LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Ectopic intestinal colonization by an oral commensal promotes C. difficile infection in Crohn’s disease'.
Answer: Crohn’s disease is a severe inflammatory disorder of the intestine for which there is no cure. People suffering from Crohn’s disease are at increased risk of developing Clostridioides difficile infection (CDI), which considerably exacerbates symptoms. Using a prospective observational clinical study combined with animal models of intestinal inflammation, we show that ectopic colonization of the intestine by Veillonella, an oral commensal, promotes CDI in Crohn’s disease. We discovered that Veillonella suppresses expression of the main transporter facilitating bile acid reabsorption, which leads to increased bile acid-dependent triggering of C. difficile germination. Our results further indicate that high pro-inflammatory capacity of its lipopolysaccharide render Veillonella exceptionally potent to trigger that mechanism. These findings highlight the potential of otherwise innocuous oral commensals to exacerbate intestinal disease and will assist in the design of therapeutics to treat CDI as a main complication of Crohn’s disease patients.
Question: Write a study description for the study titled 'Diallyl disulfide (DADS) ameliorates intestinal Candida albicans infection by modulating the gut microbiota and metabolites and providing intestinal protection in mice'.
Answer: Diallyl disulfide (DADS), a garlic extract also known as allicin, has been reported to have numerous biological activities, including anticancer, antifungal, and inflammation-inhibiting activities, among others. Although many studies have assessed whether DADS can treat Candida albicans infection in vitro, its in vivo function and the underlying mechanism are still not clear. Accumulated evidence has implicated the gut microbiota as an important factor in the colonization and invasion of C. albicans. Thus, this study aimed to identify the mechanism by which DADS ameliorates dextran sulfate (DSS)-induced intestinal C. albicans infection based on the systematic analysis of the gut microbiota and metabolomics in mice. Here, we determined the body weight, survival, colon length, histological score, and inflammatory cytokine levels in the serum and intestines of experimental mice. Fecal samples were collected for gut microbiota and metabolite analysis by 16S rRNA gene sequencing and LC-MS metabolomics, respectively. DADS significantly alleviated DSS-induced intestinal C. albicans infection and altered the gut microbial community structure and metabolic profile in the mice. The abundances of some pathogenic bacteria, such as Proteobacteria, Escherichia-Shigella, and Streptococcus, were notably decreased after treatment with DADS. In contrast, SCFA-producing bacteria, namely, Ruminiclostridium, Oscillibacter, and Ruminococcaceae_UCG-013, greatly increased in number. The perturbance of metabolites in infectious mice was improved by DADS, with increases in secondary bile acids, arachidonic acid, indoles and their derivatives, which were highly related to the multiple differentially altered metabolic pathways, namely, bile secretion, arachidonic acid metabolism, and tryptophan metabolism. This study indicated that DADS could modulate gut microbiota and metabolites and protect the gut barrier to alleviate DSS-induced intestinal C. albicans infection in mice. Moreover, this work might also provide novel insight into the treatment of C. albicans infection using DADS.
Question: Write a study description for the study titled 'Metabolomic responses to long-term salt stress in related Lotus species (A)'.
Answer: The legume genus Lotus includes glycophytic forage crops and other species adapted to extreme environments, such as saline soils. Understanding salt tolerance mechanisms will contribute to the discovery of new traits which may enhance the breeding efforts towards improved performance of legumes in marginal agricultural environments. Here, we used a combination of ionomic and gas chromatography-mass spectrometry (GC-MS)-based metabolite profilings of complete shoots (pooling leaves, petioles and stems) to compare the extremophile Lotus creticus, adapted to highly saline coastal regions, and two cultivated glycophytic grassland forage species, Lotus corniculatus and Lotus tenuis. L. creticus exhibited better survival after exposure to long-term lethal salinity and was more efficient at excluding Cl- from the shoots than the glycophytes. In contrast, Na+ levels were higher in the extremophile under both control and salt stress, a trait often observed in halophytes. Ionomics demonstrated a differential rearrangement of shoot nutrient levels in the extremophile upon salt exposure. Metabolite profiling showed that responses to NaCl in L. creticus shoots were globally similar to those of the glycophytes, providing little evidence for metabolic pre-adaptation to salinity. This study is the first comparing salt acclimation responses between extremophile and non-extremophile legumes, and challenges the generalization of the metabolic salt pre-adaptation hypothesis.
Question: Write a study description for the study titled 'Metabolo-transcriptomics analyses reveal alfalfa adaptation to combined saline-alkali and low-temperature stress in the field'.
