LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Comprehensive evaluation of untargeted metabolomics data processing software in feature detection, quantification and discriminating marker selection'.
Answer: Data analysis represents a key challenge for untargeted metabolomics studies and it commonly requires extensive processing of more than thousands of metabolite peaks included in raw high-resolution MS data. Although a number of software packages have been developed to facilitate untargeted data processing, they have not been comprehensively scrutinized in the capability of feature detection, quantification and marker selection using a well-defined benchmark sample set. In this study, we acquired a benchmark dataset from standard mixtures consisting of 1100 compounds with specified concentration ratios including 130 compounds with significant variation of concentrations. Five software evaluated here (MS-Dial, MZmine 2, XCMS, MarkerView, and Compound Discoverer) showed similar performance in detection of true features derived from compounds in the mixtures. However, significant differences between untargeted metabolomics software were observed in relative quantification of true features in the benchmark dataset. MZmine 2 outperformed the other software in terms of quantification accuracy and it reported the most true discriminating markers together with the fewest false markers. Furthermore, we assessed selection of discriminating markers by different software using both the benchmark dataset and a real-case metabolomics dataset to propose combined usage of two software for increasing confidence of biomarker identification. Our findings from comprehensive evaluation of untargeted metabolomics software would help guide future improvements of these widely used bioinformatics tools and enable users to properly interpret their metabolomics results.
Question: Write a study description for the study titled 'Altered metabolome and microbiome features provide clues in understanding irritable bowel syndrome and depression comorbidity'.
Answer: Irritable bowel syndrome (IBS) is one of the functional gastrointestinal disorders characterized by chronic and/or recurrent symptoms of abdominal pain and irregular defecation. Changed gut microbiota has been proposed to mediate IBS; however, contradictory results exist, and IBS-specific microbiota, metabolites, and their interactions remain poorly understood. To address this issue, we performed metabolomic and metagenomic profiling of stool and serum samples based on discovery (n = 330) and validation (n = 101) cohorts. Fecal metagenomic data showed moderate dysbiosis compared with other diseases, in contrast, serum metabolites showed significant differences with greater power to distinguish IBS patients from healthy controls. Specifically, 726 differentially abundant serum metabolites were identified, including a cluster of fatty acyl-CoAs enriched in IBS. We further identified 522 robust associations between differentially abundant gut bacteria and fecal metabolites, of which three species including Odoribacter splanchnicus, Escherichia coli, and Ruminococcus gnavus were strongly associated with the low abundance of dihydropteroic acid. Moreover, dysregulated tryptophan/serotonin metabolism was found to be correlated with the severity of IBS depression in both fecal and serum metabolomes, characterized by a shift in tryptophan metabolism towards kynurenine production. Collectively, our study revealed serum/fecal metabolome alterations and their relationship with gut microbiome, highlighted the massive alterations of serum metabolites, which empower to recognize IBS patients, suggested potential roles of metabolic dysregulation in IBS pathogenesis, and offered new clues to understand IBS depression comorbidity. Our study provided a valuable resource for future studies, and would facilitate potential clinical applications of IBS featured microbiota and/or metabolites.
Question: Write a study description for the study titled 'Mechanisms of hepatic steatosis in chickens: integrated analysis of the host genome, molecular phenomes and gut microbiome'.
Answer: Hepatic steatosis is the initial manifestation of abnormal liver functions and often leads to liver diseases such as non-alcoholic fatty liver disease in humans and fatty liver syndrome in animals. In this study, we conducted a comprehensive analysis of a large chicken population consisting of 705 adult hens by combining host genome resequencing, liver transcriptome, proteome and metabolome analysis, as well as microbial 16S rRNA gene sequencing of each gut segment. The results showed the heritability (h2 = 0.25) and duodenal microbiability (m2 = 0.26) of hepatic steatosis were relatively high, indicating a large effect of host genetics and duodenal microbiota on chicken hepatic steatosis. Individuals with hepatic steatosis had low microbiota diversity and a decreased genetic potential to process triglyceride output from hepatocytes, fatty acid β-oxidation activity and resistance to fatty acid peroxidation. Furthermore, we revealed a molecular network linking host genomic variants (GGA6: 5.59-5.69 Mb), hepatic gene/protein expression (PEMT, phosphatidyl-ethanolamine N-methyltransferase), metabolite abundances (folate, S-adenosylmethionine, homocysteine, phosphatidyl-ethanolamine and phosphatidylcholine) and duodenal microbes (genus Lactobacillus) to hepatic steatosis, which could provide new insights into the regulatory mechanism of fatty liver development.
