KEGG Metabolic Pathway Analysis Research Articles

In vitro digestion and fecal fermentation of Tremella fuciformis exopolysaccharides from basidiospore-derived submerged fermentation

Tremella fuciformis polysaccharides (TFPS) belong to natural bioactive macromolecule with both edible and medicinal value, possessing much bioactivities such as anti-tumor, antioxidant, antidiabetics, and immunomodulatory. Currently, the production of TFPS through submerged fermentation (TFPS-1) is gradually replacing the polysaccharides extracted from the fruiting body due to improved fermentation efficiency and reduced separation costs. However, it is still unclear about the effect of TFPS-1 on gastrointestinal digestion and gut microbial fermentation, which is directly related to the function of its biological activity. This study aimed to illustrate the effect of TFPS-1 on digestive process through in vitro digestion and fecal fermentation. TFPS-1 was indigestible during the simulated gastrointestinal tract. But TFPS-1 can be digested by intestinal flora leading to alterations in the total polysaccharides content, molecular weight, and apparent viscosity. Moreover, TFPS-1 regulated the composition of gut microbial, lowering the proportion of Firmicutes to Bacteroidetes and enhancing the abundances of Parabacteroides and Bacteroides. The change of intestinal flora produced more short chain fatty acids and lowered the pH. The KEGG metabolic pathway analysis indicated that TFPS-1 enriched lipid metabolism, glycan biosynthesis and metabolism, and biosynthesis of other secondary metabolites. This study demonstrated that T. fuciformis fermented polysaccharide can be a potential prebiotic to optimize intestinal flora homeostasis and maintain host intestinal health.

Role of Epigenetic Factors in Determining the Biological Behavior and Prognosis of Hepatocellular Carcinoma.

The current study's objective is to evaluate the molecular genetic mechanisms influencing the biological behavior of hepatocellular carcinoma (HCC) by analyzing the transcriptomic and epigenetic signatures of the tumors. Transcriptomic data were downloaded from the NCBI GEO database. We investigated the expression differences between the GSE46444 (48 cirrhotic tissues versus 88 HCC tissues) and GSE63898 (168 cirrhotic tissues versus 228 HCC tissues) data sets using GEO2R. Differentially expressed genes were evaluated using GO and KEGG metabolic pathway analysis websites. Whole genome bisulfite sequencing (WGBS) and Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq) data sets (26 HCC tissues versus 26 adjacent non-tumoral tissues) were also downloaded from the NCBI SRA database. These data sets were analyzed using Bismark and QSEA, respectively. The methylation differences between the groups were assessed using functional enrichment analysis. In the GSE46444 data set, 80 genes were upregulated, and 315 genes were downregulated in the tumor tissue (HCC tissue) compared to the non-tumor cirrhotic tissue. In the GSE63898 data set, 1261 genes were upregulated, and 458 genes were downregulated in the cirrhotic tissue compared to the tumor tissues. WGBS revealed that 20 protein-coding loci were hypermethylated. while the hypomethylated regions were non-protein-coding. The methylated residues of the tumor tissue, non-tumorous cirrhotic tissue, and healthy tissue were comparable. MeDIP-Seq, conducted on tumoral and non-tumoral tissues, identified hypermethylated or hypomethylated areas as protein-coding regions. The functional enrichment analysis indicated that these genes were related to pathways including peroxisome, focal adhesion, mTOR, RAP1, Phospholipase D, Ras, and PI3K/AKT signal transduction. The investigation of transcriptomic and epigenetic mechanisms identified several genes significant in the biological behavior of HCC. These genes present potential targets for the development of targeted therapy.

Transcriptomic and Metabolomic Analysis Reveals the Potential Roles of Polyphenols and Flavonoids in Response to Sunburn Stress in Chinese Olive (Canarium album).