Answer: Metabolomics analysis revealed specific accumulation of amino acids, organic acids, carbohydrates, fatty acids and flavonoids in ZD compared with that in BM. The core differential metabolites associated with ZD stress resistance included isoleucine, fumaric acid, raffinose and isovitexin. Integrated metabolomics and transcriptomics analysis highlighted flavonoid, carbohydrate, glutathione and salicylic acid biosynthesis as key pathways in alfalfa stress response.
Question: Write a study description for the study titled 'Alterations of fecal microbiota and plasma metabolome in patients with Parkinson's disease with rapid eye movement sleep disorder'.
Answer: Objectives: Patients with Parkinson's disease (PD) with probable Rapid eye movement sleep Behavior Disorder (RBD) (PD-RBD), a specific subtype of PD, is characterized by the presence of more severe motor and non-motor symptoms. This study aimed to elucidate the characteristics and interactions of gut microbiota and plasma metabolic characteristics of PD-RBD, thus screening for the disease mechanisms. Methods: A total of 100 PD patients, 50 healthy controls (HC) and 16 probable idiopathic RBD (iRBD) patients were collected. There were 33 PD-RBD and 67 patients without probable RBD (PD-nRBD) in PD patients. DNA extraction, PCR amplification and high-throughput sequencing were used for intestinal microbiota analysis and ultra-high liquid chromatography tandem mass spectrometry was used for metabolome analysis. Spearman analysis was applied to investigate the correlation of fecal microbiota and plasma metabolome. Results: Our findings revealed Lactobacillaceae (P = 0.017), Christensenellaceae (P = 0.017), Fusobacteriaceae (P = 0.018), Lactobacillus (P = 0.035), Christensenellaceae R-7 group (P = 0.035) and Fusobacterium (P = 0.035) were significant different in PD-RBD, PD-nRBD and HC. Moreover, the differential metabolites identified in both PD-nRBD and PD-RBD were 3-Hydroxy-2-methylpyridine-4,5-dicarboxylate (VIP = 5.802) and 3-Methoxy-4-Hydroxyphenylglycol sulfate (VIP = 5.732). Furthermore, our analysis revealed that 3-Methoxy-4-Hydroxyphenylglycol sulfate showed a positive correlation with Lactobacillus (r = 0.197, P = 0.049). Finally, functional analysis indicated that these distinctive microbiota and metabolites were primarily associated with phenylalanine metabolism and vitamin B6 metabolism. Conclusions: We managed to show that the differential microbiota, differential metabolites and their interactions in PD-RBD compared to PD-nRBD and HC. This furthers our understanding of disease pathogenesis, and offers fresh perspectives on its detection and treatment.
Question: Write a study description for the study titled 'Plant hosts modify belowground microbial community response to extreme drought'.
Answer: Drought stress negatively impacts microbial activity, but the magnitude of stress responses are likely dependent on a diversity of below ground interactions. Populus trichocarpa individuals and no plant bulk soils were exposed to extended drought (~0.03% gravimetric water content (GWC) after 12d), re-wet, and a 12-d 'recovery' period to determine the effects of plant presence in mediating soil microbiome stability to water stress. Plant metabolomic analyses indicated that drought exposure increased host investment in C and N metabolic pathways (amino acids, fatty-acids, phenolic glycosides) regardless of recovery. Several metabolites positively correlated with root-associated microbial alpha diversity, but not those of soil communities. Soil bacterial community composition shifted with P. trichocarpa presence and with drought relative to irrigated controls, whereas soil fungal composition only shifted with plant presence. However, root fungal communities strongly shifted with drought, whereas root bacterial communities changed to a lesser degree. The proportion of bacterial water-stress opportunistic OTUs (enriched counts in drought) were high (~11%) at the end of drying phases, and maintained after re-wet, and recovery phases in bulk soils, but declined over time in soils with plants present. For root fungi opportunistic OTUs were high at the end of recovery in drought treatments (~17% abundance), although relatively not responsive in soils, particularly planted soils (< 0.5% abundance for sensitive or opportunistic). These data indicate that plants modulate soil and root associated microbial drought responses via tight plant-microbe linkages during extreme drought scenarios, but trajectories after extreme drought vary with plant habitat and microbial functional groups.
Question: Write a study description for the study titled 'A metabolomic study of urinary changes in type 2 diabetes in human compared to the control group'.
