LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Identification and validation of poly-metabolite scores for diets high in ultra-processed food: An observational study and post-hoc randomized controlled crossover-feeding trial.'.
Answer: BACKGOUND: Ultra-processed food (UPF) accounts for a majority of calories consumed in the United States, but the impact on human health remains unclear. We aimed to identify poly-metabolite scores in blood and urine that are predictive of UPF intake.METHODS AND FINDINGS: Of the 1082 Interactive Diet and Activity Tracking in AARP (IDATA) Study (clinicaltrials.gov ID NCT03268577) participants, aged 50-74 years, who provided biospecimen consent, n=718 with serially collected blood and urine and one to six 24-hour dietary recalls (ASA-24s), collected over 12-months, met eligibility criteria and were included in the metabolomics analysis. Ultra-high performance liquid chromatography with tandem mass spectrometry was used to measure >1000 serum and urine metabolites. Average daily UPF intake was estimated as percentage energy according to the Nova system. Partial Spearman correlations and Least Absolute Shrinkage and Selection Operator (LASSO) regression were used to estimate UPF-metabolite correlations and build poly-metabolite scores of UPF intake, respectively. Scores were tested in a previously conducted randomized, controlled, crossover-feeding trial (clinicaltrials.gov ID NCT03407053) of 20 subjects who were admitted to the NIH Clinical Center and randomized to consume ad libitum diets that were 80% or 0% energy from UPF for 2 weeks immediately followed by the alternate diet for 2 weeks; eligible subjects were between 18-50 years old with a body mass index of >18.5 kg/m2 and weight-stable. IDATA participants were 51% female, and 97% completed 4 ASA-24s. Mean intake was 50% energy from UPF. UPF intake was correlated with 191 (of 952) serum and 293 (of 1044) 24-hour urine metabolites (FDR-corrected P-value < 0.01), including lipid (n=56 serum, n=22 24-hour urine), amino acid (n=33, 61), carbohydrate (n=4, 8), xenobiotic (n=33, 70), cofactor and vitamin (n= 9, 12), peptide (n=7, 6), and nucleotide (n=7, 10) metabolites. Using LASSO regression, 28 serum and 33 24-hour urine metabolites were selected as predictors of UPF intake; biospecimen-specific scores were calculated as a linear combination of selected metabolites. Overlapping metabolites included (S)C(S)S-S-methyl cysteine sulfoxide (rs= -0.19, -0.23), N2-N5-diacetylornithine (rs= -0.26, -0.27), pentoic acid (rs= -0.28, -0.31), and N6-carboxymethyllysine (rs=0.15, 0.21). Within the cross-over feeding trial, the poly-metabolite scores differed, within individual, between UPF diet phases (P-value for paired t-test <0.001). IDATA Study participants were older US adults whose diets may not be reflective of other populations.CONCLUSIONS: Poly-metabolite scores, developed in IDATA participants with varying diets, are predictive of UPF intake and could advance epidemiological research on UPF and health. Poly-metabolite scores should be evaluated and iteratively improved in populations with a wide range of UPF intake.
Question: Write a study description for the study titled 'Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms'.
Answer: Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars), wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomics and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g., glycolate) and fermentation (e.g., acetate, propionate, and lactate) products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gasses (e.g., H2 and CO2) in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: (1) the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; (2) photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; (3) glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and (4) fluctuations in many metabolite pools (e.g., waxesters) at different times of day result from species found at different depths within the mat responding to temporal differences in their niches.
Question: Write a study description for the study titled 'Oral Engineered Microalgae- Biosystem Targeting Intestinal Villi for Irritable Bowel Syndrome'.
Answer: Irritable Bowel Syndrome (IBS) is a chronic gastrointestinal disorder associated with dysregulation of the gut-brain axis. Current treatment approaches often lack long-term efficacy and target specificity, and there are no drugs or formulations specifically targeting this disease. Owing to chronic and intermittent gastrointestinal motility disturbances, the pharmacokinetic parameters of IBS patients change significantly. In this research, we develop an oral engineered microalgae biosystem by integrating microalgae with myricetin nanoparticles to enhance the treatment of IBS. After cultivation and micro-nano transformation, the engineered microalgae can be captured by intestinal villi and remained attached. The nano-coating further enhances the adhesion to intestinal tissue and resistance to gastric acid. Ultimately, this biosystem addresses the pharmacokinetic complications in IBS that are not resolvable by enteric-coated capsules. Interestingly, microalgae seem to exert their prebiotic potential, assisting myricetin in increasing short-chain fatty acids levels and further regulating IBS multi-organ symptoms comprehensively through the gut-brain axis.
