LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Companilactobacillus alimentarius Y4 alleviates salmonella-induced intestinal inflammation by regulating gut microbiota and its metabolites'.
Answer: The emergence of ciprofloxacin-resistant Salmonella poses a significant challenge to the development of new drugs. Probiotics that inhibit ciprofloxacin-resistant Salmonella offer a safer alternative with fewer side effects than chemical antibiotics and drugs. Here, a strain of Companilactobacillus alimentarius Y4, isolated from kimchi, demonstrated strong antibacterial activity against Salmonella C1, E. coli and other intestinal pathogens. The results of the biological characteristics experiment show that the survival rate of C. alimentarius Y4 was 80% at pH 3.0 and 87.13% at 0.3% bile salt concentration. It retained antibacterial activity even after exposure to pepsin, trypsin, protease K, and catalase. Additionally, C. alimentarius Y4 down-regulates the inflammatory cytokines IL-1β, TNF-α, and IL-6 while upregulating the anti-inflammatory cytokine IL-10. It effectively repaired intestinal damage caused by ciprofloxacin-resistant Salmonella C1. Gut flora analysis revealed that C. alimentarius Y4 colonized the intestine and increased the abundance of beneficial gut microbes such Lachnospiraceae bacterium-COE1 and Muribaculaceae-CAG-485. Furthermore,analysis of intestinal metabolites indicated that C. alimentarius Y4 Up-regulate L-leucine, L-lysine and Tryptophan and other metabolites and then restored intestinal metabolic balance. In summary, C. alimentarius Y4 by regulating inflammatory cytokines, repairing intestinal damage, rebalancing gut flora, and correcting intestinal metabolic disorders,it is holds promise as an effective probiotic for managing intestinal inflammation caused by ciprofloxacin-resistant Salmonella. This study lays a foundation for the clinical development of probiotic products.
Question: Write a study description for the study titled 'Metabolic Profiling of Volatile Organic Compounds (VOCs) Emitted by the Pathogens Francisella tularensis and Bacillus anthracis in Liquid Culture'.
Answer: We conducted comprehensive (untargeted) metabolic profiling of volatile organic compounds (VOCs) emitted in culture by bacterial taxa Francisella tularensis (F. tularensis) subspecies novicida and Bacillus anthracis (B. anthracis) Sterne, surrogates for potential bacterial bioterrorism agents, as well as selective measurements of VOCs from their fully virulent counterparts, F. tularensis subspecies tularensis strain SCHU S4 and B. anthracis Ames. F. tularensis and B. anthracis were grown in liquid broth for time periods that covered logarithmic growth, stationary, and decline phases. VOCs emitted over the course of the growth phases were collected from the headspace above the cultures using solid phase microextraction (SPME) and were analyzed using gas chromatography-mass spectrometry (GC-MS). We developed criteria for distinguishing VOCs originating from bacteria versus background VOCs (originating from growth media only controls or sampling devices). Analyses of collected VOCs revealed methyl ketones, alcohols, esters, carboxylic acids, and nitrogen- and sulfur-containing compounds that were present in the bacterial cultures and absent (or present at only low abundance) in control samples indicating that these compounds originated from the bacteria. Distinct VOC profiles where observed for F. tularensis when compared with B. anthracis while the observed profiles of each of the two F. tularensis and B. anthracis strains exhibited some similarities. Furthermore, the relative abundance of VOCs was influenced by bacterial growth phase. These data illustrate the potential for VOC profiles to distinguish pathogens at the genus and species-level and to discriminate bacterial growth phases. The determination of VOC profiles lays the groundwork for non-invasive probes of bacterial metabolism and offers prospects for detection of microbe-specific VOC biomarkers from two potential biowarfare agents.
Question: Write a study description for the study titled 'A Prototypic Small Molecule Database for Bronchoalveolar Lavage-Based Metabolomics'.