Answer: Type 2 diabetes mellitus is the result of a combination of impaired insulin secretion with reduced insulin sensitivity of target tissues. There are an estimated 150 million affected individuals worldwide, of whom a large proportion remains undiagnosed because of a lack of specific symptoms early in this disorder and inadequate diagnostics. In this study, NMR-based metabolomic analysis in conjunction with uni- and multivariate statistics was applied to examine the urinary metabolic changes in Human type 2 diabetes mellitus patients compared to the control group. The human population were un medicated diabetic patients who have good daily dietary control over their blood glucose concentrations by following the guidelines on diet issued by the American Diabetes Association. Note: This is part of a larger study, please refer to the original paper below.
Question: Write a study description for the study titled 'Analysis of glucose-independent metabolic pathways associated with anti-proliferative effect of metformin and their reversibility in liver cancer cells'.
Answer: Several studies indicated anti-cancer effects of metformin in liver cancer. This was attributed to the activation of LKB-AMPK axis, which is associated with anti-hyperglycaemic effect and cytotoxicity. However, glucose- and central carbon-independent effects of metformin and their reversibility remain unexplored. The dose-dependent effects of metformin on HepG2 cells were examined in presence and absence of glucose. The longitudinal evolution of metabolome was analyzed along with gene and protein expression as well as their correlations with and reversibility of cellular phenotype and metabolic signatures. Metformin concentrations ≤2.5mM were found to be non-cytotoxic but anti-proliferative irrespective of presence of glucose. Mitochondrial impairment along with derangement of one-carbon, glutathione and polyamine metabolism was associated with non-cytotoxic metformin treatment irrespective of glucose supplementation. Depletion of pantothenic acid, upregulation of fatty acid desaturation and downregulation of essential amino acid uptake, metabolism and purine salvage were identified as novel glucose-independent effects of metformin. These were significantly correlated with cMyc expression and reduction in proliferation. Rescue experiments established reversibility upon metformin withdrawal and tight association between proliferation, metabotype and cMyc expression. Taken together, derangement of novel glucose-independent pathways and concomitant cMyc downregulation coordinately contribute to anti-proliferative effect, which is reversible and may influence therapeutic utility of metformin.
Question: Write a study description for the study titled 'RA-MAP: mapping the molecular immunological landscape in early rheumatoid arthritis with vaccine controls'.
Answer: Rheumatoid arthritis (RA) is a chronic inflammatory disorder with poorly defined aetiology characterised by synovial inflammation with variable disease severity and drug responsiveness. To investigate the peripheral blood immune cell landscape of RA, we performed comprehensive clinical and molecular profiling of 267 RA patients and 52 healthy vaccine recipients for up to 18 months to establish a high quality sample biobank including plasma, serum, peripheral blood cells, urine, genomic DNA, RNA from whole blood, lymphocyte and monocyte subsets. We have performed extensive multi-omic immune phenotyping, including genomic, metabolomic, proteomic, transcriptomic and autoantibody profiling. We anticipate that these detailed clinical and molecular data will serve as a fundamental resource offering insights into immune-mediated disease pathogenesis, progression and therapeutic response, ultimately contributing to the development and application of targeted therapies for RA.
Question: Write a study description for the study titled 'Flow cytometry has a significant impact on the cellular metabolome (Lipidomic LC-MS assay)'.
Answer: The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyse the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signalling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry.  The Lipidomic LC-MS assay is reported in the current study MTBLS631.  The General LC-MS assay is reported in MTBLS629.  The CE-MS assay is reported in MTBLS633.  The GC-MS assay is reported in MTBLS634.  Linked Studies: MTBLS629 MTBLS633 MTBLS634
Question: Write a study description for the study titled 'Characterization of white tea metabolome: comparison against green and black tea by a nontargeted metabolomics approach'.
Answer: White tea is considered the least processed form of tea and is reported to have a series of potent bioactivities, such as antioxidant, anti-inflammatory, anti-mutagenic, and anti-cancer activities. However, the chemical composition of white tea and the dynamic changes of the metabolites during the manufacturing process are far from clear. In this study, we applied a nontargeted metabolomics approach based on ultra-high performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry to comprehensively profile the characteristic metabolites of white tea. There were significant differences in the content of amino acids, catechins, dimeric catechins, flavonol and flavone glycosides, and aroma precursors in white tea compared with green and black teas that were manufactured from the same fresh tea leaves. Furthermore, the dynamic changes of the metabolites in the tea samples with various withering durations of 0, 4, 8, 12, 16, 20, 24, 28, and 36 h were also profiled. To the best of our knowledge, this study offers the most comprehensive characterization of the metabolites and their changes in white tea.
