LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Absolute quantification of metabolites in tomato fruit extracts by fast 2D NMR (Tomato 700 MHz samples)'.
Answer: Quantitative NMR metabolomics is a powerful tool to have access to valuable information on metabolism. Unfortunately, the quantitative analysis of metabolic samples is often hampered by peak overlap. Two-dimensional (2D) spectroscopy offers a promising alternative and quantitative results can be obtained provided that a calibration approach is employed. However, the duration of 2D NMR experiments is barely compatible with the metabolomic study of a large number of samples. This drawback can be circumvented by relying on “ultrafast” experiments capable of recording 2D spectra in a single-scan. While such experiments are not sensitive enough to match the concentrations of metabolic samples, a compromise can be reached by hybrid strategies capable of recording 2D NMR spectra of extracts in a few minutes only. The purpose of this study is to demonstrate that these multi-scan single-shot experiments can be successfully applied to the absolute quantification of major metabolites in plant extracts. Fast COSY experiments are recorded in 5 min on tomato fruit pericarp extracts at different stages of development. The concentration of eight major metabolites is determined with a trueness better than 10 % and a technical repeatability of a few percent. The experiments performed at two magnetic fields lead to similar quantitative results, in coherence with the metabolism of tomato fruit. The results show that fast 2D NMR methods form a promising tool for fast targeted metabolomics, and open promising perspective towards the automated and high-throughput quantitative analysis of large groups of plant and other samples for metabolomics and for the modelling of metabolism.Tomato 700 MHz samples protocols and data are reported in the current study MTBLS132.Tomato 500 MHz samples protocols and data are reported in MTBLS131.Calibration Standard 500 MHz samples protocols and data are reported in MTBLS133.Calibration Standard 700 MHz samples protocols and data are reported in MTBLS134.
Question: Write a study description for the study titled 'Salmonella Typhimurium reprograms macrophage metabolism via T3SS effector SopE2 to promote intracellular replication and virulence'.
Answer: Salmonella Typhimurium establishes systemic infection by replicating in host macrophages. Here we show that macrophages infected with S. Typhimurium exhibit upregulated glycolysis and decreased serine synthesis, leading to accumulation of glycolytic intermediates. The effects on serine synthesis are mediated by bacterial protein SopE2, a type III secretion system (T3SS) effector encoded in pathogenicity island SPI-1. The changes in host metabolism promote intracellular replication of S. Typhimurium via two mechanisms: decreased glucose levels lead to upregulated bacterial uptake of 2- and 3-phosphoglycerate and phosphoenolpyruvate (carbon sources), while increased pyruvate and lactate levels induce upregulation of another pathogenicity island, SPI-2, known to encode virulence factors. Pharmacological or genetic inhibition of host glycolysis, activation of host serine synthesis, or deletion of either the bacterial transport or signal sensor systems for those host glycolytic intermediates impairs S. Typhimurium replication or virulence.
Question: Write a study description for the study titled 'Gut Microbiome Composition Is Associated With Future Onset of Crohn's Disease in Healthy First-Degree Relatives.'.
Answer: BACKGROUND & AIMS: The cause of Crohn's disease (CD) is unknown, but the current hypothesis is that microbial or environmental factors induce gut inflammation in genetically susceptible individuals, leading to chronic intestinal inflammation. Case-control studies of patients with CD have cataloged alterations in the gut microbiome composition; however, these studies fail to distinguish whether the altered gut microbiome composition is associated with initiation of CD or is the result of inflammation or drug treatment.METHODS: In this prospective cohort study, 3483 healthy first-degree relatives (FDRs) of patients with CD were recruited to identify the gut microbiome composition that precedes the onset of CD and to what extent this composition predicts the risk of developing CD. We applied a machine learning approach to the analysis of the gut microbiome composition (based on 16S ribosomal RNA sequencing) to define a microbial signature that associates with future development of CD. The performance of the model was assessed in an independent validation cohort.RESULTS: In the validation cohort, the microbiome risk score (MRS) model yielded a hazard ratio of 2.24 (95% confidence interval, 1.03-4.84; P = .04), using the median of the MRS from the discovery cohort as the threshold. The MRS demonstrated a temporal validity by capturing individuals that developed CD up to 5 years before disease onset (area under the curve > 0.65). The 5 most important taxa contributing to the MRS included Ruminococcus torques, Blautia, Colidextribacter, an uncultured genus-level group from Oscillospiraceae, and Roseburia.CONCLUSION: This study is the first to demonstrate that gut microbiome composition is associated with future onset of CD and suggests that gut microbiome is a contributor in the pathogenesis of CD.
