LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'CE-MS Metabolomic and LC-MS Proteomic Analyses of Breast Cancer Exosomes Reveal Alterations in Purine and Carnitine Metabolism'.
Answer: A nano sheath-flow capillary electrophoresis mass spectrometry (CE-MS) system with electrospray ionization was used to profile cationic metabolite cargo in exosomes secreted by non-tumorigenic MCF-10A and tumorigenic MDA-MB-231 breast epithelial cells. CE-MS-based metabolomics revealed increased purine synthesis intermediates and increased carnitine synthesis metabolites in MDA-MB-231-derived exosomes, with pathway enrichment indicating activation of de novo purine pathways and upregulating of carnitine metabolism. In addition, nanoLC-MS-based proteomics revealed differential expression of ecto-5’-nucleotidase (NT5E) and mitochondrial aldehyde dehydrogenase (ALDH9A1) demonstrated metabolic alterations in related enzymatic steps. This study demonstrates the application of nano sheath-flow CE-MS for comprehensive and quantitative exosome metabolomics, uncovering metabolic reprogramming in purine and carnitine pathways between normal and cancerous breast cell lines and providing insight into exosome-mediated signaling of breast cancer metabolism.
Question: Write a study description for the study titled 'Gut microbiota ameliorates hepatic fibrosis through modulating intestinal bile acid metabolism and hepatocyte pyroptosis (Hepatic fibrosis feces)'.
Answer: Hepatic fibrosis decreased feces bile acid level. Hepatic fibrosis increased serum bile acid. This result showed that hepatic fibrosis inhibited the excretion of bile acid in clinical patients. This result provided phenotype for hepatic fibrosis patients. Bile acid was important indexes for liver injury. TCDCA was important, and it play toxicity effect through ferroptosis and apoptosis. The research for other bile acid such CA, UDCA, TUDCA, TDCA, LCA, TLCA would be important.Hepatic fibrosis feces (sample 2) analysis is reported in the current study MTBLS6742.Hepatic fibrosis serum (sample 1) analysis is reported in MTBLS6732.Hepatic fibrosis serum+feces (sample 3) analysis is reported in MTBLS6728.
Question: Write a study description for the study titled '13C metabolomics reveals widespread change in carbon fate during coral bleaching'.
Answer: INTRODUCTION: Rising seawater temperatures are threatening the persistence of coral reefs; where above critical thresholds, thermal stress results in a breakdown of the coral-dinoflagellate symbiosis and the loss of algal symbionts (coral bleaching). As symbiont-derived organic products typically form a major portion of host energy budgets, this has major implications for the fitness and persistence of symbiotic corals.  OBJECTIVES: We aimed to determine change in autotrophic carbon fate within individual compounds and downstream metabolic pathways in a coral symbiosis exposed to varying degrees of thermal stress and bleaching.  METHODS: We applied gas chromatography–mass spectrometry coupled to a stable isotope tracer (13C), to track change in autotrophic carbon fate, in symbiont and host individually, following exposure to elevated water temperature.  RESULTS: Thermal stress resulted in partner-specific changes in carbon fate, which progressed with heat stress duration. We detected modifications to carbohydrate and fatty acid metabolism, lipogenesis, and homeostatic responses to thermal, oxidative and osmotic stress. Despite pronounced photodamage, remaining in hospite symbionts continued to produce organic products de novo and translocate to the coral host. However as bleaching progressed, we observed minimal 13C enrichment of symbiont long-chain fatty acids, also reflected in 13C enrichment of host fatty acid pools.  CONCLUSION: These data have major implications for our understanding of coral symbiosis function during bleaching. Our findings suggest that during early stage bleaching, remaining symbionts continue to effectively translocate a variety of organic products to the host, however under prolonged thermal stress there is likely a reduction in the quality of these products.
Question: Write a study description for the study titled 'The Impact of Ethnicity and Intra-Pancreatic Fat on the Postprandial Metabolome Response to Whey Protein in Overweight Asian Chinese and European Caucasian Women with Prediabetes'.