Question: Write a study description for the study titled 'Inositol triphosphate-triggered calcium release blocks lipid exchange at endoplasmic reticulum-Golgi contact sites'.
Answer: Vesicular traffic and membrane contact sites between organelles enable the exchange of proteins, lipids, and metabolites. Recruitment of membrane tethers to contact sites between the endoplasmic reticulum (ER) and the plasma membrane is often triggered by calcium. In contrast, we reveal here a function for calcium in the repression of cholesterol export at membrane contact sites between the ER and the Golgi complex. We show that calcium efflux from ER stores induced by inositol-triphosphate [IP3] accumulation upon loss of the inositol 5-phosphatase INPP5A or sustained receptor signaling triggers the depletion of cholesterol and associated complex glycosphingolipids from the cell surface, resulting in a blockade of clathrin-independent endocytosis (CIE) of bacterial Shiga toxin. This phenotype is caused by the calcium-induced dissociation of oxysterol binding protein (OSBP) from the Golgi complex and from VAP-containing membrane contact sites. Our findings reveal a crucial function for INPP5A-mediated IP3 hydrolysis in the control of lipid exchange at membrane contact sites.
Question: Write a study description for the study titled 'Landscape of gut microbiota and metabolites and their interaction in comorbid heart failure and depressive symptoms: a random forest analysis study'.
Answer: Depression is an individual risk factor for poor prognosis in patients with heart failure (HF). Recent studies show that gut microbiota and metabolites have critical role in comorbid HF and depressive symptoms. We recruited 95 subjects including 35 HF patients with depressive symptoms (HF-DS), 36 HF patients without depressive symptoms (HF-NDS) and 24 healthy controls (HC). The 16S rRNA, metagenome sequencing and untargeted metabolomic analysis were employed to test fecal samples. Our analysis found there was a significant difference composition of gut microbiota in HF-DS, HF-NDS and HC populations. At the genus level, Mediterranea, Tolumona and Parabacteroides were significantly increased in HF-DS patients compared with HF-NDS patients, while Pedobacter, Azospirillum and Ruminiclostridium were significantly decreased. Furthermore, anti-inflammatory mediators (abietic acid, quinic acid, linoleic acid, etc) and neurotransmitters (catechin, serotonin, tryptamine, phenylethylamine, etc) were reduced in HF-DS. The enrichment analysis revealed that the gut microbiota highly conformed with the functional pathways of metabolites, and amino acid-related metabolism, fatty acid-related metabolism and cAMP signaling pathways may be crucial biological mechanisms involved in the development of comorbid depression and HF. Finally, Cloacibacillus and alpha-tocopherol were determined as diagnostic markers for HF-DS patients.IMPORTANCE: There is increasing evidence that alterations in gut microbial composition and function are associated with cardiovascular or psychiatric disease. Therefore, it is meaningful to investigate the taxonomic and functional characterization of the microbiota in HF patients who also have depressive symptoms. In this cross-sectional study, Cloacibacillus and alpha-tocopherol were determined as new diagnostic markers. Furthermore, intestinal microecosystem disorders are closely linked to depressive symptoms in HF patients, providing a new reference viewpoint for understanding the gut-heart/brain axis.
Question: Write a study description for the study titled 'High-fat diet increases circulating palmitic acid produced by gut Bacteroides thetaiotaomicron to promote thrombosis'.
Answer: Circulating palmitic acid (PA) is generally considered to be provided from diets and endogenous synthesis, and is adversely correlated with cardiovascular disease (CVD). It is unknown, however, if gut microbiota modulates circulating PA and potentiate CVD risk. Here we demonstrate that in CVD patients, elevated circulating PA is accompanied with hypercoagulability and high gut Bacteroides thetaiotaomicron (BT) abundance. PA promotes coagulation by inhibiting a major endogenous anticoagulant activated-protein-C (APC) and enhancing platelet activation. Importantly, BT is capable of synthesizing PA, and high-fat diet amplifies gut BT colonization. Our findings show that BT transplantation elevates plasma PA and triggers hypercoagulation without alternating host lipogenesis. Hesperidin, a dietary flavonoid, inhibits PA-APC interaction to prevent hypercoagulation induced by PA or BT transplantation. Collectively, we reveal the promotion of high-fat diet on gut BT colonization that elevates circulating PA and CVD, suggesting an approach controlling CVD by targeting PA and BT.
Question: Write a study description for the study titled 'Growth control of the eukaryote cell: a systems biology study in yeast'.
Answer: Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth.