LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'The impact of rumen and hindgut microbiomes on the persistent productivity of dairy cows'.
Answer: BackgroundPersistent productivity and productive lifespan determine the lifetime output of dairy cows and influence overall herd profitability. The composition and metabolic activity of the gastrointestinal microbiota of dairy cows influence persistent productivity. However, the processes by which host-microbiome crosstalk drives dairy cow persistent productivity remain unclear. Therefore, we performed an integrative comparative analysis of rumen and rectum metagenomes and metabolomes, together with serum and milk metabolomes, in long-lived dairy cows that exhibited divergent persistent productivity levels to elucidate the potential mechanisms that underpin modulation of persistent productivity by the rumen and rectum microbiota. ResultsSerum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group, but rectum fermentation parameters and rumen and rectum microbiota diversity showed no significant differences between LH and LL cows. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows’ rumen and rectum microbial interaction networks exhibited dependence on key nodes and streamlined inter-node connectivity that enhanced local functional synergy, with robustness, cohesion, and vulnerability levels similar to LL cows. The rumen Acidaminococcaceae bacterium and rectum Parabacteroides sp. exerted a positive effect on MY via microbiota-host co-metabolism of the purine metabolites guanosine and D-ribose-1-phosphate. Furthermore, the specific rumen microbiome module enhanced the levels of circulating eicosapentaenoic acid (EPA), thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively impacted MY. ConclusionsThe rumen and rectum microbiota positively influence production levels of long-lived dairy cows via microbiota and host co-metabolites of purine metabolites. Additionally, rumen microbiota improves production levels by enhancing host synthesis of EPA through the modulation of α-linolenic acid metabolism. The study reveals the potential role of rumen and rectum microbiota in regulating productivity of cows with sustained production capacity, providing insights for nutritional management strategies aimed at improving the health status and persistent production capacity of dairy cows.
Question: Write a study description for the study titled 'A single gene mutation underpins metabolic adaptation and acquisition of filamentous competence in the emerging fungal pathogen Candida auris'.
Answer: Filamentous cell growth is a vital property of fungal pathogens. The mechanisms of filamentation in the emerging multidrug-resistant fungal pathogen Candida auris are poorly understood. Here, we show that exposure of C. auris to glycerol triggers a rod-like filamentation-competent (RL-FC) phenotype, which forms elongated filamentous cells after a prolonged culture period. Whole-genome sequencing analysis reveals that all RL-FC isolates harbor a mutation in the C2H2 zinc finger transcription factor-encoding gene GFC1 (Gfc1 variants). Deletion of GFC1 leads to an RL-FC phenotype similar to that observed in Gfc1 variants. We further demonstrate that GFC1 mutation causes enhanced fatty acid β-oxidation metabolism and thereby promotes RL-FC/filamentous growth. This regulation is achieved through a Multiple Carbon source Utilizer (Mcu1)-dependent mechanism. Interestingly, both the evolved RL-FC isolates and the gfc1Δ mutant exhibit an enhanced ability to colonize the skin. Our results reveal that glycerol-mediated GFC1 mutations are beneficial during C. auris skin colonization and infection.
Question: Write a study description for the study titled 'Multi-Omics Approach to Elucidate Cerebrospinal Fluid Changes in Dogs with Intervertebral Disc Herniation'.
Answer: Herniation of the intervertebral disc (IVDH) is the most common cause of neurological and intervertebral disc degeneration-related diseases. Since the disc starts to degenerate before it can be observed by currently available diagnostic methods, there is an urgent need for novel diagnostic approaches. To identify molecular networks and pathways which may play important roles in intervertebral disc herniation, as well as to reveal the potential features which could be useful for monitoring disease progression and prognosis, multi-omics profiling including high-resolution LC-MS-based metabolomics and proteomics was performed. Furthermore, multi-omics data were integrated to decipher a complex interaction between individual omic layers leading to improved prediction model. Together with metabolic pathways related to amino acids and lipid metabolism, and coagulation cascades, our integromics prediction model identified the key features in IVDH, namely the proteins FSTL1, SCG5, NUCB1 and CRSP2 and the metabolites N-acetyl-D-glucosamine and adenine, involved in neuropathic pain, myelination, neurotransmission and inflammatory response, respectively. Their clinical application is to be further investigated. The utilization of novel integrative interdisciplinary strategy may provide opportunities to apply the innovative diagnostic and monitoring methods for degenerative spinal disorders.
Question: Write a study description for the study titled 'Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community; Interaction between the kefir isolates Lactococcus lactis and Acetobacter fabarum (GC-MS)'.