Answer: The 'Thin on the Outside Fat on the Inside' TOFI_Asia study found Asian Chinese to be more susceptible to Type 2 Diabetes (T2D) compared to European Caucasians matched for gender and body mass index (BMI). This was influenced by degree of visceral adipose deposition and ectopic fat accumulation in key organs, including liver and pancreas, leading to altered fasting plasma glucose, insulin resistance, and differences in plasma lipid and metabolite profiles. It remains unclear how intra-pancreatic fat deposition (IPFD) impacts TOFI phenotype-related T2D risk factors associated with Asian Chinese. Cow’s milk whey protein isolate (WPI) is an insulin secretagogue which can suppress hyperglycemia in prediabetes. In this dietary intervention, we used untargeted metabolomics to characterize the postprandial WPI response in 24 overweight women with prediabetes. Participants were classified by ethnicity (Asian Chinese, n=12; European Caucasian, n=12) and IPFD (low IPFD < 4.66%, n=10; high IPFD ≥ 4.66%, n=10). Using a cross-over design participants were randomized to consume three WPI beverages on separate occasions; 0 g (water control), 12.5 g (low protein, LP) and 50 g (high protein, HP), consumed when fasted. An exclusion pipeline for isolating metabolites with temporal (T0-240mins) WPI responses was implemented, and a support vector machine-recursive feature elimination (SVM-RFE) algorithm was used to model relevant metabolites by ethnicity and IPFD classes. Metabolic network analysis identified glycine as a central hub in both ethnicity and IPFD WPI response networks. A depletion of glycine relative to WPI concentration was detected in Chinese and high IPFD participants independent of BMI. Urea cycle metabolites were highly represented among the ethnicity WPI metabolome model, implicating a dysregulation in ammonia and nitrogen metabolism among Chinese participants. Uric acid and purine synthesis pathways were enriched within the high IPFD cohort’s WPI metabolome response, implicating adipogenesis and insulin resistance pathways. In conclusion, the discrimination of ethnicity from WPI metabolome profiles was a stronger prediction model than IPFD in overweight women with prediabetes. Each models’ discriminatory metabolites enriched different metabolic pathways that help to further characterize prediabetes in Asian Chinese women and women with increased IPFD, independently.
Question: Write a study description for the study titled 'Metabolic Profiles Under Hypoxic Stress: Adolescent Athletes' Experience'.
Answer: Hypoxic training is a method by athletes to enhance their performance at sea level or improve their cardiovascular endurance in moderate-altitude competitions. Comparative studies involving populations from low and moderate altitudes offer an opportunity to understand the mechanisms behind adaptation to hypoxia. Data from GC-MS and LC-MS were combined to compare metabolic profiles of plasma between moderate- and low-altitude adolescent athletes. A total of 161 differential metabolites were identified, including 84 up-regulated and 77 down-regulated metabolites in moderate-altitude adolescents compared to their low-altitude counterparts. Pathway analysis revealed that the significantly different metabolites were associated with carbohydrate, amino acid and lipid metabolism. Lipid metabolism pathways such as linolenic and linoleic acid metabolism, sphingolipid metabolism and arachidonic acid metabolism, as well as processes involving the transfer of acetyl groups into mitochondria and fatty acid biosynthesis, were significantly altered in the moderate-altitude athletes. Receiver operating characteristic analysis detected glycerol and oxo-proline metabolites with a good range of sensitivity and specificity. These metabolites were chosen as biomarker of chronic adaptation to moderate altitude. This study demonstrates differences in metabolic profiles between moderate- and low-altitude populations and highlights the potential of these differential metabolites and metabolic pathways to provide new insights into the mechanisms of adaptation to moderate-altitude
Question: Write a study description for the study titled 'Achyranthes bidentata alleviates hypertension with regulating gut microbiota'.
