LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Known Metabolite Annotation in Different Biological Samples using Ion Mobility Collision Cross-Section Atlas (AllCCS)'.
Answer: The metabolome includes not just known but also unknown metabolites; however, metabolite annotation remains the bottleneck in untargeted metabolomics. Ion mobility – mass spectrometry (IM-MS) has emerged as a promising technology by providing multi-dimensional characterizations of metabolites. Here, we curated an ion mobility CCS atlas, namely AllCCS, and developed an integrated strategy for metabolite annotation using known or unknown chemical structures. The AllCCS atlas covers vast chemical structures with >5000 experimental CCS records and ~12 million calculated CCS values for >1.6 million small molecules. We demonstrated the high accuracy and wide applicability of AllCCS with medium relative errors of 0.5-2% for a broad spectrum of small molecules. AllCCS combined with in-silico MS/MS spectra facilitated multi-dimensional match and substantially improved the accuracy and coverage of both known and unknown metabolite annotation from biological samples. Together, AllCCS is a versatile resource that enables confident metabolite annotation, revealing comprehensive chemical and metabolic insights towards biological processes.Known Metabolite Annotation in Different Biological Samples assays are reported in the current study MTBLS1693.Unknown Metabolite Annotation in Mouse Aging assay is reported in MTBLS1622.
Question: Write a study description for the study titled 'Individual variability in human blood metabolites identifies age-related differences - determination of coefficients of variation for each metabolite (3 injections of same sample, 3 independent sample preparations)'.
Answer: Metabolites present in human blood document individual physiological states influenced by genetic, epigenetic, and lifestyle factors. Using high-resolution liquid chromatography-mass spectrometry (LC-MS), we performed nontargeted, quantitative metabolomics analysis in blood of 15 young (29 ± 4 y of age) and 15 elderly (81 ± 7 y of age) individuals. Coefficients of variation (CV = SD/mean) were obtained for 126 blood metabolites of all 30 donors. Fifty-five RBC-enriched metabolites, for which metabolomics studies have been scarce, are highlighted here. We found 14 blood compounds that show remarkable age-related increases or decreases; they include 1,5-anhydroglucitol, dimethyl-guanosine, acetyl-carnosine, carnosine, ophthalmic acid, UDP-acetyl-glucosamine, N-acetyl-arginine, N6-acetyl-lysine, pantothenate, citrulline, leucine, isoleucine, NAD+, and NADP+. Six of them are RBC-enriched, suggesting that RBC metabolomics is highly valuable for human aging research. Age differences are partly explained by a decrease in antioxidant production or increasing inefficiency of urea metabolism among the elderly. Pearson’s coefficients demonstrated that some age-related compounds are correlated, suggesting that aging affects them concomitantly. Although our CV values are mostly consistent with those CVs previously published, we here report previously unidentified CVs of 51 blood compounds. Compounds having moderate to high CV values (0.4–2.5) are often modified. Compounds having low CV values, such as ATP and glutathione, may be related to various diseases because their concentrations are strictly controlled, and changes in them would compromise health. Thus, human blood is a rich source of information about individual metabolic differences.  Validation of experimental procedures was performed as follows. First, we evaluated the contribution of sample handling to within-sample variation. The same blood sample preparation was injected 3x into the LC-MS at 80-min intervals. We thus obtained within-sample CVs (designated as CVwi), which were less than 0.1 in 107 of 126 compounds (85%). Only 10 compounds showed CVwi of 0.1-0.2, while 9 had CVwi >0.2. Second, we also examined sample-to-sample variation caused by sample preparation. Three samples were independently prepared from the same blood sample (one person), and CVs thus determined were designated as CVss. CVss values of HEPES and PIPES in the blood samples were very small (0.06~0.08 for HEPES and 0.04~0.08 for PIPES). The great majority (116/126=92%) of CVss were  Blood samples drawn from four volunteers four times within 24 h are available under accession number MTBLS264. Whole blood metabolomic data from all 30 subjects are available under accession number MTBLS265. Plasma and RBC data from all 30 subjects can be found under MTBLS266 and MTBLS267, respectively.
Question: Write a study description for the study titled 'Sex-specific metabolic shifts in plasma of COVID-19 patients after cure'.
Answer: Metabolic profiling in COVID-19 patients has been associated with disease severity, but there is no report on sex-specific metabolic changes in discharged survivors. Herein we used an integrated approach of LC-MS-and GC-MS-based untargeted metabolomics to analyze plasma metabolic characteristics in men and women with non-severe COVID-19 at both acute period and 30 days after discharge. The results demonstrate that metabolic alterations in plasma of COVID-19 patients during the recovery and rehabilitation process were presented in a sex specific manner. Overall, the levels of most metabolites were increased in COVID-19 patients after the cure relative to acute period. The major plasma metabolic changes were identified including fatty acids in men and glycerophosphocholines and carbohydrates in women. In addition, we found that women had shorter length of hospitalization than men and metabolic characteristics may contribute to predict the duration from positive to negative in non-severe COVID-19 patients. Collectively, this study shed light on sex-specific metabolic shifts in non-severe COVID-19 patients during the recovery process, suggesting a sex bias in prognostic and therapeutic evaluations based on metabolic profiling.