Answer: Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear, as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures, or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community of prokaryotes and yeasts, realizes stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open metabolic niches for followers. Through metabolomics and large-scale mapping of inter-species interactions, we show how microbes poorly suited for milk survive in — and even dominate — the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.Linked metabolomics studies:MTBLS1823 Spent-medium assay, measured untargeted (FIA-qTOF) and targeted (HILIC, LC-MS)MTBLS1829 Kefir fermentation curve (FIA-MS)Linked cross omic data:Genomes of isolated kefir species are available in the NCBI database under the accession: PRJNA375758 (bioproject ID: 375758).Metatranscriptomic sequencing reads can be accessed from ENA under the project id PRJEB37001.Genome-scale metabolic models for kefir bacteria can be found at github.com/cdanielmachado/kefir_models.
Question: Write a study description for the study titled 'Integrating two chromatographies in a co-fractionation mass spectrometry approach improved protein-metabolite interactions (PMIs) mapping capabilities and revealed novel protein-ligand pairings in Escherichia coli.'.
Answer: The protein-metabolite interactome remains understudied. We previously developed a co-fractionation mass-spectrometry-based approach called PROMIS to address this gap. PROMIS relies on size separation chromatography of protein-metabolite complexes from lysates, followed by proteomics and metabolomics analysis of the obtained fractions. Co-elution of metabolites and proteins is used to infer interactions. However, in a single separation, a metabolite cofractionates with hundreds of proteins, of which one or a few are 'true interactors,' whereas all others represent coincidental co-elution. Identifying the true binders represents the most significant challenge in using CF-MS-based methods for mapping PMIs. To address this challenge, we decided to integrate two chromatographies, size exclusion, and ion exchange, to improve PMI mapping capabilities and generate a PMI network in a model bacteria Escherichia coli. Although many complexes will have a similar size or charge, only a few should share both characteristics. The resulting interactome, comprising 994 interactions between 51 metabolites and 465 proteins, is enriched for known and predicted interactions, supporting the starting premise of this work that integrating different separation methods can assist in constructing protein-metabolite interactomes. Analysis of the protein targets predicted for the different metabolites revealed novel functional insights, such as the association between proteinogenic dipeptides and fatty acid metabolism. Moreover, we identified a novel, inhibitory interaction between riboflavin degradation product lumichrome and de novo pyrimidine synthesis enzyme, orotate phosphoribosyltransferase (pyrE). Lumichrome supplementation inhibited biofilm formation, on par with the known phenotype of ΔpyrE mutant strain. Based on published and our data, we hypothesize that lumichrome functions to integrate pyrimidine and riboflavin metabolism with quorum sensing and biofilm formation.
Question: Write a study description for the study titled 'Seed Metabolome Analysis of a Transgenic Rice Line Expressing Cholera Toxin B-subunit'.
Answer: Rice (Oryza sativa L.) is a candidate crop for production of plant-based vaccines by genetic engineering technologies. MucoRice-CTB has been developed as a rice-seed-based vaccine against cholera by transgenic expression of modified cholera toxin B-subunit (CTB) under the RNA interference (RNAi)-mediated suppression of endogenous seed storage proteins. Here, we performed non-targeted metabolomic profiling of MucoRice-CTB to understand the overall effects of the genetic engineering on rice seed metabolism using gas chromatography/time-of-flight mass spectrometry.
Question: Write a study description for the study titled 'Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection'.
Answer: The metabolic effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on human blood plasma were characterized using multi-platform metabolic phenotyping with Nuclear Magnetic Resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Quantitative measurements of lipoprotein sub-fractions, a-1-acid glycoprotein, glucose and biogenic amines were made on samples from symptomatic coronavirus disease 19 (COVID-19) patients who had tested positive for the SARS-CoV-2 virus  (n = 17) and from age and gender-matched controls (n = 25). Data were analyzed using an orthogonal-projections to latent structures (O-PLS) method and used to construct an exceptionally strong (AUROC=1) hybrid NMR-MS model that enabled detailed metabolic discrimination between the groups and their biochemical relationships. Key discriminant metabolites included markers of inflammation including elevated a-1 acid glycoprotein and an increased kynurenine/tryptophan ratio. There was also an abnormal lipoprotein, glucose and amino acid signature consistent with diabetes and coronary artery disease (low total and HDL Apolipoprotein A1, low HDL triglycerides, high LDL and VLDL triglycerides). Plus, multiple highly significant amino acid markers of liver dysfunction (including the elevated glutamine/glutamate and Fischer’s ratios) that present themselves as part of a distinct SARS-CoV-2 infection pattern. A multivariate training-test set model was validated using independent samples from additional SARS-CoV-2 positive patients and controls. The predictive model showed a sensitivity of 100% for SARS-CoV-2 positivity. The breadth of the disturbed pathways indicates a systemic signature of SARS-CoV-2 positivity that includes elements of liver dysfunction, dyslipidaemia, diabetes, and coronary heart disease risk that are consistent with recent reports that COVID-19 is a systemic disease affecting multiple organs and systems.