Sunburn stress is one of the main environmental stress factors that seriously affects the fruit development and quality of Chinese olive, a tropical and subtropical fruit in south China. Therefore, the understanding of the changes in physiological, biochemical, metabolic, and gene expression in response to sunburn stress is of great significance for the industry and breeding of Chinese olive. In this study, the different stress degrees of Chinese olive fruits, including serious sunburn injury (SSI), mild sunburn injury (MSI), and ordinary (control check, CK) samples, were used to identify the physiological and biochemical changes and explore the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) by using transcriptomics and metabolomics. Compared with CK, the phenotypes, antioxidant capacity, and antioxidant-related enzyme activities of sunburn stress samples changed significantly. Based on DEG-based KEGG metabolic pathway analysis of transcriptomics, the polyphenol and flavonoid-related pathways, including phenylpropanoid biosynthesis, sesquiterpenoid, and triterpenoid biosynthesis, monoterpene biosynthesis, carotenoid biosynthesis, isoflavonoid biosynthesis, flavonoid biosynthesis, were enriched under sunburn stress of Chinese olive. Meanwhile, 33 differentially accumulated polyphenols and 99 differentially accumulated flavonoids were identified using metabolomics. According to the integration of transcriptome and metabolome, 15 and 8 DEGs were predicted to regulate polyphenol and flavonoid biosynthesis in Chinese olive, including 4-coumarate-CoA ligase (4CL), cinnamoyl-CoA reductase (CCR), cinnamoyl-alcohol dehydrogenase (CAD), chalcone synthase (CHS), flavanone-3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS). Additionally, the content of total polyphenols and flavonoids was found to be significantly increased in MSI and SSI samples compared with CK. Our research suggested that the sunburn stress probably activates the transcription of the structural genes involved in polyphenol and flavonoid biosynthesis in Chinese olive fruits to affect the antioxidant capacity and increase the accumulation of polyphenols and flavonoids, thereby responding to this abiotic stress.

Metabolomics study on fermentation of Lactiplantibacillus plantarum ST-III with food grade proliferators in milk

Milk is a naturally complex medium that is suitable for the growth of most lactic acid bacteria. Unfortunately, Lactiplantibacillus plantarum ST-III grow poorly in milk without supplementation. To solve this problem, we use fresh pineapple and mung beans juice to develop an edible proliferator for L. plantarum ST-III. Our comparative analysis of metabolomics changes before and after fermentation reveals that amino acids and dipeptides are the most consumed compounds, with other substances including nucleotides and vitamins, implying the mechanism of proliferation. Combining the KEGG metabolic pathway analysis, substances that may promote the growth of L. plantarum ST-III in milk were screened. To explore which component of the proliferator is required for L. plantarum ST-III cultivate, we supplemented with several combinations of molecules aforementioned in milk. The simulation addition experiment results of L. plantarum ST-III in milk show that if any additions are missing, the concentration of viable bacteria is lower. Only when it contains all additives can the highest concentration of viable bacteria be obtained. Compared with the control, the fold change of the viable bacteria is about 32. Thus, it proves that milk primarily lacked available amino acids, dipeptides, uracil, xanthine, nicotinamide, and manganese for the growth of L. plantarum ST-III.

Metabolomics of Strongylocentrotus intermedius fatty acid metabolism under high-temperature stress conditions

