LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'From Herbarium to life: Implications of Reviving Historical Fungi for Modern Plant Pathology and Agriculture.'.
Answer: The Green Revolution (GR) profoundly altered plant–microorganism interactions through widespread agrochemical use and crop breeding. Phytopathogenic fungi present major challenges to agriculture by reducing yield and quality, increasing production costs, and impacting food security and environmental sustainability. Historical biological collections preserving pre-GR diversity are key to understanding how modern intensive agriculture has shaped these interactions. In this study, we revived two Botrytis cinerea strains from the early 1940s and performed phenotypic, genomic, transcriptomic, and metabolomic analyses. Comparisons with modern strains revealed significant differences, including adaptations likely driven by fungicide use and environmental pressures such as host-specific pathogenicity and pH tolerance. Our findings highlight the value of natural history collections and demonstrate how archived pathogens can be revisited with advanced omic technologies to reveal long-term ecological and evolutionary changes. These insights are crucial for plant disease management, outbreak prediction, biodiversity conservation, and advancing sustainable agriculture practices.
Question: Write a study description for the study titled 'Impact of acute lymphoblastic leukemia induction therapy: findings from metabolomics on non-fasted plasma samples from a biorepository'.
Answer: INTRODUCTION: Acute lymphoblastic leukemia (ALL) is among the most common cancers in children. With improvements in combination chemotherapy regimens, the overall survival has increased to over 90%. However, the current challenge is to mitigate adverse events resulting from the complex therapy. Several chemotherapies intercept cancer metabolism, but little is known about their collective role in altering host metabolism.OBJECTIVES: We profiled the metabolomic changes in plasma of ALL patients initial- and post- induction therapy.METHODS: We exploited a biorepository of non-fasted plasma samples derived from the Dana Farber Cancer Institute ALL Consortium; these samples were obtained from 50 ALL patients initial- and post-induction therapy. Plasma metabolites and complex lipids were analyzed by high resolution tandem mass spectrometry and differential mobility tandem mass spectrometry. Data were analyzed using a covariate-adjusted regression model with multiplicity adjustment. Pathway enrichment analysis and co-expression network analysis were performed to identify unique clusters of molecules.RESULTS: More than 1200 metabolites and complex lipids were identified in the total of global metabolomics and lipidomics platforms. Over 20% of those molecules were significantly altered. In the pathway enrichment analysis, lipids, particularly phosphatidylethanolamines (PEs), were identified. Network analysis indicated that the bioactive fatty acids, docosahexaenoic acid (DHA)-containing (22:6) triacylglycerols (TAGs), were decreased in the post-induction therapy.CONCLUSION: Metabolomic profiling in ALL patients revealed a large number of alterations following induction chemotherapy. In particular, lipid metabolism was substantially altered. The changes in metabolites and complex lipids following induction therapy could provide insight into the adverse events experienced by ALL patients.
Question: Write a study description for the study titled 'Fate and PPARγ and STATs-driven effects of the mitochondrial complex I inhibitor tebufenpyrad in liver cells revealed with multi-omics.'.
Answer: The biological effects of the pesticide and mitochondrial complex I inhibitor tebufenpyrad (TEBU) on liver cells were investigated by combining proteomics and metabolomics. Both cell culture media and cellular lysates were analyzed in dose-response and kinetic experiments on the HepaRG cell line. Responses were compared with those obtained on primary human and rat hepatocytes. A multitude of phase I and II metabolites (>80) mainly common to HepaRG cells and primary hepatocytes and an increase in metabolization enzymes were observed. Synthesis of mitochondrion and oxidative phosphorylation complex constituents, fatty acid oxidation, and cellular uptake of lipids were induced to compensate for complex I inhibition and the decrease in ATP intracellular contents caused by TEBU. Secretion of the 20 S circulating proteasome and overall inhibition of acute inflammation followed by IL-6 secretion in later stages were observed in HepaRG cells. These effects were associated with a decrease in STAT1 and STAT3 transcription factor abundances, but with different kinetics. Based on identified TEBU targets, docking experiments, and nuclear receptor reporter assays, we concluded that liver cell response to TEBU is mediated by its interaction with the PPARγ transcription factor.