Question: Write a study description for the study titled 'A multi-omic profiles of fruits regarding the maturation of Olive (Olea europaea L.) (GC-MS assay)'.
Answer: "Olive (Olea europaea) has a long history of medicinal and nutritional values own to it rich in polyphenol and fatty acids (FAs) in fruits. In order to better understand the biosynthesis important of these metabolites, we generated comprehensive Iso-Seq full-length and illumina RNA-seq transcriptome, and targeted metabolomics dataset of different olive fruits maturity. The targeted metabolomics by using both GC/MS and LC/MS were totally quantified 35 FAs and 13 polyphenols. Iso-Seq library was constructed and sequenced by PacBio Sequel System, and a total of 5,891,652 (10.55 G) with an average length of 1,791 subreads were obtained. 492,350 circular consensus sequences (CCSs) were formed after merging and error correction through subread comparison. Of the 492,350 CCSs, 399,263 were found to be full-length non chimera (FLNC) reads, and 187,517 consensus reads were finally obtained by using clustering algorithm of Iterative clustering for error (IEC). These multiomics data provide a foundation to elucidate the mechanisms regulating biosynthesis of polyphenol and FAs during the maturation of olive fruits.GC-MS protocols and data are reported in the current study MTBLS855.Polyphenols UPLC-MS protocols and data associated to this study are reported in MTBLS814.Tyrosol only UPLC-MS protocols and data associated to this study are reported in MTBLS1127."
Question: Write a study description for the study titled 'Metabolomic analysis on Microcystis aeruginosa cells under various amino acid supplementation conditions'.
Answer: Threonine, an essential amino acid for translation, exhibits toxicity towards slow-growing cyanobacteria. This prompted us to perform transcriptomic and proteomic analyses using Microcystis aeruginosa cells treated with threonine, revealing a noteworthy upregulation of thrC, annotated as pyridoxal 5’-phosphate (PLP)-dependent threonine synthase. PyMoL-based structural prediction and in vitro biochemical assays unveiled the moonlighting functions of ThrC in both threonine biosynthesis and deamination. The production of α-ketobutyrate from threonine, both in vivo and in vitro, provided strong support for the role of ThrC as a threonine deaminase. The kinetics of ThrC as a threonine synthase using O-phospho-homoserine were consistent with the Michaelis-Menten kinetics of ThrC in Thermus thermophilus, albeit with a slightly lower Vmax value. However, the in vitro deaminase activity of ThrC, exhibiting sigmoidal kinetics, suggests the potential production of α-ketobutyrate under threonine oversupply conditions in slow-growing cyanobacteria. The phylogenetic lineage of our ThrC is positioned distinctively apart from canonical threonine synthase and threonine deaminase. Gene duplication and subsequent divergence of thrC, followed by gene deletion, could have contributed to the possession of moonlighting ThrC protein in aquatic bacteria including cyanobacterial lineages. Metabolomic data revealed that the presence of threonine and α-ketobutyrate disrupted the balance of amino acids (alanine and methionine) and DNA biosynthetic pathways via feedback inhibition. Interestingly, the addition of exogenous alanine or methionine could alleviate threonine toxicity. Our data revealed that threonine does not uniformly support the growth of freshwater cyanobacteria to the same extent, but rather can be toxic to certain groups within this bacterial family.
Question: Write a study description for the study titled 'Chronic exposure to tire rubber-derived contaminant 6PPD-quinone impairs sperm quality and induces the damage of reproductive capacity in male mice'.
Answer: The study investigates the effects of 6PPDQ on male fertility in adult mice. The findings of this study are essential as the effects of low-dose environmental factors of 6PPDQ on adult male infertility are unclear, with the increasing in male infertility. The results suggest that 6PPDQ adversely affects sperm quality and male fertility possibly through affecting the proliferation of germ cells and sperm function. Future study is warranted to investigate the molecular mechanisms by which 6PPDQ affects germ cell and mature sperm functions. This study provides essential information for further study on the influence of 6PPDQ on sperm function and protective measures
Question: Write a study description for the study titled 'Structure of gut microbiota and characteristics of fecal metabolites in people living with HIV'.
