbonic anhydrase 3, Parvalbumin alpha, Major urinary protein 20 (Mup20), Thrombospondin-1, and Apolipoprotein C-IV. On the other hand, metabolomics analysis showed altered metabolites among the groups such as inosine, hypoxanthine, xanthosine, sphinganine, l-valine, 3,4-Dihydroxyphenylglycol, and l-Glutamic acid. The joint data analysis revealed that HU conditions mainly impacted pathways such as ABC transporters, complement and coagulation cascades, nitrogen metabolism, and purine metabolism. Overall, our results indicate that microgravity environment induces significant alterations in the function, proteins, and metabolites of these mice. These observations suggest the potential utilization of these proteins and metabolites as novel biomarkers for assessing and mitigating cardiovascular and skeletal muscle deconditioning associated with such conditions.

Physio-biochemical and metabolomic responses of the woody plant Dalbergia odorifera to salinity and waterlogging

BACKGROUND

Trees have developed a broad spectrum of molecular mechanisms to counteract oxidative stress. Secondary metabolites via phenolic compounds emblematized the hidden bridge among plant kingdom, human health, and oxidative stress. Although studies have demonstrated that abiotic stresses can increase the production of medicinal compounds in plants, research comparing the efficiency of these stresses still needs to be explored. Thus, the present research paper provided an exhaustive comparative metabolomic study in Dalbergia odorifera under salinity (ST) and waterlogging (WL).

RESULTS

High ST reduced D. odorifera's fresh biomass compared to WL. While WL only slightly affected leaf and vein size, ST had a significant negative impact. ST also caused more significant damage to water status and leaflet anatomy than WL. As a result, WL-treated seedlings exhibited better photosynthesis and an up-regulation of nonenzymatic pathways involved in scavenging reactive oxygen species. The metabolomic and physiological responses of D. odorifera under WL and salinity ST stress revealed an accumulation of secondary metabolites by the less aggressive stress (WL) to counterbalance the oxidative stress. Under WL, more metabolites were more regulated compared to ST. ST significantly altered the metabolite profile in D. odorifera leaflets, indicating its sensitivity to salinity. WL synthesized more metabolites involved in phenylpropanoid, flavone, flavonol, flavonoid, and isoflavonoid pathways than ST. Moreover, the down-regulation of L-phenylalanine correlated with increased p-coumarate, caffeate, and ferulate associated with better cell homeostasis and leaf anatomical indexes under WL.

CONCLUSIONS

From a pharmacological and medicinal perspective, WL improved larger phenolics with therapeutic values compared to ST. Therefore, the data showed evidence of the crucial role of medical tree species' adaptability on ROS detoxification under environmental stresses that led to a significant accumulation of secondary metabolites with therapeutic value.

Integrated microbiota and multi-omics analysis reveal the differential responses of earthworm to conventional and biodegradable microplastics in soil under biogas slurry irrigation

As one of the promising alternatives of conventional plastic mulching film (C-PMF), biodegradable plastic mulching films (B-PMF) were employed in agronomy production to alleviate the environmental burden of C-PMF. However, information regarding the potential toxicity effects of biodegradable microplastics (MPs) in soil still in scarcity, and the available findings were found to be controversial. Additionally, little is known about the molecular toxicity effects of conventional and biodegradable MPs on terrestrial organisms. Thus, 5 % (w/w) biodegradable (polylactic acid, PLA) and conventional (polyvinylchloride, PVC; low-density polyvinylchloride, LDPE) MPs were employed to assess the toxicity effects on Eisenia fetida in agricultural soil with biogas slurry irrigation. In the present study, transcriptomic, metabolomic profiles and individual indexes were selected to reveal the toxicity mechanisms from molecular level to the individual response. Furthermore, dysbiosis of bacterial community in gut was also investigated for obtaining comprehensive knowledge on the MPs toxicity. At the end of the exposure, the number of survival earthworms after MPs exposure was significantly reduced. Compared with the initial body weight, PLA and LDPE increased the biomass of earthworms after MPs exposure, while no significant influence on the biomass was observed in PVC treatment. Microbacterium, Klebsiella and Chryseobacterium were significantly enriched in earthworm gut after PLA, PVC and LDPE exposure, respectively (p < 0.05). Transcriptomic and metabolomic analysis revealed that PLA exposure induced neurotransmission disorder and high energetic expenditure in earthworms. However, PVC and LDPE inhibited the nutrient absorption efficiency and activated the innate immunity responses of earthworms. The PLS-SEM results showed that the effects of MPs were dominated by the polymer types, and hence, significantly and directly influence the gut bacterial community of earthworms. This study provides a better understanding of the similarities and discrepancies in toxicity effects of biodegradable and conventional MPs from the perspectives of individual, gut bacterial community, transcriptome and metabolome.