Answer: The analysis of bronchoalveolar lavage fluid (BALF) using mass spectrometry-based metabolomics can provide insight into lung diseases, such as asthma. However, the important step of compound identification is hindered by the lack of a small molecule database that is specific for BALF. Here we describe prototypic, small molecule databases derived from human BALF samples (n=117). Human BALF was extracted into lipid and aqueous fractions and analyzed using liquid chromatography mass spectrometry. Following filtering to reduce contaminants and artifacts, the resulting BALF databases (BALF-DBs) contain 11,737 lipid and 658 aqueous compounds. Over 10% of these were found in 100% of samples. Testing the BALF-DBs using nested test sets produced a 99% match rate for lipids and 47% match rate for aqueous molecules. Searching an independent dataset resulted in 45% matching to the lipid BALF-DB compared to < 25% when general databases are searched. Overall, the BALF-DBs can reduce false positives and improve confidence in compound identification compared to when general databases are used.
Question: Write a study description for the study titled 'Mirabegron displays anticancer effects by globally browning adipose tissues'.
Answer: Metabolic reprogramming in malignant cells is a hallmark of cancer that relies on augmented glycolytic metabolism to support their growth, invasion and metastasis. However, the impact of global adipose metabolism on tumor growth and the drug development by targeting adipose metabolism remain largely unexplored. Here we show that a therapeutic paradigm of drugs is effective for treating various cancer types by browning adipose tissues. Mirabegron, a clinically available drug for overactive bladders, displays potent anticancer effects in various animal cancer models, including untreatable cancers such as pancreatic ductal adenocarcinoma and hepatocellular carcinoma, via the browning of adipose tissues. Genetic deletion of the uncoupling protein 1 (UCP1), a key thermogenic protein in adipose tissues, ablates the anticancer effect. Similarly, the removal of brown adipose tissue (BAT), which is responsible for non-shivering thermogenesis, attenuates the anticancer activity of mirabegron. These findings demonstrate that mirabegron represents a paradigm of anticancer drugs with a distinct mechanism for the effective treatment of multiple cancers.
Question: Write a study description for the study titled 'Metabolic fingerprinting reveals roles of Arabidopsis thaliana BGLU1, BGLU3, and BGLU4 in glycosylation of various flavonoids'.
Answer: Flavonoids are specialized metabolites that play important roles in plants, including interactions with the environment. The high structural diversity of this metabolite group is largely due to enzyme-mediated modifications of flavonoid core skeletons. In particular, glycosylation with different sugars is very common. In this study, the functions of the Arabidopsis thaliana glycoside hydrolase family 1-type glycosyltransferase proteins BGLU1, BGLU3, and BGLU4 were investigated, using a reverse genetics approach and untargeted metabolic fingerprinting. We screened for metabolic differences between A. thaliana wild type, loss-of- function mutants, and overexpression lines and partially identified differentially accumulating metabolites, which are putative products and/or substrates of the BGLU enzymes. Our study revealed that the investigated BGLU proteins are glycosyltransferases involved in the glycosylation of already glycosylated flavonoids using different substrates. While BGLU1 appears to be involved in the rhamnosylation of a kaempferol diglycoside in leaves, BGLU3 and BGLU4 are likely involved in the glycosylation of quercetin diglycosides in A. thaliana seeds. In addition, we present evidence that BGLU3 is a multifunctional enzyme that catalyzes other metabolic reactions with more complex substrates. This study deepens our understanding of the metabolic pathways and enzymes that contribute to the high structural diversity of flavonoids.
Question: Write a study description for the study titled 'Diurnal Dynamics Shape Plant Defense Responses: Temporal Variations in Disease Progression and Metabolic Reprogramming in Brassica oleracea'.
Answer: Plants synchronize their immune responses with the circadian cycle, yet the impact of diurnal timing on disease resistance remains poorly understood in crop species. In this study, we investigated how diurnal variation modulates defense responses in Brassica oleracea against Xanthomonas campestris pv. campestris (Xcc). Using a resistant cabbage variety (Badger Inbred-16) and a susceptible broccoli variety (Early Big), we found that plants inoculated in the evening exhibited significantly reduced disease severity compared to morning infections. Metabolomic and gene expression analyses revealed that the circadian clock orchestrates metabolic reprogramming during infection, influencing key defense-related compounds. Lipid metabolism, particularly the accumulation of fatty acid amides such as oleamide, was strongly associated with evening resistance. Additionally, genes involved in jasmonic acid biosynthesis and energy metabolism were upregulated at night, suggesting a coordinated defense response. Exogenous application of oleamide mimicked the evening resistance phenotype, reducing lesion size and inhibiting bacterial growth in vitro. These findings indicate that diurnal immune regulation is a critical factor in plant-pathogen interactions and that leveraging circadian-driven metabolic shifts could enhance crop disease management strategies.
