Screening Of Metabolites Research Articles

ABCoRT: Retention Time Prediction for Metabolite Identification via Atom-Bond Co-Learning.

Liquid chromatography retention time (RT) prediction plays a crucial role in metabolite identification, a challenging and essential task in untargeted metabolomics. Accurate molecular representation is vital for reliable RT prediction. To address this, we propose a novel molecular representation learning framework, ABCoRT(Atom-Bond Co-learning for Retention Time prediction), designed for predicting metabolite retention times. Our model transforms molecular graphs into dual hypergraphs, enabling the collaborative updating of atomic and bond information within both molecular graphs and hypergraphs, thereby producing highly informative molecular representations. We evaluated ABCoRT on a large-scale Small Molecule Retention Time (SMRT) data set comprising 80,038 molecules. Our model achieved a mean absolute error (MAE) of 25.75 s and a mean relative error (MRE) of 3.24% after removing nonretained molecules. Additionally, we fine-tuned pretrained ABCoRT models on six additional data sets from PredRet, achieving the lowest MAEs on five of them. Additionally, in metabolite screening conducted on the MetaboBASE and RIKEN_PlaSM data sets from the MassBank of North America, ABCoRT demonstrates its capability to filter out 38.35 and 28.46% of candidate compounds, respectively.

The intestinal fungus Aspergillus tubingensis promotes polycystic ovary syndrome through a secondary metabolite.

Polycystic ovary syndrome (PCOS) affects 6%-10% of women of reproductive age and is known to be associated with disruptions in the gut bacteria. However, the role of the gut mycobiota in PCOS pathology remains unclear. Using culture-dependent and internal transcribed spacer 2 (ITS2)-sequencing methods, we discovered an enrichment of the gut-colonizable fungus Aspergillus tubingensis in 226 individuals, with or without PCOS, from 3 different geographical areas within China. Colonization of mice with A.tubingensis led to a PCOS-like phenotype due to inhibition of Aryl hydrocarbon receptor (AhR) signaling and reduced interleukin (IL)-22 secretion in intestinal group 3 innate lymphoid cells (ILC3s). By developing a strain-diversity-based-activity metabolite screening workflow, we identified secondary metabolite AT-C1 as an endogenous AhR antagonist and a key mediator of PCOS. Our findings demonstrate that an intestinal fungus and its secondary metabolite play a critical role in PCOS pathogenesis, offering a therapeutic strategy for improving the management of the disease.

Evaluating the Antibacterial Potential of Commercial Herbal Mixtures against Clinical Isolate of Salmonella typhi: An In-vitro Experimental Analysis

Background: Typhoid fever incidence has continuously increased, particularly in developing countries. As a result, there has been an influx of preference for herbal remedies to meet the growing demand. However, the increasing demand for these herbal preparations has created room for false claims. Aim: This study investigated the in vitro activity of commercial herbal mixtures against a clinical isolate of S. typhi. Study Design: The study employed an experimental design to evaluate the vitro activity of four commercial herbal mixtures against a clinical isolate of S. typhi. Methods: Four herbal mixtures (IBA-ENTR5, DB-TYFO222, DY-PHB, and BIA-TABH) were screened for phytochemical and antimicrobial activity. Screening and identification of bioactive secondary metabolites were performed using standard procedures. The antimicrobial activity and minimum inhibitory concentration (MIC) were determined using the agar well diffusion and dilution method. Results: Based on photochemical screening, apart from the absence of glycosides in IBA-ENTR5, all other phytochemicals were present in the herbal mixtures. The highest activity per agar well diffusion was observed for IBA-ENTR5, followed by DB-TYFO222, DY-PHB, and BIA-TABH. The minimum inhibitory concentration values ranged from 150 to 250 mg/L, with IBA-ENTR5 and DY-PHB possessing 150 mg/L, DB-TYFO222 possessing 200 mg/L, and BIA-TABH possessing 250 mg/L. Compared with the positive control IAG-CPRO, only IBA-ENTR exhibited a higher inhibition zone. Conclusion: This study revealed that herbal mixtures contain rich phytochemical constituents. The results also confirmed that the antimicrobial activity and minimum inhibitory concentration of the herbal mixtures were concentration-dependent. That is, the herbal mixtures sampled provided good results when their concentrations were increased. In conclusion, herbal mixtures in open Ghanaian markets may provide good antimicrobial efficacy.