Question: Write a study description for the study titled 'Multiomics of yaks reveals significant contribution of microbiome into host metabolism'.
Answer: BACKGROUND: Grazing yearly on pasture is a traditional practice for yaks, which cannot meet the requirements of yak production since the insufficient forage supplied in the cold season results in a long production cycle. An intensive feeding system increasing production efficiency has been selected for beef and dairy cattle. However, its impacts on yaks are less studied, and it is unclear how the rumen microbiome, rumen metabolites and the host metabolome respond to an intensive feeding system and contribute to yak growth. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the effects and regulatory mechanisms of intensive feeding system on yaks. RESULTS: In our results, increased growth performance and rumen volatile fatty acid (VFA) concentration were observed in yaks under the intensive feeding system compared to yaks grazing on pastures. Metagenomics of the rumen microbiome revealed that species of Clostridium and Methanobrevibacter as well as Piromyces sp. E2 and Anaeromyces robustus were increased in the rumen of intensively fed yaks, interacting and contributing to amino acid and carbohydrate metabolism. The rumen of yaks grazing on pasture had more cellulolytic microbes, such as Bacteroides and Fibrobacter species. Moreover, yaks under the intensive feeding system had lower methanogens and increased methane degradation functions, suggesting that the methane emission of these yaks may be decreased. These abundant microbiomes were correlated with the pathways of 'Alanine aspartate and glutamate metabolism' and 'Pyruvate metabolism'. Similar with rumen VFA results, metabolomics found that intensively fed yaks had greater concentrations of metabolites related to carbohydrates. The methyl metabolites associated with methane production were greater in the rumen of yak grazing on pasture. Additionally, these changed rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally influencing yaks’ growth. CONCLUSIONS: This study compressively classifies the mechanism that an intensive feeding system benefits yak growth and reveals the importance of the rumen microbiome for host metabolism and performance. These findings evidence that an intensive feeding system could be used for the yak industry.
Question: Write a study description for the study titled 'Intergenerational Association of Gut Microbiota and Metabolism with Perinatal Folate Metabolism and Neural Tube Defects (Brain tissue metabolomics)'.
Answer: Neonatal hypoxic-ischemic encephalopathy (HIE) refers to nervous system damage caused by perinatal hypoxia, which is the major cause of long-term neuro-developmental disorders in surviving infants. However, the mechanisms still require further investigation. In this study, we found that the butanoate metabolism pathway exhibited significantly decreased and short chain fatty acid (SCFAs)-producing bacteria, especially butyrate-producing bacteria, were significantly decreased in fecal of neonatal hypoxic-ischemic brain damage (HIBD) rats. Surprisingly, Sodium butyrate (SB) treatment could ameliorate pathological damage both in the cerebral cortex and hippocampus and facilitate recovery of SCFAs-producing bacteria related to metabolic pathways in neonatal HIBD rats. Moreover, we found that in samples from SB treatment neonatal HIBD rats cortex with high levels of butyrate acid along with aberrant key crotonyl-CoA-producing enzymes ACADS levels was observed compared HIBD rats. We also demonstrated that a decrease in histone 3-lysine 9-crotonylation (H3K9cr) downregulated expression of the HIE-related neurotrophic genes Bdnf, Gdnf, Cdnf, and Manf in HIBD rats. Furthermore, SB restored H3K9cr binding to HIE-related neurotrophic genes. Collectively, our results indicate that SB contributes to ameliorate pathological of HIBD by altering gut microbiota and brain SCFAs levels subsequently affecting histone crotonylation-mediated neurotrophic-related genes expression. This may be a novel microbiological approach for preventing and treating HIE.Brain tissue metabolomics is reported in the current study MTBLS4894.Feces metabolomics is reported in MTBLS4893.
Question: Write a study description for the study titled 'Dysregulation of Streptococcus pneumoniae zinc homeostasis breaks ampicillin resistance in a pneumonia infection model'.