Answer: Background: Hypertension remains a significant global health challenge, with limited treatment efficacy in many patients. Emerging evidence suggests that gut microbiota plays a crucial role in blood pressure regulation. This study investigates the anti-hypertensive effects of Achyranthes bidentata (Ab) extract and its interaction with the gut microbiota, particularly focusing on the enrichment of Dubosiella sp. and its impact on arachidonic acid metabolism.Results: Here, we identified a novel microbiota-driven anti-hypertensive mechanism mediated by the Ab extract and Dubosiella sp. Ab significantly ameliorated hypertension and kidney damage by enriching Dubosiella in hypertensive mice. Metabolomics analysis revealed that Ab enhances lipid metabolic pathways, particularly arachidonic acid metabolism. In vitro, Ab significantly promoted the biofilm formation of D. newyorkensis DSM103457. Further gavage experiments confirmed that D. newyorkensis DSM103457 alleviates hypertension, cardiac and kidney injury. Combined microbial and metabolic profiling via 16S rRNA sequencing, metagenomics and metabolomics demonstrated that D. newyorkensis DSM103457 modulates gut microbiota, arachidonic acid metabolism, restoring prostaglandins and leukotrienes essential for cardiovascular homeostasis. Notably, arachidonic acid significantly promotes D. newyorkensis DSM103457 growth, enabling rapid generation and transformation of HETEs and HODEs in vitro.Conclusions: This study identified Ab-Dubosiella-arachidonic acid axis as a novel anti-hypertensive pathway, offering promise for the development of integrated herbal prebiotics and microbial probiotics for targeted hypertension therapy.
Question: Write a study description for the study titled 'Lipid Profiles of Human Brain Tumors Obtained by High-Resolution Negative Mode Ambient Mass Spectrometry'.
Answer: Alterations in cell metabolism, including changes in lipid composition occurring during malignancy, are well characterized for various tumor types. However, a significant part of studies that deal with brain tumors have been performed using cell cultures and animal models. Here, we present a dataset of 124 high-resolution negative ionization mode lipid profiles of human brain tumors resected during neurosurgery. The dataset is supplemented with 38 non-tumor pathological brain tissue samples resected during elective surgery. The change in lipid composition alterations of brain tumors enables the possibility of discriminating between malignant and healthy tissues with the implementation of ambient mass spectrometry. On the other hand, the collection of clinical samples allows the comparison of the metabolism alteration patterns in animal models or in vitro models with natural tumor samples ex vivo. The presented dataset is intended to be a data sample for bioinformaticians to test various data analysis techniques with ambient mass spectrometry profiles, or to be a source of clinically relevant data for lipidomic research in oncology.
Question: Write a study description for the study titled 'Multi-omics association analysis reveals interactions between the oropharyngeal microbiome and the metabolome in pediatric patients with influenza A virus pneumonia.'.
Answer: Children are at high risk for influenza A virus (IAV) infections, which can develop into severe illnesses. However, little is known about interactions between the microbiome and respiratory tract metabolites and their impact on the development of IAV pneumonia in children. Using a combination of liquid chromatography tandem mass spectrometry (LC-MS/MS) and 16S rRNA gene sequencing, we analyzed the composition and metabolic profile of the oropharyngeal microbiota in 49 pediatric patients with IAV pneumonia and 42 age-matched healthy children. The results indicate that compared to healthy children, children with IAV pneumonia exhibited significant changes in the oropharyngeal macrobiotic structure (p = 0.001), and significantly lower microbial abundance and diversity (p  0.05). These changes came with significant disturbances in the levels of oropharyngeal metabolites. Intergroup differences were observed in 204 metabolites mapped to 36 metabolic pathways. Significantly higher levels of sphingolipid (sphinganine and phytosphingosine) and propanoate (propionic acid and succinic acid) metabolism were observed in patients with IAV pneumonia than in healthy controls. Using Spearman's rank-correlation analysis, correlations between IAV pneumonia-associated discriminatory microbial genera and metabolites were evaluated. The results indicate significant correlations and consistency in variation trends between Streptococcus and three sphingolipid metabolites (phytosphingosine, sphinganine, and sphingosine). Besides these three sphingolipid metabolites, the sphinganine-to-sphingosine ratio and the joint analysis of the three metabolites indicated remarkable diagnostic efficacy in children with IAV pneumonia. This study confirmed significant changes in the characteristics and metabolic profile of the oropharyngeal microbiome in pediatric patients with IAV pneumonia, with high synergy between the two factors. Oropharyngeal sphingolipid metabolites may serve as potential diagnostic biomarkers of IAV pneumonia in children.