Structure-based virtual screening of Trachyspermum ammi metabolites targeting acetylcholinesterase for Alzheimer's disease treatment.

In recent decades, Alzheimer's disease (AD) has garnered significant attention due to its rapid global prevalence. The cholinergic hypothesis posits that the degradation of acetylcholine by acetylcholinesterase (AChE) contributes to AD development. Despite existing anti-AChE drugs, their adverse side effects necessitate new agents. This study analyzed 150 bioactive phytochemicals from Trachyspermum ammi using structure-based drug design and various in-silico tools to identify potent anti-AChE compounds. Compounds were screened for drug-likeness (QEDw ≥50%) and bioavailability (≥55%) and underwent toxicity profiling via the ProTox-II server. Selected compounds were prepared for molecular docking with the human AChE protein as the receptor. Viridifloral, 2-Methyl-3-glucosyloxy-5-isopropyl phenol, Alpha-Curcumene, and Sterol emerged as top candidates with high AChE affinity. These results were validated by molecular dynamics simulations, confirming stable interactions. The hit compounds were further evaluated for drug-likeness using Lipinski's rule and ADMET properties, confirming favorable pharmacokinetic profiles. DFT optimization analyzed frontier molecular orbitals and electrostatic potential, demonstrating favorable chemical reactivity and stability. This study suggests that these identified compounds could be novel nature-derived AChE inhibitors, potentially contributing to AD treatment. However, further in-vitro and in-vivo studies are necessary to confirm their efficacy in biological systems. Future research will focus on developing these compounds into safe and effective drugs to combat Alzheimer's disease.

Serum metabolite profiles of thyroid autoimmunity patients in early pregnancy.

Research on serum metabolite profiles in thyroid autoimmunity (TAI) patients during early pregnancy is currently limited. The current study aimed to identify differential serum metabolites and assess the relationship between pregnancy outcomes and metabolic abnormalities in individuals with TAI. This research included 26 pregnant women with TAI and 30 healthy controls (HC). We employed a liquid chromatograph mass spectrometer (LC-MS) to analyze changes between the two groups. Newborns in the TAI patients had lower birth weights than those in the control group (P = 0.007). We identified 92 differential metabolites (including 50 upregulated and 42 downregulated) belonging to amino acids, fatty acyls, glycerophosphocholines, steroid and other categories and four significantly enrichment Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including taurine and hypotaurine metabolism, citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism and 2-oxocarboxylic acid metabolism. We further identified 15 characteristic metabolites (6-Methylquinoline, D-erythrose 4-phosphate, 4-Hydroxyisoleucine, phosphatidylcholine (PC)(16:2e/16:0), N3,N4-Dimethyl-L-arginine, N-desmethyltramadol, 3-Methoxybenzaldehyde, sphingomyelin (SM)(d14:3/28:2), gamma-Glutamylleucine, NSI-189, 3-(1-cyano-1,2-dihydroisoquinolin-2-yl)-3-oxopropyl propionate, lysophosphatidylinositol (LPI) 16:0, cis-Aconitic acid, polyamide (PA)(18:1/18:2) and fatty acyl esters of hydroxy fatty acid (FAHFA)(17:0/18:0)) using least absolute shrinkage and selection operator (LASSO) regression. Correlation analyses revealed that 6-Methylquinoline, D-erythrose 4-phosphate, gamma-Glutamylleucine, and LPI 16:0 exhibited a positive correlation with anemia before delivery, while 3-(1-cyano-1,2-dihydroisoquinolin-2-yl)-3-oxopropyl propionate had a negative correlation. LPI 16:0 displayed a positive correlation with uric acid (UA) during both middle and late pregnancy, whereas 3-Methoxybenzaldehyde exhibited a negative correlation with UA in late pregnancy. Cis-Aconitic acid showed a positive correlation with fasting blood glucose (FBG) in middle pregnancy. Conversely, 6-Methylquinoline and 4-Hydroxyisoleucine had a negative correlation with birth weight. Thyroid autoantibodies were found to be associated with 14 metabolites identified using LASSO, with the exception of PA (18:1/18:2). Our findings provide new evidence supporting the early screening of serum metabolites and their potential for predicting adverse pregnancy outcomes in women with TAI.