Question: Write a study description for the study titled 'Citrate serves as a signal molecule to modulate carbon metabolism and iron homeostasis in Staphylococcus aureus'.
Answer: Pathogenic bacteria's metabolic adaptation for survival and proliferation within hosts is a crucial aspect of bacterial pathogenesis. Here, we demonstrate that citrate, the first intermediate of the tricarboxylic acid (TCA) cycle, plays a key role as a regulator of gene expression in Staphylococcus aureus. We show that citrate activates the transcriptional regulator CcpE and thus modulates the expression of numerous genes involved in key cellular pathways such as central carbon metabolism, iron uptake and the synthesis and export of virulence factors. Citrate can also suppress the transcriptional regulatory activity of ferric uptake regulator. Moreover, we determined that accumulated intracellular citrate, partly through the activation of CcpE, decreases the pathogenic potential of S. aureus in animal infection models. Therefore, citrate plays a pivotal role in coordinating carbon metabolism, iron homeostasis and bacterial pathogenicity at the transcriptional level in S. aureus, going beyond its established role as a TCA cycle intermediate.
Question: Write a study description for the study titled 'Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure'.
Answer: The gut microbiomes communicate with kidney and may play a crucial role in the development of anemia in patients with chronic renal failure (CRF). However, the alterations in microbiota and their association with functional metabolites remain unclear. We performed metagenomics and untargeted metabolomics in a cohort of 30 patients with anemia of CRF and 20 healthy controls (HCs) to identify the characteristics of the gut microbiome and explore its potential interactions with the host. Decreased microbiota diversity and significant compositional differences were observed in the patients with anemia of CRF. We identified six gut microbiotas significantly changed in patients with anemia of CRF, particularly Faecalibacterium prausnitzii, Prevotella copri and Escherichia coli that were closely correlated with hemoglobin (Hb) levels and estimated glomerular filtration rate. And these changes were accompanied by functional alterations in distinctive microbial pathways. Further fecal and serum metabolomics revealed fecal 12-KETE-LB4 in arachidonic acid metabolism, uracil and L-aspartic acid in beta-alanine metabolism, gulonic acid in ascorbate and aldarate metabolism, accompanied by the top 15 differential serum metabolites were closely correlated with Hb levels. Furthermore, we observed a complex co-occurrence between anemia of CRF-related gut microbiota species and the characterized metabolites. Moreover, a non-invasive model incorporating Faecalibacterium prausnitzii, Prevotella copri, combined with fecal 12-KETE-LB4, uracil, L-aspartic acid and gulonic acid, distinguished patients with anemia of CRF from HCs (area under the curve: 0.879). Collectively, our results suggest that a disordered gut microbiome associated with functional metabolites may be a non-invasive diagnostic and therapeutic target for anemia of CRF.Linked studies: UPLC-MS assays of Blood Plasma samples are reported in this study.UPLC-MS assays of Fecal samples are reported in MTBLS6334.
Question: Write a study description for the study titled 'Horizontal Transfer of Bacteriocin Biosynthesis Genes Requires Metabolic Adaptation To Improve Compound Production and Cellular Fitness'.
Answer: Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread among bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds, and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging, and many BGC recipients initially produce small amounts of compound or show reduced growth rates. To assess whether transfer of BGCs between closely related Staphylococcus aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intraspecies transfer of a BGC encoding the ribosomally synthesized and posttranslationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites, including citrate and α-ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BGC acquisition requires genetic and metabolic predispositions, allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities.IMPORTANCE: Human microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human-associated communities and can cause disease when the composition of the community becomes unbalanced. Bacteriocin-producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction into human microbiomes might prevent pathogen colonization and infection. However, to develop probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Metabolic adaptations are most likely broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.
Question: Write a study description for the study titled 'Prolonged fasting times reap greater geroprotective effects when combined with caloric restriction in adult female mice'.
Answer: Emerging new evidence highlights the importance of prolonged daily fasting periods for the health and survival benefits of calorie restriction (CR) and time-restricted feeding (TRF) in male mice; however, little is known about the impact of these feeding regimens in females. We placed 14-month-old female mice on five different dietary regimens, either CR or TRF with different feeding windows, and determined the effects of these regimens on physiological responses, progression of neoplasms and inflammatory diseases, serum metabolite levels, and lifespan. Compared with TRF feeding, CR elicited a robust systemic response, as it relates to energetics and healthspan metrics, a unique serum metabolomics signature in overnight fasted animals, and was associated with an increase in lifespan. These results indicate that daytime (rest-phase) feeding with prolonged fasting periods initiated late in life confer greater benefits when combined with imposed lower energy intake.