Answer: Objective: The gut microbiome plays a pivotal role in human immunodeficiency virus (HIV) infection. However, the associated alterations in the gut microbiome-host interaction remain unclear. This study aims to investigate the gut microbiota and fecal metabolites in people living with HIV (PLWH).Method: We collected stool samples from 70 PLWH and 34 healthy controls (HCs) and performed 16S rRNA gene sequencing. Metabolite analysis was conducted using liquid chromatography-mass spectrometry.Results: Firmicutes, Proteobacteria, Actinobacteriota, and Bacteroidota were the most abundant phyla in both groups. At the genus level, Escherichia Shigella was significantly upregulated in the PLWH group, whereas Bacteroides were upregulated in the HC group. Functional prediction of the microbiota indicated significant reductions in alanine, aspartate, and glutamate metabolism, as well as histidine metabolism. Furthermore, comparison of fecal metabolites between the HC and PLWH groups identified 38 differentially abundant metabolites across four enriched human metabolic pathways. Spearman correlation analysis revealed close relationships between four differentially abundant microbiota members and five differentially abundant fecal metabolites, which may influence specific human metabolic pathways.Conclusion: Our findings provide a foundation for further experimental investigations into the contribution of the gut microbiota and its associated metabolites to HIV/AIDS, offering a novel perspective for future studies on HIV/AIDS.
Question: Write a study description for the study titled 'Individual variability in human blood metabolites identifies age-related differences - constant blood metabolite levels during 24h in 4 individuals'.
Answer: Metabolites present in human blood document individual physiological states influenced by genetic, epigenetic, and lifestyle factors. Using high-resolution liquid chromatography-mass spectrometry (LC-MS), we performed nontargeted, quantitative metabolomics analysis in blood of 15 young (29 ± 4 y of age) and 15 elderly (81 ± 7 y of age) individuals. Coefficients of variation (CV = SD/mean) were obtained for 126 blood metabolites of all 30 donors. Fifty-five RBC-enriched metabolites, for which metabolomics studies have been scarce, are highlighted here. We found 14 blood compounds that show remarkable age-related increases or decreases; they include 1,5-anhydroglucitol, dimethyl-guanosine, acetyl-carnosine, carnosine, ophthalmic acid, UDP-acetyl-glucosamine, N-acetyl-arginine, N6-acetyl-lysine, pantothenate, citrulline, leucine, isoleucine, NAD+, and NADP+. Six of them are RBC-enriched, suggesting that RBC metabolomics is highly valuable for human aging research. Age differences are partly explained by a decrease in antioxidant production or increasing inefficiency of urea metabolism among the elderly. Pearson’s coefficients demonstrated that some age-related compounds are correlated, suggesting that aging affects them concomitantly. Although our CV values are mostly consistent with those CVs previously published, we here report previously unidentified CVs of 51 blood compounds. Compounds having moderate to high CV values (0.4–2.5) are often modified. Compounds having low CV values, such as ATP and glutathione, may be related to various diseases because their concentrations are strictly controlled, and changes in them would compromise health. Thus, human blood is a rich source of information about individual metabolic differences.  In human 24 hr metabolome observation (non-fasting) four volunteers were taken blood after overnight fast without breakfast at 9:00; 10:00, 13:00 and before lunch on the first day. Volunteers had lunches and dinners as usual on that day. On the second day after overnight fast the blood was sampled again at 9:00 at Kyoto university hospital laboratory. The great majority of metabolites hardly fluctuated (117 from 126 metabolites varied less than 2.5-fold on average in four volunteers).  Data from three injections of the same sample and three samples prepared from the same donated blood are available under accession number MTBLS263. Whole blood metabolomic data from all 30 subjects are available under accession number MTBLS265. Plasma and RBC data from all 30 subjects can be found under MTBLS266 and MTBLS267, respectively.
Question: Write a study description for the study titled 'Stability in metabolic phenotypes and inferred metagenome profiles before the onset of colitis-induced inflammation'.
Answer: Inflammatory bowel disease (IBD) is associated with altered microbiota composition and metabolism, but it is unclear whether these changes precede inflammation or are the result of it since current studies have mainly focused on changes after the onset of disease. We previously showed differences in mucus gut microbiota composition preceded colitis-induced inflammation and stool microbial differences only became apparent at colitis onset. In the present study, we aimed to investigate whether microbial dysbiosis was associated with differences in both predicted microbial gene content and endogenous metabolite profiles. We examined the functional potential of mucus and stool microbial communities in the mdr1a -/- mouse model of colitis and littermate controls using PICRUSt on 16S rRNA sequencing data. Our findings indicate that despite changes in microbial composition, microbial functional pathways were stable before and during the development of mucosal inflammation. LC-MS-based metabolic phenotyping (metabotyping) in urine samples confirmed that metabolite profiles in mdr1a -/- mice were remarkably unaffected by development of intestinal inflammation and there were no differences in previously published metabolic markers of IBD. Metabolic profiles did, however, discriminate the colitis-prone mdr1a -/- genotype from controls. Our results indicate resilience of the metabolic network irrespective of inflammation. Importantly as metabolites differentiated genotype, genotype-differentiating metabolites could potentially predict IBD risk.