Question: Write a study description for the study titled 'Changes in the Milk Metabolome of the Giant Panda (Ailuropoda melanoleuca) with Time after Birth – Three Phases in Early Lactation and Progressive Individual Differences'.
Answer: Ursids (bears) in general, and giant pandas in particular, are highly altricial at birth. The components of bear milks and their changes with time may be uniquely adapted to nourish relatively immature neonates, protect them from pathogens, and support the maturation of neonatal digestive physiology. Serial milk samples collected from three giant pandas in early lactation were subjected to untargeted metabolite profiling and multivariate analysis. Changes in milk metabolites with time after birth were analysed by Principal Component Analysis, Hierarchical Cluster Analysis and further supported by Orthogonal Partial Least Square-Discriminant Analysis, revealing three phases of milk maturation: days 1–6 (Phase 1), days 7–20 (Phase 2), and beyond day 20 (Phase 3). While the compositions of Phase 1 milks were essentially indistinguishable among individuals, divergences emerged during the second week of lactation. OPLS regression analysis positioned against the growth rate of one cub tentatively inferred a correlation with changes in the abundance of a trisaccharide, isoglobotriose, previously observed to be a major oligosaccharide in ursid milks. Three artificial milk formulae used to feed giant panda cubs were also analysed, and were found to differ markedly in component content from natural panda milk. These findings have implications for the dependence of the ontogeny of all species of bears, and potentially other members of the Carnivora and beyond, on the complexity and sequential changes in maternal provision of micrometabolites in the immediate period after birth.
Question: Write a study description for the study titled 'Subcellular antibiotic visualization reveals a dynamic drug reservoir in infected macrophages'.
Answer: Tuberculosis, caused by the intracellular pathogen Mycobacterium tuberculosis, remains the world's deadliest infectious disease. Sterilizing chemotherapy requires at least 6 months of multidrug therapy. Difficulty visualizing the subcellular localization of antibiotics in infected host cells means that it is unclear whether antibiotics penetrate all mycobacteria-containing compartments in the cell. Here, we combined correlated light, electron, and ion microscopy to image the distribution of bedaquiline in infected human macrophages at submicrometer resolution. Bedaquiline accumulated primarily in host cell lipid droplets, but heterogeneously in mycobacteria within a variety of intracellular compartments. Furthermore, lipid droplets did not sequester antibiotic but constituted a transferable reservoir that enhanced antibacterial efficacy. Thus, strong lipid binding facilitated drug trafficking by host organelles to an intracellular target during antimicrobial treatment.
Question: Write a study description for the study titled 'Postoperative Metabolic Phenoreversion in Clear Cell Renal Cell Carcinoma'.
Answer: The ultimate goal of surgical treatment in cancer is to remove the tumor mass for restoring a healthy state. A 16-lipid panel that discriminated healthy controls from clear cell renal cell carcinoma (ccRCC) patients in a prior study was evaluated in the present work in paired-serum samples collected from patients (n = 41) before and after nephrectomy. Changes in the lipid and metabolite fingerprints from ccRCC patients were investigated and compared with fingerprints from healthy individuals obtained by means of ultra-performance liquid chromatography-high-resolution mass spectrometry. The lipid panel differentiated phenotypes associated with metabolic restoration after surgery, representing a serum signature of phenoreversion to a healthy metabolic state. In particular, PC 16:0/0:0, PC 18:2/18:2 and linoleic acid allowed discriminating serum samples from ccRCC patients with poor prognosis from those with an improved outcome during the follow-up period. Ratios of PC 16:0/0:0 and PC 18:2/18:2 with linoleic acid levels may contribute as prognostic tools to support decision-making during the patient follow-up care. The preliminary character of these results should be validated with larger cohorts, including subjects with different ethnicities, life style and diets.