Mechanism of Xiaojianzhong decoction in alleviating aspirin-induced gastric mucosal injury revealed by transcriptomics and metabolomics

ETHNOPHARMACOLOGICAL RELEVANCE

Aspirin, as a first-line drug for the treatment of cardiovascular diseases, currently has high clinical usage. However, reports of aspirin-induced gastric mucosal injury are increasing. Xiaojianzhong decoction (XJZD), a classic traditional Chinese medicine formula, has been shown to alleviate gastric mucosal injury, although its potential mechanism of action requires further study.

AIM OF THE STUDY

This study aimed to explore the effect and mechanism of XJZD in preventing aspirin-induced gastric mucosal injury.

MATERIALS AND METHODS

Aspirin was used to induce damage in the morning, while XJZD was applied as an intervention in the afternoon. The compounds in the XJZD were analyzed by means of both high-performance liquid chromatography and ultra-performance liquid chromatography-tandem mass spectrometry. The overall condition of the aspirin-related gastric mucosal injury was evaluated. The expressions of inflammatory factors and tight-junction-related proteins and apoptosis were observed via immunohistochemistry and immunofluorescence. The expression levels of the apoptosis-related proteins were detected using Western blot. Transcriptomics was used to perform the integrative analysis of gastric tissues, which was then validated. Molecular dynamics was used to explore the interaction of key compounds within the XJZD with relevant targets. Finally, non-targeted metabolomics was used to observe any metabolic changes and construct a network between the differentially expressed genes and the differential metabolites to elucidate their potential relationship.

RESULTS

XJZD can alleviate inflammation response, maintain the gastric mucosal barrier's integrity, reduce apoptosis and necroptosis levels, and promote the proliferation and repair of gastric mucosal tissues. Its mechanism of action may be related to the regulation of TNF-α signaling. Furthermore, molecular docking showed that the cinnamaldehyde within XJZD played an important role in its effects. In addition, XJZD can correct metabolic disorders, mainly regulating amino acid metabolism pathways. Moreover, six differential genes (Cyp1a2, Cyp1a1, Pla2g4c, etc.) were determined to alleviate both gastric mucosal injury and inflammation by regulating arachidonic acid metabolism, Tryptophan metabolism, etc. CONCLUSIONS: This study is the first to report that XJZD can inhibit necroptosis and gastric mucosal injury induced by aspirin, thereby revealing the complex mechanism of XJZD in relation to alleviating gastric mucosal injury from multiple levels and perspectives.

Integrative metabolome and transcriptome analyses reveal the differences in flavonoid and terpenoid synthesis between Glycyrrhiza uralensis (licorice) leaves and roots

Licorice from Glycyrrhiza uralensis roots is used in foods and medicines. Although we are aware that licorice roots and leaves have distinct material compositions, the specific reasons for these differences remain unknown. Comparison of the metabolomes and transcriptomes between the leaves and roots revealed flavonoids and triterpenoid saponins were significantly different. Isoflavones were enriched in roots because of upregulation of genes encoding chalcone isomerase and flavone synthase, which are involved in isoflavone synthesis. Six triterpenoid saponins were significantly enriched only in the roots. The leaves did not accumulate glycyrrhetinic acid because of low expression levels of genes involved in its synthesis. A gene encoding a UDP glycosyltransferase, which likely catalyzes the key step in the transformation of glycyrrhetinic acid to glycyrrhizin, was screened. Our results provide information about the differences in flavonoid and triterpenoid synthesis between roots and leaves, and highlight targets for genetic engineering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01467-y.