Question: Write a study description for the study titled 'An overlooked prebiotic: beneficial effect of dietary nucleotide supplementation on gut microbiota and metabolites in senescence-accelerated mouse prone-8 mice'.
Answer: Nucleotides (NTs) are regulatory factors in many biological processes and play important roles in the growth, development, and metabolism of living organisms. We used senescence-accelerated mouse prone-8 (SAMP8) to investigate the effects of NTs on the gut microbiota and metabolites. And the promoting effect of NTs on the growth of a probiotic (Lactobacillus casei) was explored through in vitro experiments. The results showed that the sequencing depth of 16S rDNA covered all microbial species in the feces of SAMP8. Supplementation with exogenous NTs to the diet enhanced the diversity of the gut microbiota, reduced the abundance of bacteria with negative effects on the body (such as Verrucomicrobia, Ruminococcaceae, Akkermansia and Helicobacter), and increased the abundance of the microbiota, which had beneficial effects on the mice (such as Lactobacillus, Candidatus saccharimonas and Lachnospiraceae_NK4A136_group). Metabonomic analysis showed that NT deficiency in the diet significantly affected metabolites in the mouse feces. The metabolites in mice supplemented with NTs tended to be normal (SAMR1). The differentially expressed metabolites caused by NT addition are involved in various pathways in the body, including linoleic acid metabolism, vitamin B6 metabolism, and histidine metabolism. Correlation analysis revealed a significant correlation between the gut microbiota and differentially expressed metabolites caused by the addition of NTs. In vitro experiments showed that NTs significantly promoted the growth, secretion of biofilm and extracellular polymeric substance of L. casei. NTs also promoted the ability of the crude extract of L. casei to resist the secretion of Shigella biofilm. Thus, NTs can regulate the abundance of the gut microbiota and alter the metabolic expression of the intestinal microbiome.
Question: Write a study description for the study titled 'Metagenomic and Metabolomic Analysis of Gut Microbiota's Impact on Sperm Motility in Rongchang Boars'.
Answer: This study focused on the association between gut microbiota and sperm motility, with an emphasis on analyzing differential metabolites in the intestines and blood of Rongchang boars from the high sperm motility group (group H) and low sperm motility group (group L). The results revealed that eicosapentaenoic acid (EPA) was a differential metabolite commonly present in both the intestines and blood of the two groups. Comprehensive analysis indicated that alterations in gut microbiota can promote the accumulation of EPA in the intestines and blood, and EPA may exert a positive effect on sperm motility through mechanisms such as antioxidant activity and improvement of membrane fluidity. This finding provides important clues for revealing the potential mechanism by which gut microbiota regulates sperm motility through metabolites, and has certain reference value in the field of agricultural breeding.
Question: Write a study description for the study titled 'Impact of myocardial reperfusion on human plasma lipidome'.
Answer: The primary aim of the study is to investigate the temporal changes in plasma lipidome before and after reperfusion in patients with ST-segment elevation myocardial infarction (STEMI) and their association with myocardial injury. We found that 56% of the identified lipid species were significantly altered (corrected p< 0.05) in the first 24 h following reperfusion in patients with STEMI. Three lipid species, namely, acylcarnitine 18:2, TG 51:0, and LPC 17:1 were associated with a change in troponin concentration (delta troponin) and in-hospital cardiovascular events. Of these, acylcarnitine 18:2, and LPC 17:1 and their respective whole class levels, were significantly higher (p < 0.05) in the STEMI population than the age/sex-matched control subjects. Overall, our analyses showed a large shift in plasma lipidome in patients that undergo myocardial reperfusion. The differences found for acylcarnitines and LPC species and their association with both cardiac markers and cardiac outcomes need further validation.
Question: Write a study description for the study titled 'Insights into the controls on metabolite distributions along a latitudinal transect of the western Atlantic Ocean'.