Plasma metabolomic characteristics of atrial fibrillation patients with spontaneous echo contrast

BackgroundThe spontaneous echo contrast (SEC) in patients with atrial fibrillation (AF) indicates a prethrombic state that ultimately progresses into thrombus formation. A comprehensive understanding of specific plasma metabolomics characteristics may protect AF patients from thrombus, particularly in the early stage.ObjectivesThrough the investigation of metabolic pathways, we endeavor to uncover the metabolomic characteristics associated with SEC states, and to examine the differential metabolites by which may exert their influence on thrombotic states.MethodsPatients with AF were enrolled, and the participants were divided into three groups based on the results of the echocardiogram: non-SEC, low-SEC and high-SEC group. Samples were collected and subjected to non-targeted metabolomics analysis. The analytical process included data quality control, metabolite difference analysis, component analysis, Kegg cluster analysis, etc.ResultsOur metabolic phenotype revealed a clear differential metabolic pattern between the SEC and non-SEC. Specifically, we identified 35 and 142 significantly differential metabolites in venous and atrial plasma, respectively, suggesting that SEC may be involved in pervasive metabolic dysregulation and that the degree of metabolic dysregulation in atrial plasma is more severe than that in venous blood.ConclusionPatients with SEC have a significantly different metabolic pattern compared to those without SEC. Our work promoted the understanding of mechanism of the occurrence and development of SEC, facilitated the screening of the target metabolites for its therapeutic intervention, and provided evidence for the prevention and treatment of SEC or thrombosis in AF. Our work also provided new directions for subsequent research in related fields. In conclusion, our study not only provides a theoretical basis for understanding the occurrence and development of SEC in AF, but also provides recommendations for the daily diet of AF patients with SEC, such as a balanced intake of essential amino acids, avoiding excessive intake of benzoic acid, and intake of appropriate inositol.Clinical trial numberNot applicable.

Mycosynthesis of silver nanoparticles from endophytic Aspergillus parasiticus and their antibacterial activity against methicillin-resistant Staphylococcus aureus in vitro and in vivo.

Methicillin-resistant Staphylococcus aureus (MRSA) is a drug-resistant and biofilm-forming pathogenic bacteria with severe morbidity and mortality. MRSA showed resistance against currently available antibiotics. Thus, there is an urgent need to develop novel effective treatments with minimal side effects to eliminate MRSA. In this study, we aimed to mycosynthesize silver nanoparticles (AgNPs) using the endophytic fungus Aspergillus parasiticus isolated from leaves of Reseda Arabica and to examine their antibacterial activity against MRSA. Screening of fungal secondary metabolites using gas chromatography-mass spectroscopy (GC-MS) analysis revealed the presence of high content of bioactive compounds with antibacterial activities. AP-AgNPs were mycosynthesized for the first time using ethyl acetate extract of A. parasiticus and characterized by imaging (transmission electron microscopy (TEM), UV-Vis spectroscopy, zeta potential, X-ray diffraction (XRD), energy-dispersive X-ray analysis (EDX), and Fourier transform infrared spectroscopy (FTIR)). The agar well diffusion method revealed the antibacterial activity of AP-AgNPs against MRSA with 25 μg/mL of minimum inhibitory concentration (MIC). AP-AgNPs were shown to exert antibacterial action via a bactericidal mechanism based on flow cytometry, scanning electron microscopy, and transmission electron microscopy assessment. Our data demonstrated the effective interaction of AP-AgNPs with the bacterial cell membrane, which resulted in cell membrane damage and disruption of cell surface structure. Furthermore, AP-AgNPs successfully prevented the development of MRSA biofilms by disturbing cell adhesion and destructing mature biofilm reaching over 80% clearance rate. Interestingly, topical application of AP-AgNPs to superficial skin infection induced by MRSA in mice effectively promoted wound healing and suppressed bacterial burden. Our results provide a novel green nanoparticle drug design with effective therapeutic potential against MRSA-induced skin infection.

Antiproliferative Effects of Methanolic Fruit Extract of Solanum xenthocarpum (L.) on Human Breast Cancer Cells.