Understanding quality differences between kiwifruit varieties during softening

Research into variations between kiwifruit varieties particularly their softening quality during storage is important in improving kiwifruit quality. The potential reasons for ripening quality differences between 'Cuixiang' (CX) and 'Hayward' (HWD) kiwifruit were analyzed by physiology and metabolomic data combined with the random forests learning algorithm. The results showed that the storability difference between the two varieties mainly resulted from differences in polygalacturonase (PG) and β-galactosidase activities. The 1 °C slowed the fruit softening process of both varieties by decreasing their PG activities. A total of 368 metabolites were identified and amino acid, carbohydrate, cofactors and vitamins, as well as nucleotide metabolism are key metabolic modules that affect the ripening differences of CX and HWD kiwifruit. A total of 30 metabolites showed remarkable ability in distinguish the ripening quality of CX and HWD kiwifruit, in which d-glucose, d-maltose, 2-hydroxybutyric acid, phenyllactate, and vitamin B2 were noteworthy for their potential application on the evaluation of kiwifruit taste and nutritional value. These findings provide positive insights into the underlying mechanism of ripening quality differences between CX and HWD kiwifruit and new ideas for identifying key metabolic markers in kiwifruit.

Host plant-induced changes in metabolism and osmotic regulation gene expression in Diaphorina citri adults

The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama (Hemiptera: Liviidae), is a worldwide citrus pest. It transmits the pathogen Candidatus Liberibacter spp. of Huanglongbing (HLB), causing severe economic losses to the citrus industry. Severalgenera of plants in the Rutaceae family are the hosts of D. citri. However, the impact of these hosts on the metabolism and osmotic regulation gene expression of the pest remains unexplored. In this study, the contents of total sugars, sucrose, fructose, and glucose in young shoots, old leaves, and young leaves of 'Shatangju' mandarin and Murraya exotica were analyzed. Metabolomic analysis found that sucrose and trehalose were more abundant in the gut samples of D. citri adults fed on M. exotica when compared to what's in 'Shatangju' mandarin. A total of six aquaporin genes were identified in D. citri through the genome and transcriptome data. Subsequently, the expression patterns of these genes were investigated with respect to their developmental stage and tissue specificity. Additionally, the expression levels of osmotic regulation and trehalose metabolism genes in adults fed on different plants were evaluated. Our results provide useful information on the transfer of sugar between plants and D. citri. Our results preliminary revealed the sugar metabolism regulation mechanism in D. citri adults.

Transcriptomic and metabolomic analyses reveal that lemon extract prolongs Drosophila lifespan by affecting metabolism

Ageing is an evolutionarily conserved and irreversible biological process in different species. Numerous studies have reported that taking medicine is an effective approach to slow ageing. Lemon extract (LE) is a natural extract of lemon fruit that contains a variety of bioactive phytochemicals. Various forms of LE have been shown to play a role in anti-ageing and improving ageing-related diseases. However, studies on the molecular mechanism of LE in Drosophila ageing have not been reported. In this study, we found that 0.05 g/L LE could significantly extend Drosophila lifespan and greatly improve antioxidative and anti-heat stress abilities. Furthermore, transcriptome and metabolome analyses of 10 d flies between the LE-fed and control groups suggested that the differentially expressed gene ppo1 (Prophenoloxidase 1) and metabolite L-DOPA (Levodopa) were co-enriched in the tyrosine metabolism pathway. Overall, our results indicate that affecting metabolism was the main reason for LE extending Drosophila lifespan.

by comprehensive transcriptomics and metabolomics analysis

Blindness is a physiopathy characterized by apical abortion that particularly affects the Brassica family. The occurrence of blindness has been related to exposure to low temperatures during early developmental stages. However, the causes of this selective sensitivity and how they affect the correct development remain unknown. In this study, we investigated the mechanisms involved in the occurrence of blindness in broccoli plants. The analysis of RNAseq, focused on membrane transporters and the synthesis pathways of glucosinolates and phenolics, was related with physiological changes in nutrient and water uptake, gas exchange, and metabolism. Comparative gene expression analysis between control and blindness-affected broccoli plants revealed distinct regulation patterns in roots and shoots, leading to reduced synthesis of glucosinolates and phenolics. Additionally, the expression levels of aquaporins and potassium transporters were found to be associated with mineral and water transport. In this way, our results revealed the causes of blindness by identifying differentially expressed genes, highlighting those related to secondary metabolism, as well as genes involved in water and nutrient uptake and transport as the crucial involved in the physiopathy appearance.