The gonads of sea urchins are the primary source of nutritional value; these gonads are rich in nutrients, particularly PUFAs, which are essential for the gonads' growth and development as well as their nutritional worth. Strongylocentrotus intermedius grows best at a temperature of 15 °C. However, the contemporary climate is unstable, and abrupt fluctuations in water temperature are frequently brought on by extreme weather. Therefore, S. intermedius were exposed to several temperature gradients (15 °C, 20 °C, and 25 °C) and varied stress periods (7 days, 30 days) in order to investigate the impact of temperature on the concentration of fatty acids in the gonads of S. intermedius. The following are the study's primary findings: The fatty acid (FA) content of the S. intermedius is investigated at three temperatures (15 °C (control), 20 °C, and 25 °C) after exposure for 7 and 30 days. Urchin gonads were metabolized using ultra-performance liquid chromatography coupled with high-resolution mass spectrometry. Relative to the control, after 7 d temperature stress at 20 °C, 33 FA metabolites were differentially expressed, of which mono-unsaturated fatty acids (MUFA), medium-chain fatty acids (MCFA), and most long-chain fatty acids (LCFA) were downregulated, and saturated fatty acids (SFA) and polyunsaturated fatty acids (PUFA) (ω-3 PUFA and ω-6 PUFA) were upregulated (P < 0.05); at 25 °C, 16 FA metabolites were differentially expressed, of which MCFA, ω-3 PUFA, and ω-6 PUFA were upregulated (P < 0.05), and short-chain fatty acids (SCFA), MCFA, MUFA, and some LCFA were downregulated. KEGG metabolic pathway analysis annotated FA metabolites to 62 metabolic pathways. Biosynthetic metabolic pathways that are significantly enriched in unsaturated FAs. Relative to the control, after 30 d temperature stress at 20 °C, four FA metabolites were differentially expressed, of which ω-6 PUFA was downregulated (P < 0.05), and other PUFAs were upregulated (P < 0.05); at 25 °C, 10 FA metabolites were differentially expressed, of which mid-chain SFA, ω-3 PUFA, ω-6 PUFA, and ω-6 MUFA were downgraded (P < 0.05), and short-chain MUFA and long-chain SFA were upregulated (P < 0.05). After 30 d exposure to elevated temperatures, differentially expressed metabolites of FAs are annotated to five KEGG metabolic pathways. S. intermedius may reduce energy consumption by regulating FA metabolism, where ω-3 and ω-6 PUFA may be prioritized for oxidative energy supply. As exposure to temperature stress increases, urchins are unable to synthesize more ω-3 PUFA to deal with inflammation. Changes in FA composition can be used as a sensitive early warning biometric indicator.

HPLC/ESI-QTOF-MS/MS based untargeted metabolomics authentication of Taxus × media six tissues.

Taxus media (Taxus × media Rehder) is renowned for its high paclitaxel content, serving as a major source for industrial paclitaxel production. In addition to paclitaxel, T. media contains a diverse range of metabolites, including flavonoids, alkaloids, and terpenoids, which have been shown to possess antioxidant, antibacterial, anti-inflammatory, and immunomodulatory effects. However, these compounds have not been thoroughly studied as key metabolites in T. media. The untargeted metabolomics analysis of six T. media tissues provides new insights into the development and utilization of T. media metabolites. The extracts from six tissues of T. media were analyzed and subjected to analysis using high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF-MS/MS) and chemometric techniques. Using a reliable HPLC-Q-TOF-MS/MS method, we identified 312 compounds in six T. media tissues, including 214 previously unreported in T. media. To identify characteristic compounds across different tissues, 34 metabolites were further screened. KEGG metabolic pathway analysis revealed that these compounds primarily occur in the metabolic pathways of terpene glycosides, flavans, and O-methylated flavonoids. This study initially utilized an HPLC-QTOF-MS/MS-based metabolomics approach to assess the metabolites in different tissues of T. media, providing a basis for their utilization and management.

Influence and metabolomic basis of an indigenous yeast CECA, from Ningxia wine region of China, on the aroma and flavor of Cabernet Sauvignon wines

In this study, three fermentation treatments of spontaneous fermentation (SF), direct inoculation of CECA (YF), and inoculation with CECA after addition of dimethyl dicarbonate (YDF) were carried out. Multivariate statistical analysis approved that CECA inoculation significantly influenced the composition of 141 metabolites (15 volatile organic compounds (VOCs) and 126 non-VOCs), mainly consisting of 36 acids and derivatives and 25 lipids and lipid-like molecules. YF and YDF wines exhibited similar correlations with aroma types, while there were differences in the kinds and number of VOCs. Moreover, CECA-inoculated fermentation was more favorable to the formation of aftertaste-A, umami, sourness, and richness. The KEGG metabolic pathway analysis indicated that the inoculation strategy significantly affected the amino acid metabolism. The antimicrobial treatment effectively enhanced bitterness, astringency, umami and saltiness while reducing acidity. Further studies are needed to assess the effects of antimicrobial treatment on lipid metabolism.