Solanum xanthocarpum, a perennial herb native to India, contains steroidal glycoalkaloids with notable anticancer properties. This study investigated the antioxidant and antiproliferative effects ofmethanolic fruit extract of S. xanthocarpum on human breast cancer cells (MDA-MB-231). Phytochemical screening and LC-HRMS analysis confirmedpresence of various primary and secondary metabolites. Antioxidant activity was assessed through DPPH, ABTS radical scavenging, reducing power, and phosphomolybdate assays. The extract demonstrated significant antioxidant potential with EC50 values of 60.10 ± 0.88 µg/mL (DPPH) and 392.29 ± 3.93 µg/mL (ABTS). Cytotoxicity against MDA-MB-231 cells was evaluated via morphological analysis, MTT assays, and IC50 determination (24.19 ± 0.56 µg/L). Apoptosis was confirmed using dual staining techniques (AO/EB, Hoechst 33342/PI, DAPI), revealing condensed nuclei, apoptotic bodies, and reduced mitochondrial membrane potential, as indicated by Rhodamine staining. Additionally, increased reactive oxygen species (ROS) levels were observed using H2-DCF-DA staining. The total phenolic and flavonoid contents of the extract were 127.78 ± 3.547 mg GAE/g and 98.06 ± 4.289 mg QE/g, respectively. These findings suggest that the methanolic fruit extract of S. xanthocarpum possesses strong antioxidant and anticancer activities, indicating its potential role in cancer treatment. Further studies are warranted to explore its bioactive compounds for developing novel anticancer therapies.

Identification of hypoxene metabolites in urine samples using gas chromatography–tandem mass spectrometry for anti-doping control

Objectives. Hypoxen is a drug which possesses antioxidant and antihypoxic effects. It achieves this by increasing the utilization of oxygen by mitochondria, intensifying oxidative phosphorylation, and as a result, improving tissue respiration. Athletes take it during prolonged exercise, in order to increase efficiency and reduce physical overwork. Since 2023, the World Anti-Doping Agency has included the drug in the monitoring program, in the belief that it can be used to gain a competitive advantage. It is thus a candidate for inclusion in the Prohibited List as a potential regulator of the human metabolism. Currently, there are no studies or scientific publications focusing on the identification of hypoxene in biofluids for the purpose of anti-doping control. The aim of this study is to determine the possible metabolites of the drug and their chromato-mass spectrometric characteristics in urine samples using gas chromatography–tandem mass spectrometry (GC–MS/MS) for doping control screening purposes.Methods. Sample preparation of urine samples was carried out using enzymatic hydrolysis, liquid–liquid extraction and derivatization. The GC–MS/MS method was used for analysis. Screening of hypoxene metabolites was carried out in the mode of total ion current after fragmentation of selected parent ions.Results. Three specific metabolites of hypoxene (m/z 342, 300, and 346, including trimethylsilyl derivatives) were identified in urine samples of volunteers (n = 3). They can act as markers for taking the target antihypoxant, and their possible structural formulas are given. The excretion curves of two metabolites with an m/z of 300 and 346 respectively in urine were studied. The maximum concentration is reached after 8–14 and 1.5–6 h, respectively. It was established, that these metabolites are reliably identified in urine 90 h or more after a single dose of the drug.Conclusions. Possible structures of hypoxene metabolites in urine samples from volunteers were determined for the first time and their chromato-mass spectrometric characteristics were established. The approach developed in this study can be used for screening analysis of hypoxene for the purpose of anti-doping control.

Hidden liver-joint axis: HBV infection causes rheumatoid arthritis via TRAFD1 with imbalance of HBV X protein and trans-ferulic acid