Question: Write a study description for the study titled 'Metabolomics of the interaction between PPAR-alpha and age in the PPAR-alpha-null mouse (NMR assay)'.
Answer: Regulation between the fed and fasted state in mammals is partially controlled by peroxisome proliferator activated receptor-alpha (PPAR-alpha). Expression of the receptor is high in liver, heart and skeletal muscle, but decreases with age. A combined 1H NMR spectroscopy and GC-MS metabolomic approach has been used to examine metabolism in liver, heart, skeletal muscle and adipose tissue in PPAR-alpha null mice and wild type controls during ageing between 3-13 months. For the PPAR-alpha-null mouse multivariate statistics highlighted hepatic steatosis, reductions in the concentrations of glucose and glycogen in both liver and muscle tissue, and profound changes in lipid metabolism in each tissue, reflecting known expression targets of the PPAR-alpha receptor. Hepatic glycogen and glucose also decreased with age for both genotypes. These findings indicate the development of age related hepatic steatosis in the PPAR-alpha-null mouse, with the normal metabolic changes associated with ageing exacerbating changes associated with genotype. Furthermore, the combined metabolomic and multivariate statistics approach provides a robust method for examining the interaction between age and genotype.  The GC-MS assay for this study can be found in the MetaboLights study MTBLS314.
Question: Write a study description for the study titled 'A Phosphate starvation response gene (psr1-like) is present in Micromonas pusilla and other marine algae and coordinates the metabolic response to phosphate deficiency'.
Answer: Both marine phytoplankton and terrestrial plants have to deal with limited bioavailability of the key life nutrient, phosphate. In freshwater algae and plants, a phosphate starvation response gene (psr1) has been characterized, which encodes for a transcription factor that regulates the metabolic response to phosphate deficiency. This study describes a psr1-like gene present in Micromonas pusilla and other prasinophytes as well as the haptophyte, Emiliana huxleyi. The metabolic response of M. pusilla to P-deficiency, as described from targeted and untargeted metabolomics techniques, was characteristic of an algal response to nutrient limitation with an increase in polyunsaturated fatty acids. The levels of many central metabolites, such as amino acids, vitamins, nucleosides, decreased in response to P-deficiency, with a few notable exceptions including malate, aspartate, glutamate, guanine and xanthine. Additionally, genes involved in the metabolic pathways associated with the elevated metabolites share a significant motif in their intron regions, which may be the regulatory element where the psr1 gene product binds. Results form the present study taken together with data from the literature suggests that M. pusilla, other prasionophytes and E. huxleyi, may be physiologically well poised to take advantage of a future ocean with lower nutrient levels and increased levels of pCO2.
Question: Write a study description for the study titled 'Palmitic acid-mediated TLR4/NF-κB activation drives the pathogenicity of hypervirulent Bordetella pertussis MT28 lineage'.
Answer: Whooping cough resurged globally despite the widespread vaccination. A macrolide-resistant (MR) lineage carrying the high-virulence ptxP3 allele, ptxP3 MR-MT28 (MT28), has imposed a substantial burden on pertussis epidemics, while the underlying factors driving its prevalence remain unclear. Thus, we performed an epidemiological surveillance and bacterial genomic, phenotypic, in vitro and in vivo pathogenicity analyses. We found MT28 lineage exhibits enhanced abilities of colonization and pro-inflammatory. Transcriptomic analysis revealed significant upregulation of key virulence genes (ptxA, fhaB, tcfA and bvgA), suggesting a molecular basis for its transmission and pathogenicity. Further, lipid-targeted metabolomics and liquid chromatography-mass spectrometry (LC-MS) identified B. pertussis-derived palmitic acid (PA) as a crucial pro-inflammatory mediator that promotes MT28 pathogenicity via the TLR4/NF-κB signaling pathway. These findings elucidate the mechanisms underlying the prevalence and increased pathogenicity of the MT28 lineage, and propose a novel pathogenic mechanism of B. pertussis involving PA-mediated activation of the TLR4/NF-κB inflammatory signaling pathway.
Question: Write a study description for the study titled 'A synthetic antibiotic class with a deeply-optimized design for overcoming bacterial resistance'.