Metabolomics analysis of the nutraceutical diversity and physiological quality of Torreya yunnanensis seeds during cold storage

This study investigated how cold storage affects the nutraceutical diversity and physiological quality of Torreya yunnanensis seeds, using a widely targeted UPLC-MS/MS-based metabolomics analysis. The 373 identified metabolites were divided into nine categories: lipids, phenolic acids, amino acids and derivatives, organic acids, nucleotides, saccharides, vitamins and alcohols. Among them, 49 metabolites showed significant changes after 3 months of cold storage, affecting 28 metabolic pathways. The content of amino acid-related metabolites significantly increased, while the content of sugar-related metabolites decreased during storage. Notably, the content of proline acid, shikimic acid, α-linolenic acid and branched-chain amino acids showed significant changes, indicating their potential role in seed storage. This study deepens our understanding of the nutraceutical diversity and physiological quality of T. yunnanensis seeds during storage, providing insight for conservation efforts and habitat restoration.

Metabolomic Analysis of the Desert Moss Syntrichia caninervis Provides Insights into Plant Dehydration and Rehydration Response

Desiccation-tolerant (DT) plants can survive extreme dehydration and tolerate the loss of up to 95% of their water content, making them ideal systems to determine the mechanism behind extreme drought stress and identify potential approaches for developing drought-tolerant crops. The desert moss Syntrichia caninervis is an emerging model for extreme desiccation tolerance that has benefited from high-throughput sequencing analyses, allowing identification of stress-tolerant genes; however, its metabolic response to desiccation is unknown. A liquid chromatography-mass spectrometry analysis of S. caninervis at six dehydration-rehydration stages revealed 912 differentially abundant compounds, belonging to 93 metabolic classes. Many (256) metabolites accumulated during rehydration in S. caninervis, whereas only 71 accumulated during the dehydration period, in contrast to the pattern observed in vascular DT plants. During dehydration, nitrogenous amino acids (l-glutamic acid and cysteinylglycine), alkaloids (vinleurosine) and steroids (physalin D) accumulated, whereas glucose 6-phosphate decreased. During rehydration, γ-aminobutyric acid, glucose 6-phosphate and flavonoids (karanjin and aromadendrin) accumulated, as did the plant hormones 12-oxo phytodienoic acid (12-OPDA) and trans-zeatin riboside. The contents ofl-arginine, maltose, turanose, lactulose and sucrose remained high throughout dehydration-rehydration. Syntrichia caninervis thus accumulates antioxidants to scavenge reactive oxygen species, accumulating nitrogenous amino acids and cytoprotective metabolites and decreasing energy metabolism to enter a protective state from dehydration-induced damage. During subsequent rehydration, many metabolites rapidly accumulated to prevent oxidative stress and restore physiological activities while repairing cells, representing a more elaborate rehydration repair mechanism than vascular DT plants, with a faster and greater accumulation of metabolites. This metabolic kinetics analysis in S. caninervis deepens our understanding of its dehydration mechanisms and provides new insights into the different strategies of plant responses to dehydration and rehydration.

Application of metabolomics in diagnostics and differentiation of meningitis: A narrative review with a critical approach to the literature