Unveiling the molecular basis of paracetamol-induced hepatotoxicity: Interaction of N-acetyl-p-benzoquinone imine with mitochondrial succinate dehydrogenase

Background and aimN-acetyl-p-benzoquinoneimine (NAPQI), a toxic byproduct of paracetamol (Acetaminophen, APAP), can accumulate and cause liver damage by depleting glutathione and forming protein adducts in the mitochondria. These adducts disrupt the respiratory chain, increasing superoxide production and reducing ATP. The goal of this study was to provide computational proof that succinate dehydrogenase (SDH), a subunit of complex II in the mitochondrial respiratory chain, is a favorable binding partner for NAPQI in this regard. MethodMolecular docking, molecular dynamics simulation, protein-protein interaction networks (PPI), and KEGG metabolic pathway analysis were employed to identify binding characteristics, interaction partners, and their associations with metabolic pathways. A lipid membrane was added to the experimental apparatus to mimic the natural cellular environment of SDH. This modification made it possible to develop a context for investigating the role and interactions of SDH within a cellular ecosystem that was more realistic and biologically relevant. ResultThe molecular binding affinity score for APAP and NAPQI with SDH was predicted −6.5 and −6.7 kcal/mol, respectively. Furthermore, RMSD, RMSF, and Rog from the molecular dynamics simulations study revealed that NAPQI has slightly higher stability and compactness compared to APAP at 100 ns timeframe with mitochondrial SDH. ConclusionThis study serves to predict the mechanistic process of paracetamol toxicity by using different computational approaches. In addition, this study will provide information about the drug target against APAP hepatotoxicity.

Widely targeted metabolomic and KEGG analyses of natural deep eutectic solvent-based saponins extraction from Camellia oleifera Abel.: Effects on composition

Camellia saponins are important by-products of Camellia Oleifer Abel. processing. In this study, an eco-friendly method based on natural deep eutectic solvents (NaDESs, proline and glycerol at a molar ratio of 2:5) was established to extract saponins from C.oleifera cakes. The content of saponin (702.22 ± 1.28 mg/g) obtained using NaDES was higher than those extracted using water or methanol. UPLC-Q-TOF MS analysis of chemical structure showed that the difference in the extraction technique alter individual saponins. A widely targeted metabolomic approach and KEGG metabolic pathway analysis showed that the upregulated metabolites in the NaDES-based extract mainly included flavonoids, alkaloids, and phenolic acids; and they were involved in arginine and proline metabolism, metabolic pathways, phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, and flavonoid biosynthesis. The present study proposes a selective substitute for use in the extraction of camellia saponins with composition analysis.

Transcriptome Analysis of Potential Regulatory Genes under Chemical Doubling in Maize Haploids

Maize is one of the most successful crops with regard to the utilization of heterosis. The haploid induction technique is one of the fastest methods to obtain pure maize material at the present stage. However, the molecular mechanism of haploid doubling is rarely reported. In this study, we treated B73 and ZNC442 haploid young shoots with colchicine for 0 h, 6.2 h, and 10 h, and analyzed the differentially expressed genes (DEGs). We found that colchicine treatment for 6.2 h and 10 h compared to 0 h resulted in a total of 4868 co-DEGs. GO enrichment analysis and KEGG metabolic pathway analysis found significantly enriched 282 GO terms and 31 significantly pathways, respectively. Additionally, The GO term and KEGG pathway genes of spindle, cytoskeleton, microtubules and nuclear division were selected for analysis, and three candidate genes were screened by taking intersections. Zm00001d033112, Zm00001d010525, and Zm00001d043386 were annotated as kinesin-associated protein 13, kinesin-like protein KIN-10C, and kinesin light-chain LC6, respectively. The real-time fluorescence quantification (RT-PCR) results revealed that Zm00001d033112, Zm00001d010525, and Zm00001d043386 had the same trends as RNA-seq. Interestingly, Zm00001d033112 is homologous gene AT3G20150 in Arabidopsis, which was involved in the regulation of chromosome movement and mitotic spindle assembly. Our study suggests that kinesin genes may play an important role in doubling chromosomes, thus providing valuable information for future studies on the molecular mechanisms of chromosome doubling in maize.