Answer: The lack of new drugs that are effective against antibiotic-resistant bacteria has caused increasing concern in global public health. Based on this study, we report development of a modified antimicrobial drug through structure-based drug design (SBDD) and modular synthesis. The optimal modified compound, F8, was identified, which demonstrated in vitro and in vivo broad-spectrum antibacterial activity against drug-resistant bacteria and effectively mitigated the development of resistance. F8 exhibits significant bactericidal activity against bacteria resistant to antibiotics such as methicillin, polymyxin B, florfenicol (FLO), doxycycline, ampicillin and sulfamethoxazole. In a mouse model of drug-resistant bacteremia, F8 was found to increase survival and significantly reduce bacterial load in infected mice. Multi-omics analysis (transcriptomics, proteomics and metabolomics) have indicated that ornithine carbamoyl transferase (arcB) is a antimicrobial target of F8. Further molecular docking, Isothermal Titration Calorimetry (ITC) and Differential Scanning Fluorimetry (DSF) studies verified arcB as a effective target for F8. Finally, mechanistic studies suggest that F8 competitively binds to arcB, disrupting the bacterial cell membrane and inducing a certain degree of oxidative damage. Here, we report F8 as a promising candidate drug for the development of antibiotic formulations to combat antibiotic-resistant bacteria-associated infections.
Question: Write a study description for the study titled 'Metabolomics Study of Serum and Urine Samples Reveals Metabolic Pathways and Biomarkers Associated with Pelvic Organ Prolapse'.
Answer: Pelvic organ prolapse (POP) is a common medical condition among women and involves complicated diagnostics and controversial surgical management. The exact molecular mechanism underlying POP is poorly understood, especially at the metabolism level. To explore the metabolic mechanism underlying POP and discover potential biomarkers for POP diagnosis, we applied a non-targeted metabolomics approach using ultra-high performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). Metabolomics study of serum samples from patients with POP (n = 24) and controls (n = 22) revealed a total of 59 metabolites that are significantly different (VIP ≥ 1 and p ≤ 0.05) between the two groups. Between urine samples from POP patients (n = 45) and controls (n = 59), 33 metabolites differed significantly (VIP ≥ 1 and p ≤ 0.05). Metabolic pathways affected by these differentially expressed metabolites were analyzed. In both serum and urine samples, three pathways including arginine biosynthesis and purine metabolism were found to be significantly related to POP. Six metabolites including GPC, 1-methyladenosine, maleic acid, L-pyroglutamic acid, inosine, and citrate are significantly changed (VIP ≥ 1 and p ≤ 0.05) in both serum and urine samples from patients with POP. Receiver operating characteristics (ROC) curve analysis showed that using these six metabolites as a biomarker could distinguish patients with POP from controls with good accuracy in both serum (AUC = 1) and urine samples (AUC = 0.854). Collectively, these results further extended our understanding of key regulatory metabolic pathways involved in the pathophysiology of POP, as well as provided some promising biomarkers for effective POP diagnosis.
Question: Write a study description for the study titled 'Virus-encoded glycosyltransferases hypermodify DNA with diverse glycans'.
Answer: Enzymatic modification of DNA nucleobases can coordinate gene expression, nuclease protection or mutagenesis. We recently discovered a clade of phage-specific cytosine methyltransferase (MT) and 5-methylpyrimidine dioxygenase (5mYOX) enzymes that produce 5-hydroxymethylcytosine (5hmC) as a precursor for enzymatic hypermodifications on viral genomes. Here, we identify phage MT- and 5mYOX- associated glycosyltransferases (GTs) that catalyze linkage of diverse sugars to 5hmC nucleobase substrates. Metavirome mining revealed thousands of new biosynthetic gene clusters containing enzymes with predicted roles in cytosine sugar hypermodification. We developed a platform for high-throughput screening of GT- containing pathways, relying on the E. coli metabolome as a substrate pool. We successfully reconstituted several pathways and isolated diverse sugar modifications appended to cytosine, including mono-, di-, or tri-saccharides comprised of hexoses, N-acetylhexosamines or heptose. These findings expand our knowledge of hypermodifications on nucleic acids and the origins of corresponding sugar-installing enzymes.
Question: Write a study description for the study titled 'Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a LTQ-Orbitrap mass spectrometer'.
Answer: This study deals with the annotation of the human adult urinary metabolome and metabolite identification from electrospray-mass spectrometry (ESI-MS) based metabolomics datasets. Metabolite identification was achieved using two complementary approaches: (i) formal identification by matching chromatographic retention times, mass spectra and also product ion spectra (if required) of metabolites to be characterized in biological datasets to those of reference compounds, and, (ii) putative identification from biological data thanks to MS/MS experiments for metabolites not available in our chemical library. By these means, 384 metabolites corresponding to 1484 annotated features (659 in negative ion mode and 825 in positive ion mode) were characterized in human urine samples. Of these metabolites, 191 and 67 were formally and putatively identified, respectively.