Question: Write a study description for the study titled 'Metabolomic Microbiome Modulations Induced by ZIF8@ZIF67 Supplementation in the Midgut of Bombyx mori'.
Answer: Bombyx mori is an economically crucial lepidopteran insect, and its health is closely related to the gut microbiota and metabolic status. Our previous research confirmed that metal organic frameworks nanocomposite ZIF8@ZIF67 supplementation can significantly enhance silkworm survival rates upon bacterial challenges without adversely affecting its growth or cocoon weight. To elucidate the mechanism, this study integrated non targeted metabolomics and 16S rRNA sequencing to dissect ZIF8@ZIF67 driven midgut modulations. The results showed that ZIF8@ZIF67 supplementation led to significant metabolic shifts in the midgut of B. mori, with 96 metabolites up-regulated and 54 down-regulated in the negative ion model and 117 up regulated and 43 down regulated in the positive ion model. Key pathways included glutathione metabolism, purine/pyrimidine metabolism and histidine metabolism, which are involved in antioxidant defense, nucleotide and protein synthesis for growth and immunity regulation. Furthermore, the gut microbiota composition of B. mori was significantly altered after ZIF8@ZIF67 supplementation, with a marked increase in the relative abundance of Mammaliicoccus and Enterococcus. Lastly, the correlation between metabolites and microbiomes was analyzed, including Enterococcus and 1_methylhistidine (r=0.8895, P=0.0001), Akkermansia and N_acetyl_d_galactosamine (r=0.8674, P=0.0003). These findings demonstrated that ZIF8@ZIF67 could optimize silkworm health by orchestrating metabolite-microbe interactions to enhance nutrient assimilation and oxidative stress resilience, while simultaneously activating pathways essential for growth regulation and immune function.
Question: Write a study description for the study titled 'The use of metabolomics to monitor simultaneous changes in metabolic variables following supramaximal low volume high intensity exercise'.
Answer: High intensity exercise (HIE) stimulates greater physiological remodeling when compared to workload matched low-moderate intensity exercise. This study utilized an untargeted metabolomics approach to examine the metabolic perturbations that occur following two workload matched supramaximal low volume HIE trials. In a randomized order, 7 untrained males completed two exercise protocols separated by 1 week; (1) HIE150%: 30 x 20 s cycling at 150% VO2peak, 40 s passive rest; (2) HIE300%: 30 x 10 s cycling at 300% VO2peak, 50 s passive rest. Total exercise duration was 30 min for both trials. Blood samples were taken at rest, during and immediately following exercise and at 60 min post exercise. Gas chromatography-mass spectrometry analysis of plasma identified 43 known metabolites of which 3 demonstrated significant fold changes (HIE300% compared to the HIE150% value) during exercise, 14 post exercise and 23 at the end of the recovery period. Significant changes in plasma metabolites relating to lipid metabolism [fatty acids: dodecanoate (p=0.042), hexadecanoate (p=0.001), octadecanoate (p=0.001)], total cholesterol (p=0.001), and glycolysis [lactate (p=0.018)] were observed following exercise and during the recovery period. The HIE300% protocol elicited greater metabolic changes relating to lipid metabolism and glycolysis when compared to HIE150% protocol. These changes were more pronounced throughout the recovery period rather than during the exercise bout itself. Data from the current study demonstrate the use of metabolomics to monitor intensity-dependent changes in multiple metabolic pathways following exercise. The small sample size indicates a need for further studies in a larger sample cohort to validate these findings.
Question: Write a study description for the study titled 'Bacteria encode their own post-mortem protein catabolism to enable nutrient recycling'.