Endogenous Phytohormone and Transcriptome Analysis Provided Insights into Seedling Height Growth of Pinus yunnanensis

Plant height plays a crucial role in both the structure and quality of plants. Pinus yunnanensis is a distinctive species of the forest found in Southwest China, where the height of the plants significantly influences both yield performance and plant architecture. Although the phenotypes of P. yunnanensis seedlings with different plant heights were quite different at their seedling stage, the molecular mechanisms controlling the seedling differentiation remain poorly understood. This study is aimed to investigate the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The P. yunnanensis seedlings were categorized into three grades, i.e., Grades A, B, and C, by mean ± 1/2 standard deviation method (H ± 1/2σ), and the seedling height and ground diameter were measured. We conducted the measurements of endogenous hormone levels in the young shoot apexes of seedlings at different grades during the fast-growth period (March). The DEGs were identified through transcriptome sequencing and analyzed by qRT-PCR validation. Significant differences were observed in the content and ratio of endogenous phytohormones among various grades of P. yunnanensis seedlings (p &lt; 0.05). The ABA content in Grade A was prominently more than that in Grades B and C, and the order of the content of auxins was Grade B &gt; C &gt; A. Furthermore, when compared to Grade A, the ratios of auxins/CTKs, auxins/ABA, CTKs/ABA, and (auxins + CTKs)/ABA exhibited significant increases in Grades B and C. Moreover, GO functional annotation analysis indicated the more pronounced enrichment of DEGs in molecular functions. KEGG metabolic pathway analysis revealed notable differences in enrichment pathways between the pairwise comparisons. The “plant hormone signal transduction” pathway exhibited enrichment in the two groups, followed by “plant–pathogen interaction” pathway in the organism system that was enriched in the three groups. In addition, the results for endogenous phytohormone metabolism pathways indicate a significant up-regulation in the expression of AUX1, while AHP and PP2C exhibited significant down-regulation. To sum up, we aimed at investigating the underlying mechanisms of P. yunnanensis seedling differentiation using phenotypic, transcriptomic, and endogenous phytohormone analyses. The results suggested that individual phytohormones have a limited capacity to regulate gene expression, and seedling differentiation results from the combined regulation of multiple hormones. In addition, several candidate genes associated with phytohormone biosynthesis and signal transduction pathways were identified, including AUX1, GH3, AHP, B-ARR, PP2C, etc., which provided candidate genes for the following hormone-related gene overexpression and knockout experiments. These findings provide insights into the molecular genetic control of seedling height growth of P. yunnanensis.

Genome-wide transcriptome profiling reveals molecular response pathways of Trichoderma harzianum in response to salt stress.

Trichoderma harzianum exhibits a strong biological control effect on many important plant pathogens, such as Fusarium oxysporum, Botrytis cinerea, and Meloidogyne. However, its biocontrol effectiveness is weakened or reduced under salt stress. The aim of this study was to investigate the molecular response of T. harzianum to salt stress at the whole-genome level. Here, we present a 44.47 Mb near-complete genome assembly of the T. harzianum qt40003 strain for the first time, which was assembled de novo with 7.59 Gb Nanopore sequencing long reads (~170-fold) and 5.2 Gb Illumina short reads (~116-fold). The assembled qt40003 genome contains 12 contigs, with a contig N50 of 4.81 Mb, in which four of the 12 contigs were entirely reconstructed in a single chromosome from telomere to telomere. The qt40003 genome contains 4.27 Mb of repeat sequences and 12,238 protein-coding genes with a BUSCO completeness of 97.5%, indicating the high accuracy and completeness of our gene annotations. Genome-wide transcriptomic analysis was used to investigate gene expression changes related to salt stress in qt40003 at 0, 2% (T2), and 4% (T4) sodium chloride concentrations. A total of 2,937 and 3,527 differentially expressed genes (DEGs) were obtained under T2 and T4 conditions, respectively. GO enrichment analysis showed that the T2-treatment DEGs were highly enriched in detoxification (p < 0.001), while the T4 DEGs were mainly enriched in cell components, mostly in cellular detoxification, cell surface, and cell wall. KEGG metabolic pathway analysis showed that 91 and 173 DEGs were significantly enriched in the T2 and T4 treatments, respectively (p < 0.01), mainly in the glutathione metabolism pathway. We further experimentally analyzed the differentially expressed glutathione transferase genes in the glutathione metabolic pathway, most of which were downregulated (13/15). In addition, we screened 13 genes related to active oxygen clearance, including six upregulated and seven downregulated genes, alongside five fungal hydrophobic proteins, of which two genes were highly expressed. Our study provides high-quality genome information for the use of T. harzianum for biological control and offers significant insights into the molecular responses of T. harzianum under salt-stress conditions.