Answer: Metabolites, or the small organic molecules that are synthesized by cells during metabolism, comprise a complex and dynamic pool of carbon in the ocean. They are an essential form of information, linking genotype to phenotype at the individual, population and community levels of biological organization. Characterizing metabolite distributions inside microbial cells and dissolved in seawater is essential to understanding the controls on their production and fate, as well as their roles in shaping marine microbial food webs. Here, we apply a targeted metabolomics method to quantify particulate and dissolved distributions of a suite of biologically relevant metabolites including vitamins, amino acids, nucleic acids, osmolytes, and intermediates in biosynthetic pathways along a latitudinal transect in the western Atlantic Ocean. We find that, in the euphotic zone, most particulate or intracellular metabolites positively co-vary with the most abundant microbial taxa. In contrast, dissolved metabolites exhibited greater variability with differences in distribution between ocean regions. Although fewer particulate metabolites were detected below the euphotic zone, molecules identified in the deep ocean may be linked to preservation of organic matter or adaptive physiological strategies of deep-sea microbes. Based on the identified metabolite distributions, we propose relationships between certain metabolites and microbial populations, and find that dissolved metabolite distributions are not directly related to their particulate abundances.
Question: Write a study description for the study titled 'Comparison of singlequad and Orbitrap mass analyzer coupled to gas chromatography reveals potential of high resolution GC MS for untargeted metabolomics'.
Answer: The development of improved spectrometers and supporting computational tools is expected to eventually enable the rapid annotation of whole metabolomes. However, rarely are novel mass spectrometers directly compared to the previously used ones in the field of metabolomics, thus preventing researchers from gauging the benefits of the investment. LC Orbitrap technology is now widely in use while GC-Orbitrap introduced in 2015 has remained fairly unexplored in its potential for metabolomics research. This study aims to evaluate the additional knowledge gained in a metabolomics experiment when using the GC-Orbitrap in comparison to a unit mass singlequad GC-MS. Samples from an osmotic stress treatment versus a control of the microalga Skeletonema costatum were investigated using comparative metabolomics. Samples from this treatment of a non-model organism were split and measured on both platforms with nearly identical chromatography. Resulting datasets were compared both on a statistical level and on the level of individual compound annotation. Both mass spectrometers successfully classified stressed vs non-stressed microalgae, but the GC-Orbitrap detected more than triple the number of compounds compared to the singlequad mass analyzer, resulting in more readily interpretable annotations. Additionally, one unknown was correctly annotated exploiting high resolution capabilities unavailable to the singlequad mass analyzer. While computational support that specifically utilizes high resolution GC-MS data is still underdeveloped, clear benefits of the GC-Orbitrap technology for metabolomics studies are shown here.
Question: Write a study description for the study titled 'Deep longitudinal multi-omics analysis of Bordetella pertussis cultivated in bioreactors highlights medium starvations and transitory metabolisms, associated to vaccine antigen biosynthesis variations and global virulence regulation'.
Answer: Bordetella pertussis is the bacterial causative agent of whooping cough, a serious respiratory illness. An extensive knowledge on its virulence regulation and metabolism is a key factor to ensure pertussis vaccine manufacturing process robustness. The aim of this study was to refine our comprehension of B. pertussis physiology during in vitro cultures in bioreactors. A longitudinal multi-omics analysis was carried out over 26 h small-scale cultures of B. pertussis. Cultures were performed in batch mode and under culture conditions intending to mimic industrial processes. Putative cysteine and proline starvations were, respectively, observed at the beginning of the exponential phase (from 4 to 8 h) and during the exponential phase (18 h 45 min). As revealed by multi-omics analyses, the proline starvation induced major molecular changes, including a transient metabolism with internal stock consumption. In the meantime, growth and specific total PT, PRN and Fim2 antigen productions were negatively affected. Interestingly, the master virulence-regulating two-component system of B. pertussis (BvgASR) was not evidenced as the sole virulence regulator in this in vitro growth condition. Indeed, novel intermediate regulators were identified as putatively involved in the expression of some virulence-activated genes (vags). Such longitudinal multi-omics analysis applied to B. pertussis culture process emerges as a powerful tool for characterization and incremental optimization of vaccine antigen production.