Question: Write a study description for the study titled 'A molecular index for biological age identified from the metabolome and senescence-associated secretome in humans.'.
Answer: Unlike chronological age, biological age is a strong indicator of health of an individual. However, the molecular fingerprint associated with biological age is ill-defined. To define a high-resolution signature of biological age, we analyzed metabolome, circulating senescence-associated secretome (SASP)/inflammation markers and the interaction between them, from a cohort of healthy and rapid agers. The balance between two fatty acid oxidation mechanisms, β-oxidation and ω-oxidation, associated with the extent of functional aging. Furthermore, a panel of 25 metabolites, Healthy Aging Metabolic (HAM) index, predicted healthy agers regardless of gender and race. HAM index was also validated in an independent cohort. Causal inference with machine learning implied three metabolites, β-cryptoxanthin, prolylhydroxyproline, and eicosenoylcarnitine as putative drivers of biological aging. Multiple SASP markers were also elevated in rapid agers. Together, our findings reveal that a network of metabolic pathways underlie biological aging, and the HAM index could serve as a predictor of phenotypic aging in humans.
Question: Write a study description for the study titled 'Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization'.
Answer: BACKGROUND: The human intestinal microbiome plays a central role in overall health status, especially in early life stages. 16S rRNA amplicon sequencing is used to profile its taxonomic composition; however, multiomic approaches have been proposed as the most accurate methods for study of the complexity of the gut microbiota. In this study, we propose an optimized method for bacterial diversity analysis that we validated and complemented with metabolomics by analyzing fecal samples.METHODS: Forty-eight different analytical combinations regarding (1) 16S rRNA variable region sequencing, (2) a feature selection approach, and (3) taxonomy assignment methods were tested. A total of 18 infant fecal samples grouped depending on the type of feeding were analyzed by the proposed 16S rRNA workflow and by metabolomic analysis.RESULTS: The results showed that the sole use of V4 region sequencing with ASV identification and VSEARCH for taxonomy assignment produced the most accurate results. The application of this workflow showed clear differences between fecal samples according to the type of feeding, which correlated with changes in the fecal metabolic profile.CONCLUSION: A multiomic approach using real fecal samples from 18 infants with different types of feeding demonstrated the effectiveness of the proposed 16S rRNA-amplicon sequencing workflow.
Question: Write a study description for the study titled 'Metabolic Effects of a Chronic Dietary Exposure to a Low-Dose Pesticide Cocktail in Mice: Sexual Dimorphism and Role of the Constitutive Androstane Receptor (Untargeted urine UPLC-MS assay)'.
Answer: BACKGROUND: Epidemiological evidence suggests a link between pesticide exposure and the development of metabolic diseases. However, most experimental studies have evaluated the metabolic effects of pesticides using individual molecules, often at non relevant doses or in combination with other risk factors such as high fat diets.OBJECTIVES: We aimed to evaluate, in mice, the metabolic consequences of chronic dietary exposure to a pesticide mixture at non-toxic doses, relevant to consumers’ risk assessment. METHODS: A mixture of six pesticides commonly used in France i.e. boscalid, captan, chlorpyrifos, thiofanate, thiacloprid, and ziram was incorporated in a standard chow diet, at doses exposing mice to the acceptable daily intake (ADI) of each pesticide. Wild-type (WT) and Constitutive Androstane Receptor knock-out (CAR-/-) C57Bl6/J male and female mice were exposed for 52 weeks. We assessed metabolic parameters (body-weight, food and water consumption, glucose tolerance, urinary metabolome) throughout the experiment. At the end of the experiment, we evaluated liver metabolism (histology, transcriptomics, metabolomics) and pesticide detoxification using LC/MS.RESULTS: In males, pesticide exposure increased body weight and adiposity and induced hepatic steatosis and glucose intolerance. Exposed females exhibited fasted hyperglycaemia, hepatic oxidative stress and perturbations of gut microbiota-related urinary metabolites. The Constitutive Androstane Receptor is involved in the sexually dimorphic response to pesticide exposure. CONCLUSIONS: We show for the first time the sexually dimorphic obesogen and diabetogen effects of a chronic dietary exposure to a realistic mixture of pesticides, which are partially mediated through CAR. This raises questions about the relevance of ADI for individual pesticides when present in a mixture.Untargeted urine UPLC-MS assay protocols and data are reported in the current study MTBLS596.Untargeted urine, plasma and liver NMR assay protocols and data associated to this study are reported in MTBLS602.
Question: Write a study description for the study titled 'Metabolomic profiling reveals pipecolic acid-related pathways involved in Rlm1-mediated resistance in Canola'.
Answer: Study of pipecolic acid-related pathways involved in Rlm1-mediated resistance in Canola
Question: Write a study description for the study titled 'NMR-based metabolic profiling of children with premature adrenarche'.
Answer: INTRODUCTION: Premature adrenarche (PA) for long time was considered a benign condition but later has been connected to various diseases in childhood and adulthood which remains controversial.OBJECTIVE: To investigate the effect of premature adrenarche on the metabolic phenotype, and correlate the clinical and biochemical data with the metabolic profile of children with PA.METHODS: Nuclear magnetic resonance (NMR)-based untargeted and targeted metabolomic approach in combination with multivariate and univariate statistical analysis applied to study the metabolic profiles of children with PA. Plasma, serum, and urine samples were collected from fifty-two children with Idiopathic PA and forty-eight age-matched controls from the division of Pediatric Endocrinology of the University Hospital of Patras were enrolled.RESULTS: Metabolomic results showed that plasma and serum glucose, myo-inositol, amino acids, a population of unsaturated lipids, and esterified cholesterol were higher and significantly different in PA children. In the metabolic profiles of children with PA and age-matched control group a gradual increase of glucose and myo-inositol levels was observed in serum and plasma, which was positively correlated their body mass index standard deviation score (BMI SDS) values respectively. Urine 1H NMR metabolic fingerprint of PA children showed positive correlation and a clustering-dependent relationship with their BMI and bone age (BA) respectively.CONCLUSION: This study provides evidence that PA driven metabolic changes begin during the childhood and PA may has an inductive role in a BMI-driven increase of specific metabolites. Finally, urine may be considered as the best biofluid for identification of the PA metabolism as it reflects more clearly the PA metabolic fingerprint.
Question: Write a study description for the study titled 'Microbial -Enzymatic Mucin Metabolic Relay Suppresses Tumor Progression in Apcmin/+ mice'.
Answer: Compelling evidence established the gut microbiota as a pivotal regulator of colorectal cancer (CRC) progression, although stage-specific mechanisms remain unclear. Our investigation in Apcmin/+ mice mapped tumor growth and microbial shifts across early, intermediate, and advanced stages. In Apcmin/+ mice, tumor growth exhibited an initial rapid phase followed by a gradual deceleration. Our study elucidated a niche complementarity model of gut microbiota in suppressing CRC progression: both critical gut bacteria (Akkermansia muciniphila, Muribaculaceae and other taxa) and their enzymes (hexosaminidase and SusD) exhibited the relay pattern in metabolizing intestinal mucin and producing N-acetylglucosamine (GlcNAc). Furthermore, rectal administration of GlcNAc suppressed Wnt/β-catenin signaling activation, might potentially contributing to the deceleration of tumor growth in the mid-to-late stages of cancer. This interplay between gut bacteria may reflect the significance of functional redundancy in maintaining the stability of microbial function.
Question: Write a study description for the study titled 'Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis'.
Answer: Translation fidelity is the limiting factor in the accuracy of gene expression. With an estimated frequency of 10-4, errors in mRNA decoding occur in a mostly stochastic manner. Little is known about the response of higher eukaryotes to chronic loss of ribosomal accuracy as per an increase in the random error rate of mRNA decoding. Here, we present a global and comprehensive picture of the cellular changes in response to translational accuracy in mammalian ribosomes impaired by genetic manipulation. In addition to affecting established protein quality control pathways, such as elevated transcript levels for cytosolic chaperones, activation of the ubiquitin-proteasome system, and translational slowdown, ribosomal mistranslation led to unexpected responses. In particular, we observed increased mitochondrial biogenesis associated with import of misfolded proteins into the mitochondria and silencing of the unfolded protein response in the endoplasmic reticulum.This study describes the metabolomic analysis of HEK293 cells lines expressing mutant ribosomal protein RPS2 (human A226Y). RPS2 A226Y mutation has been shown to cause misreading and readthrough. Results provide insight into the response to chronic mistranslation in mammalian cells.
Question: Write a study description for the study titled 'Treatment of lean and diet-induced obesity (DIO) mice with a novel stable obestatin analogue alters plasma metabolite levels as detected by untargeted LC-MS metabolomics'.
Answer: Introduction: Obestatin is a controversial gastrointestinal peptide purported to have metabolic actions. Objectives: This study investigated whether treatment with a stable obestatin analogue (PEG-OB(Cys10, Cys13) changed plasma metabolite levels firstly in lean and subsequently in diet-induced obesity (DIO) C57BL6/J mice. Method: Untargeted LC-HRMS metabolomics experiments were carried out in ESI+ mode with plasma extracts from both groups of animals. Data were normalised, multivariate and univariate statistical analysis performed and metabolites of interest putatively identified. Result: In lean mice, 39 metabolites were significantly changed by obestatin treatment and the majority of these were increased, including various C16 and C18 moieties of phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine and monoacylglycerol, along with vitamin A, vitamin D3, tyrosine, acetylcarnitine and 2alpha-(hydroxymethyl)-5alpha-androstane-3beta,17beta-diol. Decreased concentrations of glycolithocholic acid, 3-dehydroteasterone and various phospholipids were observed. In DIO mice, 25 metabolites were significantly affected and strikingly, the magnitudes of changes here were generally much greater in DIO mice than in lean mice, and in contrast, the majority of metabolite changes were decreases. Four metabolites affected in both groups included glycolithocholic acid, and three different long-chain (C18) phospholipid molecules (phosphatidylethanolamine, platelet activating factor (PAF), and monoacylglycerol). Metabolites exclusively affected in DIO mice included various phosphatidylcholines, lysophosphatidylcholines and fatty acyls, as well as creatine and oxidised glutathione. Conclusion: This investigation demonstrates that obestatin treatment affects phospholipid turnover and influences lipid homeostasis, whilst providing convincing evidence that obestatin may be acting to ameliorate diet-induced impairments in lipid metabolism, and it may influence steroid, bile acid, PAF and glutathione metabolism.
Question: Write a study description for the study titled 'Impact of Tomato Grafts on the Potato Tuber Metabolome and Skin Colour'.
Answer: INTRODUCTION: Grafting is a traditional research and plant production technique used to study the long-distance movement of molecules and reduce disease susceptibility, respectively. Tomato/potato grafts are rare examples of successful interspecies grafting, even resulting in commercially available products. Nevertheless, information on the effect of tomato on the quality parameters of potato tubers is scarce.MATERIALS AND METHODS: The tomato cultivar ‘Mobil’ was grafted with the potato cultivars ‘White Lady’, ‘Hópehely’ and ‘Désirée’, and the phenotype, metabolite composition, and starch and protein contents of tubers were analysed. Anthocyanins were isolated from the tuber skins, and the expression level of the transcription factor ANTHOCYANIN1 (StAN1) was evaluated.RESULTS: Out of the 112 identified metabolites, the concentrations of twelve compounds were altered in the same direction in all three cultivars. The starch content of tubers was increased, while the protein level remained unaltered in ‘White Lady’ and ‘Hópehely’. The oval tubers became roundish. The tomato scion increased the anthocyanin content of ‘Hópehely’ and ‘Désirée’ tuber skins, which was correlated with the upregulation of StAN1 expression.CONCLUSION: Tomato has a significant impact on the quality parameters of potato tubers and reduces the asparagine concentration and risk of acrylamide formation.