UHPLC-QTOF-MS-based untargeted metabolomic authentication of Chinese red wines according to their grape varieties

Wine is a very popular alcoholic drink owing to its health benefits of antioxidant effects. However, profits-driven frauds of wine especially false declarations of variety frequently occurred in markets. In this work, an UHPLC-QTOF-MS-based untargeted metabolomics method was developed for metabolite profiling of 119 bottles of Chinese red wines from four varieties (Cabernet Sauvignon, Merlot, Cabernet Gernischt, and Pinot Noir). The metabolites of red wines from different varieties were assessed using orthogonal partial least-squares discriminant analysis (OPLS-DA) and analyzed using KEGG metabolic pathway analysis. Results showed that the differential compounds among different varieties of red wines are mainly flavonoids, phenols, indoles and amino acids. The KEGG metabolic pathway analysis showed that indoles metabolism and flavonoids metabolism are closely related to wine varieties. Based on the differential compounds, OPLS-DA models could identify external validation wine samples with a total correct rate of 90.9 % in positive ionization mode and 100 % in negative ionization mode. This study indicated that the developed untargeted metabolomics method based on UHPLC-QTOF-MS is a potential tool to identify the varieties of Chinese red wines.

UHPLC-MS/MS metabolomics analysis of sea cucumber (Apostichopus japonicus) processed using different methods

The effects of different processing methods on the nutritional components of sea cucumber (Apostichopus japonicus) are of concern to consumers who select sea cucumber products. This study employed liquid chromatography tandem mass spectrometry to examine the metabolites in fresh, unsoaked salted, soaked salted, and instant sea cucumber body wall samples sourced from Dalian, China. Metabolites were evaluated utilizing partial least squares discriminant analysis (PLS-DA) and subsequently subjected to KEGG metabolic pathway analysis for further investigation. PLS-DA effectively discriminated the body wall metabolites of sea cucumbers obtained via various processing techniques. The differential metabolites identified predominantly encompassed amino acids, lipids, and carbohydrates. Subsequent KEGG metabolic pathway analysis demonstrated a significant association between lipid, carbohydrate, and amino acid metabolism and the specific processing methods employed. The assessment of nutritional differences corresponding to the various A. japonicus processing methods was conducted. The findings of this study can assist in the choice of sea cucumber products and the selection of suitable processing methods.

Effect of CO2 on the preservation effectiveness of chilled fresh boneless beef knuckle in modified atmosphere packaging and microbial diversity analysis

To explore the effect of different concentrations of CO2 in modified atmosphere packaging (MAP) on the preservation shelf life of boneless beef knuckle (BBK), and to deeply study the changes in the bacterial community. In the controlled atmosphere combination, the proportion of O2 in each group is kept at 40%, CO2: 20%–45%, and N2: 15%–60%, the blank control group is set to 40%O2+0%CO2+60%N2. Sensory evaluation, headspace gas, total colony, and physicochemical indicators were measured at the 1st, 3rd, 5th, 7th, 9th, and 11th days of storage, respectively. The results showed that group 25%CO2+35%N2 had the longest shelf life is 9 days. In the analysis of the bacterial community, CO2 significantly inhibited the growth of Pseudomonas from the 3rd day onwards in the group 25%CO2+35%N2. After 4 days of storage, Lactobacillus was the main dominant bacterium, followed by Carnobacterium. Through KEGG metabolic pathway analysis, it was found that during the storage and preservation process, the expression levels of genes related to carbohydrate metabolism and amino acid metabolism in cold fresh BBK were higher than those in other metabolites.

Fecal metabolomics combined with 16S rRNA gene sequencing to analyze the effect of Jiaotai pill intervention in type 2 diabetes mellitus rats.

The occurrence and development of type 2 diabetes mellitus (T2DM) are closely related to gut microbiota. Jiaotai pill (JTP) is used to treat type 2 diabetes mellitus, with definite efficacy in clinical practice. However, it is not clear whether the therapeutic effect is produced by regulating the changes in gut microbiota and its metabolism. In this study, T2DM rat models were established by a high-fat diet and low-dose streptozotocin (STZ). Based on the pharmacodynamic evaluation, the mechanism of JTP in the treatment of type 2 diabetes mellitus was investigated by fecal metabolism and 16S rRNA gene sequencing. The results showed that JTP decreased blood glucose (FBG, HbA1c) and blood lipid (TC, TG, and LDL) levels and alleviated insulin resistance (FINS, IL-10) in T2DM rats. 16S rRNA gene sequencing results revealed that JTP increased microbiota diversity and reversed the disorder of gut microbiota in T2DM rats, and therefore achieved the therapeutic effect in T2DM. JTP regulated 13 differential flora, which were Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, Eubacteriaceae, Prevotellaceae, Ruminococcaceae, Clostridium_IV, Clostridium_XlVa, Eubacterium, Fusicatenibacter, Romboutsia, and Roseburia. Metabolomics analysis showed that JTP interfered with 13 biomarkers to play a therapeutic role in type 2 diabetes mellitus. They were L-Valine, Choline, L-Aspartic acid, Serotonin, L-Lysine, L-Histidine, 3-Hydroxybutyric acid, Pyruvic acid, N-Acetylornithine, Arachidonic acid, L-Tryptophan, L-Alanine, and L-Methionine. KEGG metabolic pathway analysis of the above differential metabolites and gut microbiota by using the MetaboAnalyst database and Picrust software. It was found that JTP treated type 2 diabetes mellitus by affecting metabolic pathways such as amino acid metabolism, carbohydrate metabolism, and lipid metabolism. Spearman correlation analysis revealed high correlations for 7 pharmacological indicators, 12 biomarkers, and 11 gut microbiota. In this study, the therapeutic effect and potential mechanism of JTP on type 2 diabetes mellitus were preliminarily demonstrated by gut microbiota and metabolomics, which could provide a theoretical basis for the treatment of T2DM with JTP.

Transcriptome analysis of the biofilm formation mechanism of Vibrio parahaemolyticus under the sub-inhibitory concentrations of copper and carbenicillin

Biofilm formation of Vibrio parahaemolyticus enhanced its tolerance to the environment, but caused many serious problems to food safety and human health. In this paper, the effects of copper and carbenicillin (CARB) stress on the formation of the biofilms of V. parahaemolyticus organisms were studied, and RNA sequencing technology was used to compare the differences in transcriptome profiles of the biofilm-related genes of V. parahaemolyticus organisms under different sub-inhibitory stresses. The results proved that V. parahaemolyticus had a large growth difference under the two stresses, copper and CARB at 1/2 minimal inhibitory concentration (MIC), and it could form a stable biofilm under both stress conditions. The amount of biofilm formed under CARB stress was significantly higher than that of copper stress (p < 0.05). Based on the analysis of transcriptome sequencing results 323, 1,550, and 1,296 significantly differential expressed genes were identified in the three treatment groups namely 1/2 MIC CARB, Cu2+, and Cu2++CARB. Through COG annotation, KEGG metabolic pathway analysis and gene expression analysis related to biofilm formation, the functional pathways of transcriptome changes affecting V. parahaemolyticus were different in the three treatment groups, and the CARB treatment group was significantly different from the other two groups. These differences indicated that the ABC transport system, two-component system and quorum sensing were all involved in the biofilm formation of the V. parahaemolytic by regulating flagellar motility, extracellular polysaccharides and extracellular polymer synthesis. Exploring the effects of different stress conditions on the transcriptome of V. parahaemolyticus could provide a basis for future research on the complex network system that regulates the formation of bacterial biofilms.

Effect of ultrasound combined with exogenous GABA treatment on polyphenolic metabolites and antioxidant activity of mung bean during germination

Mung bean seeds were treated by a combination of ultrasound and γ-aminobutyric acid (GABA). Effect of these treatments on the free polyphenols content, antioxidant activity, and digestibility of mung bean sprouts was evaluated. Additionally, phenolic compounds were analyzed and identified using a metabolomics approach. The combined ultrasound and GABA treatments significantly enhanced the free polyphenols and flavonoids content (P < 0.05) of mung bean sprouts depending on sprouting duration. Besides, a positive correlation (P < 0.05) was found between the polyphenols content and in vitro antioxidant activity of mung bean sprouts. Moreover, a total number of 608 metabolites were detected, and 55 polyphenol compounds were identified, including flavonoids, isoflavones, phenols, and coumarins. Also, the KEGG metabolic pathway analysis revealed 10 metabolic pathways of phenols, including flavonoid, isoflavone, and phenylpropanoid biosynthesis. Powder of 48 h sprouted mung bean released polyphenols during simulated gastric digestion and possessed antioxidant activity.

Effects of Light Intensity on Physiological Characteristics and Expression of Genes in Coumarin Biosynthetic Pathway of Angelica dahurica.

Plants are affected by changes in light and adaptation mechanisms can affect secondary metabolite synthesis. In this study, the physiological response and regulation of the coumarin biosynthetic pathway of Angelica dahurica to different light intensities (natural light (CK), shade rate 50% (L1), shade rate 70% (L2), and shade rate 90% (L3)) were examined. The chlorophyll content, level of the enzymes of the antioxidant system, extent of lipid peroxidation, and concentrations of the osmoregulatory solute levels were determined in potted plants. Root transcriptome under different light intensities was sequenced using high-throughput technology, and differentially expressed genes (DEGs) related to coumarin biosynthesis were analyzed by quantitative real-time PCR (qRT-PCR). With increasing shade, Chl a, Chl b, Chl a + b, and Chl a/b content increased, while the Chl a/b ratio decreased. The antioxidant enzyme system activity and extent of membrane lipid peroxidation increased. The soluble protein (SP) and proline (Pro) content decreased with the reduction in the light intensity, and soluble sugar (SS) content was found to be highest at 50% shade. The RNA-seq analysis showed that 9388 genes were differentially expressed in the L3 group (7561 were upregulated and 1827 were downregulated). In both the L1 and L2 groups, DEGs were significantly enriched in "Ribosome biosynthesis"; meanwhile, in the L3 group, the DEGs were significantly enriched in "Amino and ribonucleotide sugar metabolism" in KEGG metabolic pathway analysis. Additionally, 4CL (TRINITY_DN40230_c0_g2) and COMT (TRINITY_DN21272_c0_g1) of the phenylpropanoid metabolic pathway were significantly downregulated in the L3 group. In conclusion, A. dahurica grew best under 50% shade and the secondary-metabolite coumarin biosynthetic pathway was inhibited by 90% shade, affecting the yield and quality of medicinal compounds.

Impact of a hexafluoropropylene oxide trimer acid (HFPO-TA) exposure on impairing the gut microbiota in mice.

Hexafluoropropylene oxide trimer acid (HFPO-TA) has been used as an alternative of perfluorooctanoic acid (PFOA) in the fluoropolymer industry for several years. HFPO-TA is reported to have high capability of bioaccumulation, widespread environmental distribution, and multiple toxicities. However, its potential toxicity on the intestines and gut microbiota remains unknown. In the present study, male mice were orally exposed to 200μg/L HFPO-TA for 6 weeks, and after total genomic DNA extraction, 16S rRNA amplicon pyrosequencing was performed. Our results demonstrated that HFPO-TA exposure resulted in the imbalance of cecal microbiota and alterations of cecal microbiota diversity. At the phylum level, the relative abundances of Proteobacteria, Deferribacteres, and Tenericutes increased in mice after exposure to HFPO-TA, while the relative abundances of Verrucomicrobia, Cyanobacteria, and TM7 decreased. At the genus level, the relative abundances of Ver Akkermansia, Pre Prevotella, Lac Coprococcus, Por_Parabacteroides, and Lac Dorea decreased in HFPO-TA exposed mice. Meanwhile, the increased relative abundances of Def_Mucispirillum, Des_Desulfovibrio and Odo Odoribacter were observed in HFPO-TA exposed mice. Additionally, KEGG metabolic pathway analysis revealed that HFPO-TA exposure changed the unsaturated fatty acid synthesis, fatty acid metabolism, glyoxylic acid and dicarboxylic acid metabolism, galactose metabolism pathway and other metabolic pathways. Collectively, all these findings indicate the potential gut toxicity of HFPO-TA and is perceived as a risk of health on gut microbiota. Future investigations should be warranted.