Question: Write a study description for the study titled 'A Murine Model of Maternal Micronutrient Deficiencies and Gut Inflammatory Host-microbe Interactions in the Offspring.'.
Answer: BACKGROUND & AIMS: Micronutrient deficiency (MND) (ie, lack of vitamins and minerals) during pregnancy is a major public health concern. Historically, studies have considered micronutrients in isolation; however, MNDs rarely occur alone. The impact of co-occurring MNDs on public health, mainly in shaping mucosal colonization by pathobionts from the Enterobacteriaceae family, remains undetermined due to lack of relevant animal models.METHODS: To establish a maternal murine model of multiple MND (MMND), we customized a diet deficient in vitamins (A, B12, and B9) and minerals (iron and zinc) that most commonly affect children and women of reproductive age. Thereafter, mucosal adherence by Enterobacteriaceae, the associated inflammatory markers, and proteomic profile of intestines were determined in the offspring of MMND mothers (hereafter, low micronutrient [LM] pups) via bacterial plating, flow cytometry, and mass spectrometry, respectively. For human validation, Enterobacteriaceae abundance, assessed via 16s sequencing of 3-month-old infant fecal samples (n = 100), was correlated with micronutrient metabolites using Spearman's correlation in meconium of children from the CHILD birth cohort.RESULTS: We developed an MMND model and reported an increase in colonic abundance of Enterobacteriaceae in LM pups at weaning. Findings from CHILD cohort confirmed a negative correlation between Enterobacteriaceae and micronutrient availability. Furthermore, pro-inflammatory cytokines and increased infiltration of lymphocyte antigen 6 complex high monocytes and M1-like macrophages were evident in the colons of LM pups. Mechanistically, mitochondrial dysfunction marked by reduced expression of nicotinamide adenine dinucleotide (NAD)H dehydrogenase and increased expression of NAD phosphate oxidase (Nox) 1 contributed to the Enterobacteriaceae bloom.CONCLUSION: This study establishes an early life MMND link to intestinal pathobiont colonization and mucosal inflammation via damaged mitochondria in the offspring.
Question: Write a study description for the study titled 'Co-Housed Mice Reveal the Tumor-Promoting Potential of Akkermansia muciniphila'.
Answer: Specific pathogen-free laboratory mice are widely used in biomedical research; however, their neonatal-like physiological state often limits their ability to model adult human conditions. Here, we induced adult-like physiological characteristics in laboratory mice by co-housing them with naturally raised mice obtained from pet stores. Co-housing resulted in significant changes in the gut microbiota composition and a marked suppression of tumor growth in multiple tissues. We discovered reduction in Akkermansia muciniphila was a contributing factor to the observed tumor suppression. Furthermore, decreased serum indole metabolite levels were linked to both Akkermansia muciniphila and the tumor-suppressive effects. These findings suggest that Akkermansia muciniphila may, under certain situations, be tumor-promoting and highlight the value of using adult-like mouse models in uncovering critical environmental factors in cancer and other health conditions.
Question: Write a study description for the study titled 'An Unbiased Lipid Phenotyping Approach To Study the Genetic Determinants of Lipids and Their Association with Coronary Heart Disease Risk Factors'.
Answer: Direct infusion high-resolution mass spectrometry (DIHRMS) is a novel, high-throughput approach to rapidly and accurately profile hundreds of lipids in human serum without prior chromatography, facilitating in-depth lipid phenotyping for large epidemiological studies to reveal the detailed associations of individual lipids with coronary heart disease (CHD) risk factors. Intact lipid profiling by DIHRMS was performed on 5662 serum samples from healthy participants in the Pakistan Risk of Myocardial Infarction Study (PROMIS). We developed a novel semi-targeted peak-picking algorithm to detect mass-to-charge ratios in positive and negative ionization modes. We analyzed lipid partial correlations, assessed the association of lipid principal components with established CHD risk factors and genetic variants, and examined differences between lipids for a common genetic polymorphism. The DIHRMS method provided information on 360 lipids (including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, and sterol lipids), with a median coefficient of variation of 11.6% (range: 5.4-51.9). The lipids were highly correlated and exhibited a range of associations with clinical chemistry biomarkers and lifestyle factors. This platform can provide many novel insights into the effects of physiology and lifestyle on lipid metabolism, genetic determinants of lipids, and the relationship between individual lipids and CHD risk factors.