Answer: Streptococcus pneumoniae is the primary cause of community-acquired bacterial pneumonia with rates of penicillin and multi-drug resistance exceeding 80% and 40%, respectively. The innate immune response generates a variety of antimicrobial agents to control infection including zinc stress. Here, we characterized the impact of zinc intoxication on S. pneumoniae, revealing disruptions in central carbon metabolism, lipid biogenesis and peptidoglycan biosynthesis. Characterization of the pivotal peptidoglycan biosynthetic enzyme GlmU revealed an exquisite sensitivity to zinc inhibition. Disruption of the sole zinc efflux pathway, czcD, rendered S. pneumoniae highly susceptible to β-lactam antibiotics. To dysregulate zinc homeostasis in the wild-type strain, we investigated the safe-for-human use ionophore PBT2. PBT2 rendered wild-type S. pneumoniae strains sensitive to a range of antibiotics. Using an invasive ampicillin-resistant strain, we demonstrate in a murine pneumonia infection model the efficacy of PBT2+ampicillin treatment. These findings present a therapeutic modality to break resistance of drug-resistant S. pneumoniae.
Question: Write a study description for the study titled 'Fecal Metabolomics and Potential Biomarkers for Systemic Lupus Erythematosus'.
Answer: The role of metabolomics in autoimmune diseases has been a rapidly expanding area in researches over the last decade, while its pathophysiologic impact on systemic lupus erythematosus (SLE) remains poorly elucidated. In this study, we analyzed the metabolic profiling of fecal samples from SLE patients and healthy controls based on ultra-high-performance liquid chromatography equipped with mass spectrometry for exploring the potential biomarkers of SLE. The results showed that 23 differential metabolites and 5 perturbed pathways were identified between the two groups, including aminoacyl-tRNA biosynthesis, thiamine metabolism, nitrogen metabolism, tryptophan metabolism, and cyanoamino acid metabolism. In addition, logistic regression and ROC analysis were used to establish a diagnostic model for distinguishing SLE patients from healthy controls. The combined model of fecal PG 27:2 and proline achieved an area under the ROC curve of 0.846, and had a good diagnostic efficacy. In the present study, we analyzed the correlations between fecal metabolic perturbations and SLE pathogenesis. In summary, we firstly illustrate the comprehensive metabolic profiles of feces in SLE patients, suggesting that the fecal metabolites could be used as the potential non-invasive biomarkers for SLE.
Question: Write a study description for the study titled 'Neurotransmitter acetylcholine mediates the mummification of Ophiocordyceps sinensis-infected Thitarodes xiaojinensis larvae (Metabolome data)'.
Answer: Parasites can manipulate host behavior to facilitate parasite transmission. One such host-pathogen interaction occurs between the fungus Ophiocordyceps sinensis (O. sinensis) and the ghost moth Thitarodes xiaojinensis. O. sinensis is involved in the mummification process of infected host larvae. However, the underlying molecular and chemical mechanism for this phenomenon is unknown. We characterized the small molecules regulating host behavior and the altered metabolites in infected and mummified host larvae. Lipid-related metabolites, such as phosphatidylcholine (PC) were identified in infected and mummified larvae. Decreased levels of the neurotransmitter acetylcholine (ACh) and elevated choline levels were observed in the brains of both the infected and mummified larvae. The aberrant activity of acetylcholinesterase (AChE) and relative mRNA expression of ACE2 (acetylcholinesterase) may mediate the altered transformation between ACh and choline, leading to the brain dysfunction of mummified larvae. Caspofungin treatment inhibited the mummification of infected larvae and the activity of AChE. These findings indicate the importance of ACh in the mummification of host larvae after O. sinensis infection.Metabolome data is reported in the current study MTBLS9929.Lipidome data is reported in MTBLS9930.
Question: Write a study description for the study titled 'Small Polar Hits against S. aureus: Screening, Initial Hit Optimization, and Metabolomic Studies'.