Answer: For many organisms, death is a tangible, visible event. In bacteria, death can be a natural or an induced process 1. Death permits genes conferring a survival advantage to be selected in a bacterial population. Furthermore, biomolecule recycling from dead bacteria is crucial under nutrient limitation across ecosystems 2. However, the underlying mechanisms that permit macromolecule recycling after bacterial death are largely unknown. Here, we show that bacteria encode their own post-mortem protein catabolism. We observed that live bacteria cannot recycle the lysates of dead bacteria from which the Lon protease-encoding lon gene is deleted. The nutrient recycling function of the Lon protease manifests itself after the death of the bacteria that produced it and is ATP-independent. We demonstrate that the post-mortem Lon protease is a cooperative trait susceptible to exploitation by cheating 3. However, we propose that, in addition to a kin selected benefit of helping related cells, the fitness benefit of cheating is outweighed by the fitness benefit of producing Lon protease under stress. This finding of an unexpected post-mortem biochemistry fundamentally revises our understanding of the nutrient recycling process. Further, we suggest a solution to an evolutionary puzzle of how a phenotype that manifests after death can exist in a population. Nutrient recycling is a vital aspect of all ecosystems, and our results demonstrate a potential new molecular target for modulating bacterial growth that does not directly target the live bacteria.
Question: Write a study description for the study titled 'Improvement of prediction ability by integrating multi-omic datasets in barley'.
Answer: BACKGROUND: Genomic prediction (GP) based on single nucleotide polymorphisms (SNP) has become a broadly used tool to increase the gain of selection in plant breeding. However, using predictors that are biologically closer to the phenotypes such as transcriptome and metabolome may increase the prediction ability in GP. The objectives of this study were to (i) assess the prediction ability for three phenotypic traits using different omic datasets including sequence variants (SV), deleterious SV (dSV), tolerant SV (tSV), expression presence/absence variation (ePAV), gene expression (GE), transcript expression (TE), and metabolites (M) as single predictors in comparison to those using a SNP array; (ii) investigate the improvement in prediction ability when combining multiple omic datasets information to predict phenotypic variation in barley breeding programs; (iii) explore the relationship between genes and metabolites to unravel the metabolic pathway of the three above mentioned phenotypic traits.RESULTS: The prediction ability from genomic best linear unbiased prediction (GBLUP) for the three traits using dSV information was higher than when using tSV, all SV information, or the SNP array. Any predictors from the transcriptome (GE, TE, as well as ePAV) and metabolome provided higher prediction abilities compared to the SNP array and SV on average across the three traits. In addition, some (di)-similarity existed between different omic datasets, and therefore provided complementary biological perspectives to phenotypic variation. Optimal combining the information of dSV, TE, ePAV, as well as metabolites into GP models could improve the prediction ability over that of the single predictors alone.CONCLUSIONS: The use of integrated omic datasets in GP model is highly recommended. Furthermore, we evaluated a cost-effective approach generating 3’end mRNA sequencing with transcriptome data extracted from seedling without losing prediction ability in comparison to the full-length mRNA sequencing, paving the path for the use of such prediction methods in commercial breeding programs.
Question: Write a study description for the study titled 'The Bardet-Biedl protein Bbs1 controls photoreceptor outer segment protein and lipid composition'.
Answer: SummaryPrimary cilia are key sensory organelles whose dysfunction leads to ciliopathy disorders such as Bardet-Biedl syndrome (BBS). Retinal degeneration is common in ciliopathies, since the outer segments (OSs) of photoreceptors are highly specialized primary cilia. BBS1, encoded by the most commonly mutated BBS-associated gene, is part of the BBSome protein complex. Using a new bbs1 zebrafish mutant, we show that retinal development and photoreceptor differentiation are unaffected by Bbs1-loss, supported by an initially unaffected transcriptome. Quantitative proteomics and lipidomics on isolated OSs show that Bbs1 is required for BBSome-entry into OSs and that Bbs1-loss leads to accumulation of membrane-associated proteins in OSs, with enrichment in proteins involved in lipid homeostasis. Disruption of the tightly regulated OS lipid composition with increased OS cholesterol content are paralleled by early functional visual deficits, which precede progressive OS morphological anomalies. Our findings identify a new role for Bbs1/BBSome in OS lipid homeostasis and suggest a new pathomechanism underlying retinal degeneration in BBS.Data availability:The proteomic data generated in this study have been deposited in PRIDE repository under accession code PXD026646 for the OS proteome and PXD030522 for the whole eye lysate proteome [https://www.ebi.ac.uk/pride].The RNAseq data generated in this study have been deposited in the SRA repository under the BioProject accession number PRJNA789116 [https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA789116].