Due to its high mortality rate associated with various life-threatening sequelae, meningitis poses a vital problem in contemporary medicine. Numerous algorithms, many of which were derived with the aid of artificial intelligence, were brought up in a strive for perfection in predicting the status of sepsis-related survival or exacerbation. This review aims to provide key insights on the contextual utilization of metabolomics. The aim of this the metabolomic approach set of methods can be used to investigate both bacterial and host metabolite sets from both the host and its microbes in several types of specimens - even in one's breath, mainly with use of two methods - Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR). Metabolomics, and has been used to elucidate the mechanisms underlying disease development and metabolic identification changes in a wide range of metabolite contents, leading to improved methods of diagnosis, treatment, and prognosis of meningitis. Mass spectrometry (MS) and Nuclear Magnetic Resonance (NMR) are the main analytical platforms used in metabolomics. Its high sensitivity accounts for the usefulness of metabolomics in studies into meningitis, its sequelae, and concomitant comorbidities. Metabolomics approaches are a double-edged sword, due to not only their flexibility, but also - high complexity, as even minor changes in the multi-step methods can have a massive impact on the results. Information on the differential diagnosis of meningitis act as a background in presenting the merits and drawbacks of the use of metabolomics in context of meningeal infections.

The role of milk fat globule size in modulating the composition of postbiotics produced by Bacillus subtilis and their effect on mammary epithelial cells

Milk lipids are secreted into the milk collecting ducts as milk fat globule (MFG) where they are exposed to microflora of the udder. We hypothesized that MFG size modulates the metabolic fingerprint of B. subtilis. Accordingly, small and large (2.3 and 7.0 µm, respectively) MFG were isolated from cow milk and used as a substrate for B. subtilis. Small MFG enhanced growth, whereas large MFG enhanced biofilm formation. Bacteria incubated with small MFG had increased concentration of metabolites related to energy production whereas metabolome of the bacteria incubated with large MFG had reduced concentrations of metabolites important for biofilm formation. Postbiotics from bacteria grown on large MFG exacerbated the proinflammatory response of MEC to LPS, and changed the expression of key enzymes involved in lipid and protein synthesis. Our results suggest that MFG size modulate growth trajectories and metabolome of B. subtilis, and consequently the stress response of host cells.

Metabolomic and microbiome analysis of the protective effects of Puerarin against Salmonella Enteritidis Infection in chicks

BACKGROUND

Salmonella Enteritidis is a zoonotic pathogen and poses a substantial risk to human health, as well as significant financial losses to the livestock and poultry industries. It is currently urgent to identify alternatives to antibiotic treatment.

RESULTS

In this study, we explored the influence of Puerarin on the immunological response, intestinal flora, serum metabolome, and growth performance of chicks infected with Salmonella Enteritidis. Chicks were weighed at specific time points and the average daily gain (ADG) was calculated. Serum, intestinal, and cecal content samples were collected on days 10 and 17. The results showed that 100 mg/kg of Puerarin significantly suppressed inflammation and enhanced immune function. Metabolomic analysis showed significant differences in serum metabolites after Puerarin treatment and suggested that Puerarin may regulate abnormal amino acid and lipid metabolism after Salmonella Enteritidis infection through the autophagic and ABC transporter pathways. In addition, Puerarin suppressed Salmonella Enteritidis-induced intestinal flora dysbiosis through modulation of the microbial community structures (increased Lactobacillus, Faecalibacterium, and Subdoligranulum), as demonstrated by 16S rRNA analysis.

CONCLUSIONS

In conclusion, Puerarin can improve growth performance in chicks, suppress the inflammatory response in vivo, enhance immunity, and regulate lipid and amino acid metabolism and the intestinal flora.

Combining stable isotope, multielement and untargeted metabolomics with chemometrics to discriminate the geographical origins of ginger (Zingiber officinale Roscoe)

Ginger (Zingiber officinale Roscoe) is a high-value food and herb worldwide. The quality of ginger is often related to its production regions. In this study, stable isotopes, multiple elements, and metabolites were investigated together to realize ginger origin traceability. Chemometrics showed that ginger samples could be preliminarily separated, and 4 isotopes (δ13C, δ2H, δ18O, and δ34S), 12 mineral elements (Rb, Mn, V, Na, Sm, K, Ga, Cd, Al, Ti, Mg, and Li), 1 bioelement (%C), and 143 metabolites were the most important variables for discrimination. Furthermore, three algorithms were introduced, and the fused dataset based on VIP features led to the highest accuracies for origin classification, with predictive rates of 98% for K-nearest neighbor and 100% for support vector machine and random forest. The results demonstrated that isotopic, elemental, and metabolic fingerprints were useful indicators for the geographical origins of Chinese ginger.