ABSTRACT Liver metabolites are involved in the progression of rheumatoid arthritis (RA), indicating a connection between the liver and joints. However, the impact and mechanism of Hepatitis B virus (HBV), a hepatotropic virus, on RA are still unclear. We investigated the correlation between HBV and RA using Mendelian randomization analysis. Single-cell transcriptome analysis was conducted to investigate changes in cell subtypes in synovial tissue of HBV-RA patients. Fibroblast-like synoviocytes (FLS) were used to create a cell model, and the transcriptome was examined to identify the key downstream molecules of FMT regulated by HBx. CIA model was constructed using HBV transgenic, HBx transgenic, and TRADF1 knockout mice to investigate the impact and mechanism of HBV on CIA. The results of our study revealed a significant positive correlation between HBV and RA. The functional studies identified a crucial role of fibroblast-myofibroblast transition (FMT) in the progression of RA. The results suggest that HBV-encoded HBx may promote FMT in RA by upregulating TRAFD1. Furthermore, trans-ferulic acid (TFA) was identified by screening for common metabolites in the liver, joints, and peripheral blood using the metabolome and WGCNA. Interestingly, we found that TFA ameliorated HBx-induced RA by suppressing TRAFD1 expression. Our study demonstrates that hidden liver-joint axis, an imbalance between TFA and HBx, plays a critical role in HBV-induced RA, which could be a potential strategy for preventing RA development.

Chemical composition of anti-microbially active fractions derived from extract of filamentous fungus Keratinophyton Lemmensii including three novel bioactive compounds

Screening for new bioactive microbial metabolites, we found a novel okaramine derivative, for which we propose the trivial name lemmokaramine, as well as two already known okaramine congeners – okaramine H and okaramine J - responsible for antimicrobial activity of the recently described microscopic filamentous fungus, Keratinophyton lemmensii BiMM-F76 (= CCF 6359). In addition, two novel substances, a new cyclohexyl denominated lemmensihexol and a new tetrahydroxypyrane denominated lemmensipyrane, were purified and characterized. The compounds were isolated from the culture extract of the fungus grown on modified yeast extract sucrose medium by means of flash chromatography followed by preparative HPLC. The chemical structures were elucidated by NMR and LC-MS. The new okaramine (lemmokaramine) exerted antimicrobial activity against Gram-positive and Gram-negative bacteria, yeasts and fungi and anticancer activity against different mammalian cell lines (Caco-2, HCT116, HT29, SW480, MCM G1, and MCM DLN). Furthermore, we found a significant antioxidant effect of lemmokaramine following H2O2 treatment indicated by activation of the Nrf2 pathway. This is the first report describing analysis and structural elucidation of bioactive metabolites for the onygenalean genus Keratinophyton.

Combining culture optimization and synthetic biology to improve production and detection of secondary metabolites in Myxococcus xanthus: application to myxoprincomide.

Microbial secondary metabolites play crucial ecological roles in governing species interactions and contributing to their defense strategies. Their unique structures and potent bioactivities have been key in discovering antibiotics and anticancer drugs. Genome sequencing has undoubtedly revealed that myxobacteria constitute a huge reservoir of secondary metabolites as the well-known producers, actinomycetes. However, because most secondary metabolites are not produced in the laboratory context, the natural products from myxobacteria characterized to date represent only the tip of the iceberg. By combining the engineering of a dedicated Myxococcus xanthus DZ2 chassis strain with a two-step growth medium protocol, we provide a new approach called two-step Protocol for Resource Integration and Maximization-Biomolecules Overproduction and Optimal Screening Therapeutics (2PRIM-BOOST) for the production of non-ribosomal peptides synthetases (NRPS)/polyketides synthases (PKS) secondary metabolites from myxobacteria. We further show that the 2PRIM-BOOST strategy will facilitate the screening of secondary metabolites for biological activities of medical interest. As proof of concept, using a constitutive strong promoter, the myxoprincomide from M. xanthus DZ2 has been efficiently produced and its biosynthesis has been enhanced using the 2PRIM-BOOST approach, allowing the identification of new features of myxoprincomide. This strategy should allow the chances to produce and discover new NRPS, PKS, and mixed NRPS/PKS hybrid natural metabolites that are currently considered as cryptic and are the most represented in myxobacteria.IMPORTANCEMicrobial secondary metabolites are important in species interactions and are also a prolific source of drugs. Myxobacteria are ubiquitous soil-dwelling bacteria constituting a huge reservoir of secondary metabolites. However, because most of these molecules are not produced in the laboratory context, one can estimate that only one-tenth have been characterized to date. Here, we developed a new strategy called two-step Protocol for Resource Integration and Maximization-Biomolecules Overproduction and Optimal Screening Therapeutics (2PRIM-BOOST) that combines the engineering of a dedicated Myxococcus xanthus chassis strain together with growth medium optimization. By combining these strategies with the insertion of a constitutive promoter upstream the biosynthetic gene cluster (BGC), the production of myxoprincomide, a characterized low-produced secondary metabolite, was successfully and significantly increased. The 2PRIM-BOOST enriches the toolbox used to produce previously cryptic metabolites, unveil their ecological role, and provide new molecules of medical interest.