Question: Write a study description for the study titled 'A Randomized Controlled Trial of Shengji Ointment Combined with Bromelain in Promoting Healing of Tendon-Exposed Diabetic Foot Wounds: Metabolomics Profiling Analysis'.
Answer:  Background: Diabetic foot tendon exposures are prone to infection, necrosis, and prolonged treatment cycles, not only hindering wound healing but potentially leading to amputation and life-threatening complications. Shengji ointment combined with bromelain has demonstrated preliminary efficacy in treating these wounds, but its mechanisms of action and impact on wound metabolites require further investigation. Methods: Thirty patients with diabetic foot tendon exposure wounds received four-week treatment with Shengji ointment combined with bromelain. Clinical outcomes including granulation tissue coverage and wound healing rates were evaluated. Wound exudates collected pretreatment and posttreatment underwent metabolomics analysis to characterize treatment-induced metabolic changes. Results: Following treatment, significant improvements were observed in granulation tissue coverage and wound healing rates compared to pretreatment baseline. Metabolomic profiling identified 4034 differential metabolites (1907 upregulated, 2127 downregulated), revealing significant alterations in key metabolic pathways including phenylpropanoid biosynthesis, tyrosine metabolism, and amino acid biosynthesis pathways. Conclusion: Shengji ointment combined with bromelain effectively promotes healing of diabetic foot wounds with tendon exposure through significant modulation of the wound metabolic environment, particularly via regulation of critical metabolic pathways. These metabolomics findings provide mechanistic insights supporting this treatment approach.
Question: Write a study description for the study titled 'Nicotinamide Riboside is Uniquely Bioavailable in People and Mice'.
Answer: Nicotinamide riboside (NR) is in wide use as an NAD+ precursor vitamin. Here we conducted experiments to determine the time and dose-dependent effects of NR on blood, liver and heart NAD+ metabolism in people and mice. We report that human blood cell NAD+ can rise as much as 2.7-fold with a single dose of NR, that NR elevates mouse hepatic NAD+ with distinct and superior pharmacokinetics to those of nicotinic acid (NA) and nicotinamide (Nam), and that single doses of 100, 300, and 1000 mg of NR provide a dose-dependent increase in the blood cell NAD+ metabolome in the first clinical trial of NR pharmacokinetics. We also report that nicotinic acid adenine dinucleotide (NAAD), which was not thought to be en route for conversion of NR to NAD+, is formed from NR and that the rise in NAAD is a highly sensitive biomarker of effective NAD+ supplementation.
Question: Write a study description for the study titled 'Metabolomic signatures discriminate horses with clinical signs of atypical myopathy from healthy co-grazing horses'.
Answer: Atypical myopathy (AM) is a severe rhabdomyolysis syndrome that occurs in grazing horses. Despite the presence of toxins in their blood, all horses from the same pasture are not prone to display clinical signs of AM. The objective of this study was to compare the blood metabolomic profiles of horses with AM clinical signs with those of healthy co-grazing (Co-G) horses. To do so, plasma samples from 5 AM horses and 11 Co-G horses were investigated using untargeted metabolomics. Metabolomic data were evaluated using unsupervised, supervised, and pathway analyses. Unsupervised principal component analysis performed with all detected features separated AM and healthy Co-G horses. Supervised analyses had identified 1276 features showing differential expression between both groups. Among them, 46 metabolites, belonging predominantly to the fatty acid, fatty ester, and amino acid chemical classes, were identified by standard comparison. Fatty acids, unsaturated fatty acids, organic dicarboxylic acids, and fatty esters were detected with higher intensities in AM horses in link with the toxins' pathological mechanism. The main relevant pathways were lipid metabolism; valine, leucine, and isoleucine metabolism; and glycine metabolism. This study revealed characteristic metabolite changes in the plasma of clinically affected horses, which might ultimately help scientists and field veterinarians to detect and manage AM. The raw data of metabolomics are available in the MetaboLights database with the access number MTBLS2579.