Question: Write a study description for the study titled 'Cell-to-cell heterogeneity drives host-virus coexistence in a bloom-forming alga'.
Answer: Algal blooms drive global biogeochemical cycles of key nutrients in the oceans and serve as hotspots for biological interactions. The massive spring blooms of the cosmopolitan coccolithophore Emiliania huxleyi (E. huxleyi) are often infected by the lytic Emiliania huxleyi specific virus (EhV) which is a major mortality agent triggering bloom demise. Nonetheless, the multi-annual 'boom and bust' pattern of E. huxleyi suggests that mechanisms of coexistence are essential for these host-virus dynamics. To investigate host-virus coexistence, we developed a new model system from an E. huxleyi culture which recovered from viral infection. The recovered population coexists with the virus, as host cells continue to grow in parallel to viral production. By applying a single-molecule fluorescence in situ hybridization (smFISH) approach to quantify the fraction of infected cells and assessing infection-specific lipid biomarkers, we identified a small subpopulation (5-7% of cells) that was infected and produced new virions, whereas the majority of the host population could resist infection. To further assess population heterogeneity, we generated monoclonal strain collections using single-cell sorting and subsequently phenotyped their susceptibility to EhV infection. This unraveled a substantial cell-to-cell heterogeneity across a continuum of susceptibility to resistance, suggesting that infection outcomes may vary depending on the individual cell. These results add a new dimension to our understanding of the complexity of host-virus interactions that are commonly assessed in bulk and described by binary definitions of resistance or susceptibility. We propose that phenotypic heterogeneity drives E. huxleyi-EhV coexistence and may potentially provide the coexisting strain an ecological advantage by killing competing susceptible strains.
Question: Write a study description for the study titled 'Stable Isotope-Assisted Metabolomics for Deciphering Xenobiotic Metabolism in Mammalian Cell Culture'.
Answer: Xenobiotics are ubiquitous in the environment and modified abundantly in the human body by phase I and II metabolism. Liquid chromatography coupled to high resolution mass spectrometry is a powerful tool to investigate these biotransformation products. Here, we present a workflow based on stable isotope-assisted metabolomics and the bioinformatics tool MetExtract II for deciphering all measureable xenobiotic metabolites produced by human cells in vitro in an untargeted manner. The value of this workflow is demonstrated by the detailed investigation of the metabolism of deoxynivalenol (DON), an abundant food contaminant, in two cell models (HepG2, HT29). Detected known metabolites included DON-3-sulfate, DON-10-sulfonate, and DON-10-glutathione as well as DON-cysteine. Conjugation with amino acids and antibiotics was observed and confirmed for the first time. The approach allows for the generic and untargeted elucidation of human xenobiotic products in tissue culture. It may be easily applied to other fields of research including drug metabolism, personalized medicine and systems biology and serves to better understand the relevance of in vitro experiments.
Question: Write a study description for the study titled 'Bacteria regulate aging physiology in microalgae via induced vesicle production and the methionine cycle (Metabolomics analysis)'.
Answer: In annually reoccurring patterns, microalgae form blooms that persist and decline thereby contributing massively to global biogeochemical cycles. The decline of blooms is mainly caused by nutrient limitation and goes ahead with the aging of individual algal cells. Nutrient intake can re-initiate proliferation, but the processes involved are poorly understood. By investigating the bloom-forming diatom Coscinodiscus radiatus, we demonstrate how algae recover after nutrient influx. The rejuvenation physiology of the algae is characterized by metabolomic re-organization and the formation of extracellular vesicles. Regulated pathways mediating aging are centered around the methionine cycle in C. radiatus. Vesicles shuttle reactive oxygen species, oxylipins and other harmful metabolites out of the old cells, thereby re-enabling their proliferation. Metabolic processes involved in aging and vesicle production are modulated by bacteria. Using chemical signaling bacteria can trigger vesicle production thereby releasing organic nutrients for their growth and supporting algal growth as well.Metabolomics analysis is reported in the current study MTBLS5368.Metabolomics profiling of FACS purified EVs is reported in MTBLS5401.
Question: Write a study description for the study titled 'Plant-to-plant variability in root metabolite profiles of 19 Arabidopsis thaliana accessions is substance-class dependent'.