Answer: The global prevalence of antibacterial resistance requires new antibacterial drugs with novel chemical scaffolds and modes of action. It is also vital to design compounds with optimal physicochemical properties to permeate the bacterial cell envelope. We described an approach of combining and integrating whole cell screening and metabolomics into early antibacterial drug discovery using a library of small polar compounds. Whole cell screening of a diverse library of small polar compounds against Staphylococcus aureus gave compound 2. Hit expansion was carried out to determine structure-activity relationships. A selection of compounds from this series, together with other screened active compounds, was subjected to an initial metabolomics study to provide a metabolic fingerprint of the mode of action. It was found that compound 2 and its analogues have a different mode of action from some of the known antibacterial compounds tested. This early study highlighted the potential of whole cell screening and metabolomics in early antibacterial drug discovery. Future works will require improving potency and performing orthogonal studies to confirm the modes of action.
Question: Write a study description for the study titled 'Sponges With Microbial Symbionts Transform Dissolved Organic Matter and Take Up Organohalides (2018 collection assay)'.
Answer: Seawater dissolved organic matter (DOM) is a large reservoir of carbon composed of a complex and poorly characterized mixture of molecules. Sponges have long been known to consume dissolved organic carbon (DOC) from this mixture, but the role of microbial sponge symbionts in this process is complex, and the molecules involved remain largely unknown. In order to better understand how sponge processing changes seawater DOM, we used untargeted metabolomics to characterize DOM in samples of incurrent and excurrent seawater taken from sponges on the fore-reef off Carrie Bow Cay, Belize, over 2 years. We collected samples from three sponge species each with either high or low microbial abundance (HMA, LMA) to explore the relationship between symbiont abundance and DOM alterations. Analyses revealed that sponges took up metabolites and changed the composition of seawater DOM, but only for the three HMA species, and none of the LMA species, implicating microbial symbionts in this uptake. Using a new mass spectra classification tool, we found that putative compositions of features depleted in the excurrent samples of HMA sponges were similar in both years and were dominated by organic acids and derivatives (74%) and organic nitrogen compounds (19%). Interestingly, HMA sponges also took up halogenated compounds (containing chlorine or bromine), providing evidence of a previously unknown mechanism of halide cycling. The metabolites taken up by HMA sponges may be used as a food source or as building blocks of chemical defenses, selective advantages that may have guided the evolution of microbial symbioses in sponges.2018 collection assay is reported in the current study MTBLS21992019 collection assay is reported in MTBLS2200
Question: Write a study description for the study titled 'Survival of the littlest: Navigating sepsis diagnosis beyond inflammation in preterm neonates'.
Answer: Background Sepsis diagnosis in preterm neonates is challenging due to symptom overlap with non-infectious inflammatory conditions, and slow, unreliable diagnostic practices. This study aims to identify metabolic biomarkers to elucidate sepsis pathophysiology, and enable timely, accurate diagnosis, which is crucial for preventing rapid health deterioration and minimizing unnecessary antibiotic use. Methods Liquid chromatography-mass spectrometry was performed on 227 plasma samples, obtained from 94 preterm neonates (<32 week gestational age), to measure 317 metabolites encompassing amines and signaling lipids. Linear mixed-effect modeling, LASSO and logistic regression models were calculated to assess metabolic alterations across the control, systemic inflammation-no sepsis (SINS), and sepsis groups. Stratification by sex and pathogen type was performed to evaluate sex-specific responses and pathogen-driven variations in sepsis. Findings We identified metabolites that (i) were similarly altered in both SINS and sepsis, (ii) exhibited a trend from control to SINS to sepsis, and (iii) were exclusively altered in sepsis. Males exhibited a pro-inflammatory phenotype while females showed an anti-inflammatory phenotype. Gram-positive and gram-negative bacterial sepsis revealed distinct metabolic profiles. A diagnostic model comprising 5 metabolic features and IL6 distinguished SINS from sepsis with an AUC of 0.80. Interpretation Our findings elucidate common mechanisms underlying systemic inflammation irrespective of causative trigger, exaggerated immune responses in sepsis, and sepsis-specific anomalies. Metabolomics holds the potential for early, accurate sepsis diagnosis with personalized treatment strategies. Funding This research was supported by Medical Delta through the MOMETA and METABODELTA scientific programs, with partial funding from X-Omics (NWO Project 184.034.019), Exposome-Scan (NWO Project 175.2019.032), and the European Funds for Regional Development (Kansen voor West II: Phenomix Fieldlab).