Analytical strategies based on untargeted and targeted metabolomics for the accurate authentication of organic milk from Jersey and Yak

Organic milk has a high risk of food fraud as it can easily be adulterated with non-organic milk. This study aimed to identify metabolite markers for assessing the authenticity of organic milk from Jersey and Yak. In the untargeted strategy, ultra-high performance liquid chromatography-Q Exactive HF-X mass spectrometer coupled with chemometrics analysis was used to screen and identify tentative markers of organic milk from Jersey and Yak. In the targeted strategy, a quick and easy method of ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was developed to quantify three markers. The peptide of Thr-Ala-Val and D-biotin were determined to be metabolite markers for distinguishing organic and non-organic Jersey milk, whereas trimethylamine N-oxide was determined to be a metabolite marker for distinguishing organic and non-organic Yak milk. These findings provide critical information to facilitate assessments of organic milk authenticity.

Small networks of expressed genes in the whole blood and relationships to profiles in circulating metabolites provide insights in inter-individual variability of feed efficiency in growing pigs

BACKGROUND

Feed efficiency is a research priority to support a sustainable meat production. It is recognized as a complex trait that integrates multiple biological pathways orchestrated in and by various tissues. This study aims to determine networks between biological entities to explain inter-individual variation of feed efficiency in growing pigs.

RESULTS

The feed conversion ratio (FCR), a measure of feed efficiency, and its two component traits, average daily gain and average daily feed intake, were obtained from 47 growing pigs from a divergent selection for residual feed intake and fed high-starch or high-fat high-fiber diets during 58 days. Datasets of transcriptomics (60 k porcine microarray) in the whole blood and metabolomics (1H-NMR analysis and target gas chromatography) in plasma were available for all pigs at the end of the trial. A weighted gene co-expression network was built from the transcriptomics dataset, resulting in 33 modules of co-expressed molecular probes. The eigengenes of eight of these modules were significantly ([Formula: see text]) or tended to be ([Formula: see text]) correlated to FCR. Great homogeneity in the enriched biological pathways was observed in these modules, suggesting co-expressed and co-regulated constitutive genes. They were mainly enriched in genes participating to immune and defense-related processes, and to a lesser extent, to translation, cell development or learning. They were also generally associated with growth rate and percentage of lean mass. In the whole network, only one module composed of genes participating to the response to substances, was significantly associated with daily feed intake and body adiposity. The plasma profiles in circulating metabolites and in fatty acids were summarized by weighted linear combinations using a dimensionality reduction method. Close association was thus found between a module composed of co-expressed genes participating to T cell receptor signaling and cell development process in the whole blood and related to FCR, and the circulating concentrations of polyunsaturated fatty acids in plasma.

CONCLUSION

These systemic approaches have highlighted networks of entities driving key biological processes involved in the phenotypic difference in feed efficiency between animals. Connecting transcriptomics and metabolic levels together had some additional benefits.

A L-glutamine binding protein modified MNM structured optical fiber biosensor based on surface plasmon resonance sensing for detection of L-glutamine metabolism in vitro embryo culture

A surface plasmon resonance (SPR) optical fiber sensor with multimode-coreless-multimode (MNM) structure was developed, which modified by L-glutamine-binding protein (QBP) for detection of L-glutamine (Gln). The QBP was immobilized on the surface of gold films by chemical cross-linking and exhibited a binding affinity for L-glutamine. The conformation of QBP can be changed from the "open" to the "closed", which led to a red-shift of the SPR peak when QBP bounded to L-glutamine. There was a good linear correlation between is a dependence of the SPR peak on and the concentration of L-glutamine concentration in the range 10-100 μM, with a sensitivity of 10.797nm/log10[Gln] for L-glutamine in the in vitro embryo culture (IVC) medium environment, and the limit of detection (LOD) is 1.187 μM. This QBP-modified MNM structure optical fiber SPR sensor provides a new idea for the developmental potential assessment of embryos in the process of in vitro embryo culture.

Metabolomic and transcriptomic analyses reveal comparisons against liquid-state fermentation of primary dark tea, green tea and white tea by Aspergillus cristatus

Liquid-state fermentation (LSF) of tea leaves is a promising way to obtain tea-based nutraceutical products rich in various bioactive compounds. In the study, the changes of bioactive compounds, tea pigments and complex metabolites from LSF of primary dark tea, green tea and white tea infusions with Aspergillus cristatus were determined. Chemical analyses revealed that soluble sugars, monosaccharide composition, total polyphenols, total flavonoids, free amino acids, soluble proteins and tea pigments were changed in different ways. An untargeted metabolomic analysis and ribonucleic acid sequencing (RNA-seq) based transcriptomic analysis were performed to investigate the metabolic differentiation and clarify the key differentially expressed genes (DEGs, fold change >2 and p < 0.05), showing that amino acid metabolism, carbohydrate metabolism and lipid metabolism were the most enriched pathways during A. cristatus fermentation of primary dark tea, green tea and white tea infusions. In addition, glycerophospholipid metabolism, linoleic acid metabolism and phenylalanine metabolism were greatly accumulated in the fermentation of primary dark tea and white tea infusions; Pyruvate metabolism, glycolysis/gluconeogenesis, fatty acid degradation, tyrosine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and valine and leucine, isoleucine degradation were greatly accumulated in the fermentation of primary dark tea and green tea infusions; Starch and sucrose metabolism was greatly accumulated in the fermentation of green tea and white tea infusions; Galactose metabolism was significantly enhanced in the fermentation of primary dark tea infusion; Amino sugar and nucleotide sugar metabolism, sphingolipid metabolism and alanine, aspartate and glutamate metabolism were significantly enhanced in the fermentation of green tea infusion. Besides, some other pathways involving aminobenzoate degradation, biosynthesis of cofactors, pyrimidine metabolism, benzoxazinoid biosynthesis and phenazine biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis and flavone and flavonol biosynthesis also differed from each other. These findings support that A. cristatus plays a vital role in the biochemical and genetic regulation of metabolite profile, and could be considered a potential prospect for better use of A. cristatus on different kinds of tea materials.

Experimental study on changes in metabolic mechanism of papillary thyroid carcinoma complicated with Hashimoto's thyroiditis

Background

Whether the mechanism of thyroid papillary carcinoma (PTC) is the same in patients with a Hashimoto's thyroiditis (HT) background as compared with patients with a normal background remains a highly debated and controversial issue. In this study, we aimed to analyze the differences and similarities of the metabolic mechanism of PTC in normal and HT background, and to explore the relationship between HT and PTC.

Methods

The ultra performance liquid chromatography-quadrupole-time of flight-mass spectrometry (UPLC-Q-TOF/MS) technology was used to analyze 61 PTC patient tissues (31 HT background and 30 normal tissue (NC) background). Potential biomarkers were screened from principal component analysis (PCA) to orthogonal partial least square (OPLS) discriminant analysis. HMDB was searched to identify potential differential metabolites and final metabolic pathway analysis was performed by MetaboAnalyst 5.0. We analyzed the differential metabolites diagnostic accuracy through receiver operating characteristic (ROC) curves analysis.

Results

Seven different metabolites were screened from HT group and NC group, including arginine, glutamic acid, cysteine, citric acid, malic acid, uracil and taurine. Logistic regression model combined with ROC analysis of these 7 biomarkers had good discriminability for PTC (area under operating characteristic curve of HT group and NC group were 0.867 and 0.973, respectively). The HT group had specific metabolic pathways, including aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism.

Conclusions

The metabolic profiles of the NC and HT groups had important similarities and differences in PTC. The correlation of PTC with HT may be related to aminoacyl-tRNA biosynthesis, serine and threonine metabolism.

Integrated metabolomic and transcriptomic analysis reveals perturbed glycerophospholipid metabolism in mouse neural stem cells exposed to cadmium

Cadmium (Cd) is a ubiquitous heavy metal with neurotoxicity. Our previous study reported that Cd could inhibit the proliferation of mouse neural stem cells (mNSCs). However, the underlying mechanisms are obscure. In recent years, the rapid growth of multi-omics techniques enables us to explore the cellular responses that occurred after toxicant exposure at the molecular level. In this study, we used a combination of metabolomics and transcriptomics approaches to investigate the effects of exposure to Cd on mNSCs. After treatment with Cd, the metabolites and transcripts in mNSCs changed significantly with 110 differentially expressed metabolites and 2135 differentially expressed genes identified, respectively. The altered metabolites were mainly involved in glycerophospholipid metabolism, arginine and proline metabolism, arginine biosynthesis, glyoxylate and dicarboxylate metabolism. Meanwhile, the transcriptomic data demonstrated perturbed membrane function and signal transduction. Furthermore, integrated analysis of metabolomic and transcriptomic data suggested that glycerophospholipid metabolism might be the major metabolic pathway affected by Cd in mNSCs. More interestingly, the supplementation of lysophosphatidylethanolamine (LPE) attenuated Cd-induced mitochondrial impairment and the inhibition of cell proliferation and differentiation in mNSCs, further supporting our analysis. Overall, the study provides new insights into the mechanisms of Cd-induced neurotoxicity.

Multi-time point metabolomics reveals key metabolic features from the ultra-early stage of intracerebral hemorrhage in mice

Despite decades of intensive research, there are still very limited options for the effective treatment of intracerebral hemorrhage (ICH). Recently, mounting evidence has indicated that the ultra-early stage (<3 h), serving as the primary phase of ICH, plays a pivotal role and may even surpass other stages in terms of its significance. Therefore, uncovering the metabolic alterations induced by ICH in the ultra-early stage is of crucial importance. To investigate this, the collagenase ICH mouse model was employed in this study. ICH or sham-operated mice were euthanized at the ultra-early stage of 3 h and the acute stage of 24 h and 72 h after the operation. Then, the metabolic changes in the perihematomal tissues were detected by liquid chromatography coupled with tandem mass spectrometry. In total, alterations in the levels of 465 metabolites were detected. A total of 136 metabolites were significantly changed at 3 h. At 24 h and 72 h, the amounts were 132 and 126, respectively. Additionally, the key corresponding metabolic pathways for these time points were analyzed through KEGG. To gather additional information, quantitative real-time transcription polymerase chain reaction, enzyme-linked immunosorbent assay and Western blots were performed to validate the metabolic changes. Overall, ICH significantly alters important physiological functions such as cysteine metabolism, purine metabolism, synaptic alterations, the synaptic vesicle cycle, and the ATP-binding cassette transporter system. These might be the key pathologic mechanisms of the ultra-early stage induced by ICH.

Suppression of hepatocellular carcinoma by Ulva lactuca ulvan via gut microbiota and metabolite interactions

INTRODUCTION

Ulva lactuca polysaccharide (ULP) is green algae extract with numerous biological activities, including anticoagulant, anti-inflammatory, and antiviral effects. However, the inhibitory ability of ULP in the development of hepatocellular carcinoma warrants further studies.

OBJECTIVES

To elucidate the anti-tumor mechanism of ULP action and evaluate its regulatory effect on gut microbiota and metabolism in H22 hepatocellular carcinoma tumor-bearing mice.

METHODS

An H22 tumor-bearing mouse model was established by subcutaneously injecting H22 hepatoma cells. The gut microbiota composition in cecal feces was assessed and subjected to untargeted metabolomic sequencing. The antitumor activity of ULP was verified further by western blot, RT-qPCR, and reactive oxygen species (ROS) assays.

RESULTS

Administration of ULP alleviated tumor growth by modulating the compositions of the gut microbial communities (Tenericutes, Agathobacter, Ruminiclostridium, Parabacteroides, Lactobacillus, and Holdemania) and metabolites (docosahexaenoic acid, uric acid, N-Oleoyl Dopamine, and L-Kynurenine). Mechanistically, ULP promoted ROS production by inhibiting the protein levels of JNK, c-JUN, PI3K, Akt, and Bcl-6, thereby delaying the growth of HepG2 cells.

CONCLUSION

ULP attenuates tumor growth in H22 tumor-bearing mice by modulating gut microbial composition and metabolism. ULP inhibits tumor growth mainly by promoting ROS generation.