Answer: Natural variation of secondary metabolism between different accessions of Arabidopsis thaliana has been studied extensively. In this study, we extended the natural variation approach by including biological variability and analyzed root metabolic patterns as well as their variability between plants and naturally occurring accessions.  To screen 19 accessions of A. thaliana, comprehensive non-targeted metabolite profiling of single plant root extracts was performed using UPLC/ESI-QTOF-MS and GC/EI-QMS. 98 (GC/MS) and 139 (LC/MS) metabolites were identified at MSI levels one or two, or characterised ad level three.  All metabolic profiles indicated that plant-to-plant-variability is greater than natural variation between accessions and non-biological variation of experimental batches. Ratios of plant-to-plant to total variability were high and distinct for the classes of known secondary metabolites, which are commonly subjected to natural variation analysis. None of the investigated accessions displayed a specifically high or low biological variability for these substance classes.
Question: Write a study description for the study titled 'Attenuate host susceptibility to respiratory virus invasion by inhibiting interactions between host proteins SLC16A3 and AP1G1'.
Answer: Modulating cell endocytosis activity to reduce host susceptibility to virus represents a promising strategy for antiviral drug development. In this study, we reveal that lactate transporter SLC16A3 as a critical host factor for reducing diverse virus invasion. By performing metabolomics, proteomics, and thermal proteome profiling experiment, AP1G1, a pivotal protein involved in cellular endocytosis, was indiscriminately screened as a chaperone of SLC16A3. SLC16A3 decides the membrane enrichment of AP1G1 by protein interaction, thereby influence host susceptibility to diverse virus. This conclusion was further validated in SLC16A3 knocked-down cells, which indicating a broad-spectrum target for anti-virus drug development to recedes virus entry by blocking the interaction between AP1G1 and SLC16A3. This conclusion has been validated with a patent medicine SFJD (Shufengjiedu). SFJD exhibits strong effect in decreasing the susceptibility of host cells to viral infections. Molecularly, SFJD administration results in disrupting the interaction between SLC16A3 and AP1G1 and reduced membrane localization of AP1G1. Consequently, achieves a receded endocytosis activity of host cells on viral particles. This provide evidence for the practicability of SLC16A3-AP1G1 strategy. Taken together, the regulation on the SLC16A3-AP1G1 interaction represents a broad-spectrum and practicable antiviral strategy. This study offers insights into novel approach for inhibiting viral infections through the alteration of host susceptibility and advances the idea for antiviral drug development.
Question: Write a study description for the study titled 'Chlorogenic acid alters ileal microbiota and metabolites in broilers under immune stress'.
Answer: Immune stress in broilers can cause severe economic losses, chlorogenic acid is an effective plant extract for alleviating immune stress. This study investigates the effect of chlorogenic acid on the intestinal microbiota and metabolites of broilers under immune stress. 312 broilers were randomly divided into 4 treatment groups, namely saline group, lipopolysaccharides (LPS) group, saline+chlorogenic acid (SCGA) group, and LPS+CGA (LCGA) group. The LPS group and LCGA group of broilers were injected with 0.5mg/kg LPS intraperitoneally at 14, 15, and 17 days of age to induce immune stress. SCGA and LCGA group fed a basal diet supplemented with 1000mg/kg CGA. At 17d, the ileal contents of broilers were collected for microbial and metabolomics analysis. Results showed that immune stress led Subdoligranulum decreased, thereby lowering the diversity of the intestinal microbial community. CGA increase the abundance of beneficial bacteria Clostridiaceae and Candidatus Arthromitus in the ileum of immune-stressed broilers, while reducing the abundance of Lachnospiraceae, Allobaculum, Desulfovibrio, Desulfovibrionales, Desulfovibrionaceae. Non-targeted metabolomics results showed that immune stress significantly increased the content of methylmalonic acid, N-Acetyl-L-aspartic acid, trans-ferulic acid, and pantothenic acid in the ileum of broilers, while significantly downregulated the content of pyroglutamic acid, L-glutamic gamma-semialdehyde, and biliverdin, indicating that LPS activated inflammation and oxidation in broilers, leading to oxidative damage in the intestine. After CGA added, the levels of corticosterone, prostaglandin B2, trans-ferulic acid, methylmalonic acid in the ileum of immune-stressed broilers were significantly lower, while the levels of pyroglutamic acid, L-glutamic gamma-semialdehyde, biliverdin, chenodeoxycholic acid, desmosterol, and 4-hydroxycinnamic acid were significantly higher, indicating that CGA can alleviate the inflammatory response induced by immune stress and enhance antioxidant capacity. Therefore, CGA can alleviate immune stress by regulating the ileal microbiota and metabolites.