Question: Write a study description for the study titled 'Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus'.
Answer: We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in Synechococcus sp. strains WH8102, WH7803, and BL107 and Prochlorococcus sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the Entner-Doudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in Prochlorococcus sp. strain SS120 and Synechococcus sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in Synechococcus sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria. The Prochlorococcus sp. strain PCC 9511 is genetically identical to MED4IMPORTANCE Glucose uptake by marine picocyanobacteria has been previously described and strongly suggests they are mixotrophic organisms (capable of using energy from the sun to make organic matter, but also to directly use organic matter from the environment when available). However, a detailed analysis of the effects of glucose addition on the proteome and metabolome of these microorganisms had not been carried out. Here, we analyzed three Prochlorococcus sp. and three Synechococcus sp. strains which were representative of several marine picocyanobacterial clades. We observed differential features in the effects of glucose availability, depending on both the genus and strain; our study illuminated the strategies utilized by these organisms to metabolize glucose and showed unexpected links to other pathways, such as circadian regulation. Furthermore, we found glucose addition had profound effects in the microbiome, favoring the growth of coexisting heterotrophic bacteria.
Question: Write a study description for the study titled 'Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease'.
Answer: Non-alcoholic fatty liver is the most common liver disease worldwide. Here, we show that the mitochondrial protein mitofusin 2 (Mfn2) protects against liver disease. Reduced Mfn2 expression was detected in liver biopsies from patients with non-alcoholic steatohepatitis (NASH). Moreover, reduced Mfn2 levels were detected in mouse models of steatosis or NASH, and its re-expression in a NASH mouse model ameliorated the disease. Liver-specific ablation of Mfn2 in mice provoked inflammation, triglyceride accumulation, fibrosis, and liver cancer. We demonstrate that Mfn2 binds phosphatidylserine (PS) and can specifically extract PS into membrane domains, favoring PS transfer to mitochondria and mitochondrial phosphatidylethanolamine (PE) synthesis. Consequently, hepatic Mfn2 deficiency reduces PS transfer and phospholipid synthesis, leading to endoplasmic reticulum (ER) stress and the development of a NASH-like phenotype and liver cancer. Ablation of Mfn2 in liver reveals that disruption of ER-mitochondrial PS transfer is a new mechanism involved in the development of liver disease.
Question: Write a study description for the study titled 'Metabolic interdependence and rewiring in radiolaria-microalgae photosymbioses'.
Answer: Marine planktonic Radiolaria harboring symbiotic microalgae are ubiquitous in the oceans and abundant in oligotrophic areas. In these low-nutrient environments, they are among the most important primary producers. Systematic studies of radiolarian biology are limited because radiolaria are non-culturable and prone to damage during sampling. To obtain insight into the mechanistic basis of radiolarian photosymbiosis,we address here the metabolic contributions ofthe partners to the performance ofthe holobiont. Therefore, we describe the metabolic inventory of two highly abundant photosymbiotic radiolaria—colony-forming Collodaria and single-celled Acantharia and compare their metabolomes to metabolomes of respective free-living algae. Most of the metabolites detected in the symbiosis are not present in the free-living algae, suggesting a significant transformation of symbionts’ metabolites by the host. The metabolites identified in the holobiont and the free-living algae encompass molecules of primary metabolism and a number of osmolytes, including dimethylsulfoniopropionate. Mass spectrometry imaging revealed the presence of dimethylsulfoniopropionate in the symbionts and host cells, indicating that the algae provide osmolytic protection to the host. Furthermore, our findings suggest a possible dependence of Collodaria on symbiotic vitamin B3. Distinctive differences in phospholipid composition between free-living and symbiotic stages indicate that the algal cell membrane may undergo rearrangement in the symbiosis. Our results demonstrate a strong interdependence and rewiring of the algal metabolism underlying radiolaria-microalgae photosymbioses.
Question: Write a study description for the study titled 'Urine Latin Square Spike-In for testing the NMR quantification tool, MetaboQuant'.
Answer: To test the quantification performance of MetaboQuant and other NMR quantification tools, a set of eight metabolites were added to replicates of a urine sample in varying concentrations. The metabolites were alanine, creatinine, histidine, betaine, acetate, phosphocreatine, β-hydroxybutyrate (BHBA) and lactate. These were added in concentrations of 6000, 3000, 1500, 750, 375, 188, 94, and 47 micromol/L in a Latin Square design. 2D 1H-13C-HSQC spectra were recorded on a 600 MHz Bruker Avance III spectrometer employing a triple-resonance cryoprobe and z-gradients.