Question: Write a study description for the study titled 'Global Analyses of Selective Insulin Resistance in Hepatocytes due to Palmitate Lipotoxicity'.
Answer: Obesity is tightly linked to hepatic steatosis and insulin resistance. One feature of this association is the paradox of selective insulin resistance: insulin fails to suppress hepatic gluconeogenesis but activates lipid synthesis in the liver. How lipid accumulation interferes selectively with some branches of hepatic insulin signaling is not well understood. Here we provide a resource, based on unbiased approaches and established in a simple cell culture system, to enable investigations of the phenomenon of selective insulin resistance. We analyzed the phosphoproteome of insulin treated human hepatoma cells and identified sites in which palmitate selectively impairs insulin signaling. As an example, we show that palmitate interferes with insulin signaling to FoxO1, a key transcription factor regulating gluconeogenesis, and identify a possible mechanism. This model system, together with our comprehensive characterization of the proteome, phosphoproteome, and lipidome changes in response to palmitate treatment, provides a novel and useful resource for unraveling the mechanisms underlying selective insulin resistance.
Question: Write a study description for the study titled 'Metagenomic and metabolomic analyses reveal the role of gut microbiome-associated metabolites in the muscle elasticity of large yellow croaker (Larimichthys crocea)'.
Answer: The large yellow croaker (LYC, Larimichthys crocea) is highly regarded for its delicious taste and unique flavor. The gut microbiota has the ability to affect the host muscle performance and elasticity by regulating nutrient metabolism. However, the mechanism by which the intestinal microbiota regulates the muscle elasticity of LYC remains poorly understood. In this study, the intestinal contents of high muscle elasticity males (IEHM), females (IEHF), and low muscle elasticity males (IELM) and females (IELF) were collected and subjected to metagenomic and metabolomic analyses. Metagenomic sequencing results showed that the intestinal flora structures of LYCs with different muscle elasticities were significantly different. The abundance of Streptophyta in the IELM ( 24.63%) and IELF (29.68%) groups was significantly higher than that in the IEHM and IEHF groups. The abundance of Vibrio scophthalmi (66.66%) in the IEHF group was the highest. Based on metabolomic analysis by liquid chromatograph-mass spectrometry, 107 differentially abundant metabolites were identified between the IEHM and IELM groups, and 100 differentially abundant metabolites were identified between the IEHF and IELF groups. Based on these metabolites, a large number of enriched metabolic pathways related to muscle elasticity were identified. Significant differences in intestinal metabolism between groups with different muscle elasticities were identified. Moreover, the model of the relationship between the intestinal flora and metabolites was constructed, and the molecular mechanism of intestinal flora regulation of nutrient metabolism was further revealed. The results help to understand the molecular mechanism of different muscle elasticities of LYC and provide an important reference for the study of the mechanism of the effects of LYC intestinal symbiotic bacteria on muscle development, and the development and application of probiotics in LYC.
Question: Write a study description for the study titled 'Metabolomics to elucidate the effects of novel sustainable feed additives in the feed of farmed salmon (HoloFood Trial D - fermented seaweed open water-dose response)'.
Answer: Testing the effect of seaweed as a novel cost-efficient feed source for Atlantic salmon feed. Fermentation of novel raw materials for fish feed is a new practice with little prior experience of direct relevance to aquaculture and fish farming. In Trial D, an alternative marine compound is included in the feed, which is based on seaweed.HoloFood Trial D - fermented seaweed open water-dose response is reported in the current study MTBLS6733.HoloFood Trial A - seaweed-dose response is reported in MTBLS4381.HoloFood Trial B - blue mussel-dose response is reported in MTBLS4382.HoloFood Trial C - blue mussel ensilage-dose response is reported in MTBLS4384.HoloFood Trial 1/2/3 is reported in MTBLS6988.Linked cross omic data sets:Nucleic acid data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJEB43192.Metagenomic data associated with this study are available from MGnify under the Super Study 'holofood'.