Characterizing the Metabolism of Tire Rubber-Derived p-Phenylenediamine Quinones to Identify Potential Exposure Biomarkers in Humans.

There is growing evidence of the frequent detection of tire rubber-derived contaminants p-phenylenediamine-derived quinones (PPD-Qs) (e.g., highly toxic N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-Q)) in the environment and biota and the adverse impact on organisms. Hence, a better understanding of their biotransformation/metabolism in humans is essential. However, relevant data are lacking owing to recent discoveries. Herein, the biotransformation patterns of 6PPD-Q and other five commonly detected PPD-Qs were characterized via combined in vitro assay and maternal cord blood screening monitoring. Rapid metabolism was found for each PPD-Q incubated with human liver S9 fraction and microsomes, resulting in the formation of abundant phase I and phase II metabolites. The subsequent screening for potential PPD-Q metabolites in blood samples showed the presence of suspect metabolites. Three detected metabolites were confirmed by matching the mass spectra and retention times of in vitro metabolites. N-Dealkylated, carboxy, carbonyl, and reductive metabolites and glucose, cysteine, and methionine conjugates were observed for the first time. The semiquantitative concentrations of metabolites were higher than those of the parent PPD-Qs, and several metabolites such as carboxy products were proposed as candidate biomarkers of PPD-Q exposure to humans. 6PPD-Q and N,N'-diphenyl-p-phenylenediamine quinone were detected in maternal and/or cord whole blood samples for the first time. This study holds great importance in elucidating the potential risks and health effects of PPD-Qs.

Rapid identification of chemical profiles in vitro and in vivo of Huan Shao Dan and potential anti-aging metabolites by high-resolution mass spectrometry, sequential metabolism, and deep learning model.

Aging is marked by the gradual deterioration of cells, tissues, and organs and is a major risk factor for many chronic diseases. Considering the complex mechanisms of aging, traditional Chinese medicine (TCM) could offer distinct advantages. However, due to the complexity and variability of metabolites in TCM, the comprehensive screening of metabolites associated with pharmacology remains a significant issue. A reliable and integrated identification method based on UPLC-Q Exactive-Orbitrap HRMS was established to identify the chemical profiles of Huan Shao Dan (HSD). Then, based on the theory of sequential metabolism, the metabolic sites of HSD in vivo were further investigated. Finally, a deep learning model and a bioactivity assessment assay were applied to screen potential anti-aging metabolites. This study identified 366 metabolites in HSD. Based on the results of sequential metabolism, 135 metabolites were then absorbed into plasma. A total of 178 peaks were identified from the sample after incubation with artificial gastric juice. In addition, 102 and 91 peaks were identified from the fecal and urine samples, respectively. Finally, based on the results of the deep learning model and bioactivity assay, ginsenoside Rg1, Rg2, and Rc, pseudoginsenoside F11, and jionoside B1 were selected as potential anti-aging metabolites. This study provides a valuable reference for future research on the material basis of HSD by describing the chemical profiles both in vivo and in vitro. Moreover, the proposed screening approach may serve as a rapid tool for identifying potential anti-aging metabolites in TCM.

Computational and in vitro analyses of the antibacterial effect of the ethanolic extract of Pluchea indica L. leaves.

The most common gram-negative, Escherichia coli, and gram-positive bacteria, Bacillus spp., have evolved different mechanisms that have caused the emergence of multi-drug resistance. As a result, drugs that block the bacterial growth cycle are needed. Here, in silico and in vitro studies were performed to assess compounds in the Pluchea indica leaf extract, a medicinal plant, that can inhibit bacterial proteins. Briefly, P. indica leaves were extracted using ethanol. The crude extract was then subjected to gas chromatography-mass spectrometry for metabolite screening. Molecular docking simulations with rhomboid protease (Rpro) (Protein data bank ID number: 3ZMI from E. coli and filamenting temperature-sensitive mutant Z (FtsZ) protein data bank ID number: 2VAM from Bacillus subtilis were performed. Moreover, the well diffusion method was used to confirm the antibacterial activity of P. indica leaf extract. A total of 10 compounds were identified in the P. indica extract and used for computational analysis. Based on drug-likeness prediction, P. indica compounds may be drug-like molecules. Binding affinity tests indicated that 10,10-Dimethyl-2,6-dimethylenebicyclo(7.2.0)undecan-5.β.-ol and 11,11-Dimethyl-4,8-dimethylenebicyclo(7.2.0)undecan-3-ol had the most negative values. Accordingly, these compounds may be potential ligands that bind to bacterial proteins. The root mean square fluctuation values was <2 Å, indicating stable fluctuation binding for the ligand-protein complex. According to in vitro antibacterial assays, a high concentration (50%) of the P. indica extract markedly inhibited E. coli and B. subtilis, with inhibitory zone diameters of 31.86±1.63 and 21.09±0.09 mm, respectively. Overall, the compounds in the P. indica leaf extract were identified as functional inhibitors of E. coli and B. subtilis proteins via in silico analysis. This may facilitate development of antibacterial agents.

Screening of Extract Secondary Metabolites of Bacteria Which Have Symbiosis with Sponges from Central Tapanuli Bakar Island as an Antibacteria

This study aims to determine the presence of antibacterial-producing bacteria from sponges from Bakar Island, Central Tapanuli Regency and to determine the antibacterial activity of methanol extracts from potential bacterial isolates against Staphylococcus aureus and Escherichiacoli. 21 pure isolates were found and it was known that 9 isolates produced antibacterial against S. aureus and 4 isolates against E. coli. Bacterial isolates with the highest inhibition zone against bothS.aureus and E. coli were found in isolates with code SP20 with each large inhibition zone are 14.5 mm and 16.04 mm. Then microscopic observations were carried out, namely gram staining and were obtained 8 isolates were gram positive, and 1 gram was negative. The biochemical test showed that SP20 showed positive results for the Motility, TSIA and Catalase Test but negative for Citrate Test. Bacterial isolates withthe code SP20 had the largest inhibition zone so that these isolates were to be extracted.The resultsof the screening test showed that the secondary metabolitesof the sponge symbiont bacterial extract from Bakar Island were positive for flavonoids and saponins. And then test the activity of secondary metabolites with 3 concentrations, 10%, 20%, and 30%.The results showed that the best concentration of the test bacteria was S. aureus at a concentration of 30% with an inhibition zone of 3.08 mm and E. coli at 5.04 mm.

Insights into flavor quality and metabolites profiles of fresh cheese with different probiotics by SPME-GC-MS and untargeted metabolomics

In this study, fresh cheeses produced with four novel probiotics (Lactobacillus casei PB-LC39, Lactobacillus rhamnosus PB-LR76, Lactobacillus helveticus HH-LH17, and Lactobacillus plantarum HH-LP56) were named as LC, LR, LH, and LP, respectively. SPME-GC-MS and untargeted metabolomics were used to compare and analyze the flavor quality, metabolites and metabolic pathways of LC, LR, LH and LP, and the potential function of differential metabolites was emphasized. The results demonstrated that the incorporation of probiotics resulted in a significant increase in the number of volatile flavor compounds and varying flavor profiles within the cheese. Especially LC, exhibited aromas reminiscent of wine, fruit and rose, and displayed the most favorable flavor qualities among all probiotic cheeses. The results of differential metabolite screening and metabolic pathway demonstrated that probiotic cheese could result in the production of 146–192 differential metabolites, mainly carbohydrates, proteins and acids. Arginine biosynthesis was a key differential metabolite pathway made by probiotics. The LC, LR, LH, and LP groups contained 22, 27, 23, and 24 functional metabolites, including L-carnitine, naringenin, and turanose et al., which might confer anti-inflammatory and improve lipid metabolism functions. These findings provide a theoretical basis for the further functional evaluation and development of probiotic cheese.

Mycobolome of Phialomyces Macrosporus Across OSMAC-Based Assorted Culture Media.

The fungus Phialomyces macrosporus was cultured using the One Strain Many Compounds (OSMAC) strategies to evaluate its metabolome. Variations in the nutrient culture media, culture regime, and cultivation parameters can significantly influence fungal extract quantity and chemical diversity. This study aimed to explore the mycobolome of P. macrosporus in five different culture media and two different cultivation conditions using NMR-based metabolomics. Principal component analysis (PCA) of 1H-NMR spectra revealed clear differentiation between these samples, highlighting the rice dextrose agar medium (RDA) and potato dextrose broth (PDB) as standard complex media for conducting a fungal metabolite screening program.

Buqi-Huoxue-Tongnao decoction drives gut microbiota-derived indole lactic acid to attenuate ischemic stroke via the gut-brain axis

BackgroundIschemic stroke belongs to “apoplexy” and its pathogenesis is characterized by qi deficiency and blood stasis combining with phlegm-damp clouding orifices. Buqi-Huoxue-Tongnao decoction (BHTD) is a traditional Chinese medicine formula for qi deficiency, blood stasis and phlegm obstruction syndrome. However, its efficacy and potential mechanism on ischemic stroke are still unclear. This study aims to investigate the protective effect and potential mechanism of BHTD against ischemic stroke.Materials and methodsMiddle cerebral artery occlusion (MCAO) surgery was carried out to establish an ischemic stroke model in rats. Subsequently, the rats were gavaged with different doses of BHTD (2.59, 5.175, 10.35 g/kg) for 14 days. The protective effects of BHTD on the brain and gut were evaluated by neurological function scores, cerebral infarction area, levels of brain injury markers (S-100B, NGB), indicators of gut permeability (FD-4) and bacterial translocation (DAO, LPS, D-lactate), and tight junction proteins (Occludin, Claudin-1, ZO-1) in brain and colon. 16S rRNA gene sequencing and metabolomic analysis were utilized to analyze the effects on gut microecology and screen for marker metabolites to explore potential mechanisms of BHTD protection against ischemic stroke.ResultsBHTD could effectively mitigate brain impairment, including reducing neurological damage, decreasing cerebral infarction and repairing the blood–brain barrier, and BHTD showed the best effect at the dose of 10.35 g/kg. Moreover, BHTD reversed gut injury induced by ischemic stroke, as evidenced by decreased intestinal permeability, reduced intestinal bacterial translocation, and enhanced intestinal barrier integrity. In addition, BHTD rescued gut microbiota dysbiosis by increasing the abundance of beneficial bacteria, including Turicibacter and Faecalibaculum. Transplantation of the gut microbiota remodeled by BHTD into ischemic stroke rats recapitulated the protective effects of BHTD. Especially, BHTD upregulated tryptophan metabolism, which promoted gut microbiota to produce more indole lactic acid (ILA). Notably, supplementation with ILA by gavage could alleviate stroke injury, which suggested that driving the production of ILA in the gut might be a novel treatment for ischemic stroke.ConclusionBHTD could increase gut microbiota-derived indole lactic acid to attenuate ischemic stroke via the gut-brain axis. Our current finding provides evidence that traditional Chinese medicine can ameliorate central diseases through regulating the gut microbiology.

A Comparative Metabolomics Study of Glucosinolates in Four Watercress (Nasturtium officinale R. Br.) Samples from Different Origins Using Ultra-High-Performance Liquid Chromatography–Electrospray Ionization–Tandem Mass Spectrometry

Glucosinolates are important plant secondary metabolites that are involved in plant defense responses and have beneficial effects on human life and health. Watercress (Nasturtium officinale R. Br.) is an aquatic vegetable rich in glucosinolates. This study utilized ultra-high-performance liquid chromatography–electrospray ionization–tandem mass spectrometry (UHPLC-ESI-MS/MS) to compare and analyze four watercress samples from different origins. A total of 35 glucosinolates were identified, including 33 differential glucosinolates, and their relative content in different samples was determined. Differential metabolite screening revealed significant differences in the watercress from Guangdong, China (GD), compared with other samples. It contained two specific glucosinolates: 2(R)-Hydroxy-2-Phenylethyl glucosinolate and 4-Benzoyloxybutyl glucosinolate. The watercress from the United States of America (MG) had the highest total glucosinolate content. Genes involved in glucosinolate biosynthesis, such as NoCYP83A1 and NoSUR1, were also expressed differently in the four samples. This study provides a reference for further investigation of glucosinolate metabolites in the four watercress samples and the utilization of glucosinolates in watercress.