Question: Write a study description for the study titled 'MaHPIC Experiment 04: Metabolomics from Macaca mulatta infected with Plasmodium cynomolgi B strain to produce and integrate clinical, hematological, parasitological, and omics measures of acute primary infection and relapses'.
Answer: Malaria-naive male rhesus macaques (Macaca mulatta), approximately three years of age, were inoculated intravenously with salivary gland sporozoites produced and isolated at the Centers for Disease Control and Prevention from multiple Anopheles species (An. dirus, An. gambiae, and An. stephensi) and then profiled for clinical, hematological, parasitological, immunological, functional genomic, lipidomic, proteomic, and metabolomic measurements. The experiment was designed for 100 days, and pre- and post-100 day periods to prepare subjects and administer curative treatments respectively. The anti-malarial drug artemether was subcuratively administered selectively to several subjects during the primary parasitemia to suppress clinical complications and to all animals for curative treatment of blood-stage infections to allow detection of relapses. One subject was euthanized during the 100-day experimental period due to clinical complications. The anti-malarial drugs primaquine and chloroquine were administered to all remaining subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively. Capillary blood samples were collected daily for the measurement of CBCs, reticulocytes, and parasitemias. Capillary blood samples were collected every other day to obtain plasma for metabolomic analysis. Venous blood and bone marrow samples were collected at seven time points for functional genomic, proteomic, lipidomic, and immunological analyses. Within the MaHPIC, this project is known as Experiment 04. This dataset was produced by Dean Jones at Emory University.To access other publicly available results from E04 and other MaHPIC Experiments, including clinical results (specifics on drugs administered, diet, and veterinary interventions), and other omics, visit http://plasmodb.org/plasmo/mahpic.jsp This page will be updated as datasets are released to the public. The experimental design and protocols for this study were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).Linked Studies: Malaria Host-Pathogen Interaction Center (MaHPIC)
Question: Write a study description for the study titled '1H NMR based urinary metabolites profiling dataset of canine mammary tumors'.
Answer: The identification of efficient and sensitive biomarkers for non-invasive tests is one of the major challenges in cancer diagnosis. To address this challenge, metabolomics is widely applied for identifying biomarkers that detects abnormal changes in cancer patients. Canine mammary tumors exhibit physiological characteristics identical to those in human breast cancer and serve as a useful animal model to conduct breast cancer research. Here, we aimed to provide a reliable large-scale metabolite dataset collected from dogs with mammary tumors, using proton nuclear magnetic resonance spectroscopy. We identified 55 metabolites in urine samples from 20 benign, 87 malignant, and 49 healthy control subjects. This dataset provides details of mammary tumor-specific metabolites in dogs and insights into cancer-specific metabolic alterations that share similar molecular characteristics.
Question: Write a study description for the study titled 'Lipid-accumulated reactive astrocytes promote disease progression in epilepsy (Human lipidomics)'.
Answer: Reactive astrocytes play an important role in neurological diseases, but their molecular and functional phenotypes in epilepsy are unclear. Here, we show that in patients with temporal lobe epilepsy (TLE) and mouse models of epilepsy, excessive lipid accumulation in astrocytes leads to the formation of lipid-accumulated reactive astrocytes (LARAs), a new reactive astrocyte subtype characterized by elevated APOE expression. Genetic knockout of APOE inhibited LARA formation and seizure activities in epileptic mice. Single-nucleus RNA sequencing in TLE patients confirmed the existence of a LARA subpopulation with a distinct molecular signature. Functional studies in epilepsy mouse models and human brain slices showed that LARAs promote neuronal hyperactivity and disease progression. Targeting LARAs by intervention with lipid transport and metabolism could thus provide new therapeutic options for drug-resistant TLE.Human lipidomics is reported in the current study MTBLS8856.Mice lipidomics reported in MTBLS8865.
Question: Write a study description for the study titled 'Innate Immune Training of Human Macrophages by Cathelicidin Analogs'.
Answer: Trained innate immunity can be induced in human macrophages by microbial ligands, but it is unknown if exposure to endogenous alarmins such as cathelicidins can have similar effects. Previously, we demonstrated sustained protection against infection by the chicken cathelicidin-2 analog DCATH-2. Thus, we assessed the capacity of cathelicidins to induce trained immunity. PMA23 differentiated THP-1 (dTHP1) cells were trained with cathelicidin analogs for 24 hours, and restimulated after a 3-day rest period. DCATH-2 training of dTHP-1 cells amplified their proinflammatory cytokine response when restimulated with TLR2/4 agonists. Trained cells displayed a biased cellular metabolism towards mTOR-dependent aerobic glycolysis and long-chain fatty acid accumulation and augmented microbicidal activity. DCATH-2-induced trained immunity was inhibited by histone acetylase inhibitors, suggesting epigenetic regulation, and depended on caveolae/lipid raft-mediated uptake, MAPK p38 and purinergic signaling. To our knowledge, this is the first report of trained immunity by host defense peptides.
Question: Write a study description for the study titled 'Piriformospora indica stimulates root metabolism of Arabidopsis thaliana'.
Answer: Piriformospora indica is a root-colonizing fungus, which interacts with a variety of plants including Arabidopsis thaliana. This interaction has been considered as mutualistic, as it leads to an increased mycelia dry weight and increased shoot fresh weight, respectively. So far, only indolic glucosinolates and phytohormones have been identified as major key players. In a comprehensive non-targeted metabolite profiling study by means of UPLC/ESI-QTOFMS and GC/EI-QMS we analyzed Arabidopsis thaliana’s roots, root exudates, and leaves of inoculated and non-inoculated plants and identified further biomarkers. Among them, the concentration of nucleosides, dipeptides, oligolignols, and glucosinolate degradation products was affected in the exudates. In the root profiles, nearly all metabolite levels increased upon co-cultivation, namely those of carbohydrates, organic acids, amino acids, glucosinolates, oligolignols, and flavonoids. In the leaf profiles, we detected by far less significant changes. We only observed an increased concentration in organic acids, carbohydrates, ascorbate, glucosinolates and hydroxycinnamic acids, and a decreased concentration in nitrogen-rich amino acids in inoculated plants.
Question: Write a study description for the study titled 'Comprehensive Metabolic Profiling of Age-Related Mitochondrial Dysfunction in the High-Fat-Fed ob/ob Mouse Heart'.
Answer: The ectopic deposition of fat is thought to lead to lipotoxicity and has been associated with mitochondrial dysfunction and diabetic cardiomyopathy. We have measured mitochondrial respiratory capacities in the hearts of ob/ob and wild-type mice on either a regular chow (RCD) or high-fat (HFD) diet across four age groups to investigate the impact of diet and age on mitochondrial function alongside a comprehensive strategy for metabolic profiling of the tissue. Myocardial mitochondrial dysfunction was only evident in ob/ob mice on RCD at 14 months, but it was detectable at 3 months on the HFD. Liquid chromatography–mass spectrometry (LC–MS) was used to study the profiles of acylcarnitines and the accumulation of triglycerides, but neither class of lipid was associated with mitochondrial dysfunction. However, a targeted LC–MS/MS analysis of markers of oxidative stress demonstrated increases in GSSG/GSH and 8-oxoguanine, in addition to the accumulation of diacylglycerols, which are lipid species linked to lipotoxicity. Our results demonstrate that myocardial mitochondria in ob/ob mice on RCD maintained a similar respiratory capacity to that of wild type until a late stage in aging. However, on a HFD, unlike wild-type mice, ob/ob mice failed to increase mitochondrial respiration, which may be associated with a complex I defect following increased oxidative damage.
Question: Write a study description for the study titled 'Brain metabolomic profiling of eastern honey bee (Apis cerana) infested with the mite Varroa destructor'.
Answer: The mite Varroa destructor is currently the greatest threat to apiculture as it is causing a global decrease in honey bee colonies. However, it rarely causes serious damage to its native hosts, the eastern honey bees Apis cerana. To better understand the mechanism of resistance of A. cerana against the V. destructor mite, we profiled the metabolic changes that occur in the honey bee brain during V. destructor infestation. Brain samples were collected from infested and control honey bees and then measured using an untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based global metabolomics method, in which 7918 and 7462 ions in ESI+ and ESI- mode, respectively, were successfully identified. Multivariate statistical analyses were applied, and 64 dysregulated metabolites, including fatty acids, amino acids, carboxylic acid, and phospholipids, amongst others, were identified. Pathway analysis further revealed that linoleic acid metabolism; propanoate metabolism; and glycine, serine, and threonine metabolism were acutely perturbed. The data obtained in this study offer insight into the defense mechanisms of A. cerana against V. destructor mites and provide a better method for understanding the synergistic effects of parasitism on honey bee colonies.
Question: Write a study description for the study titled 'The rumen metagenome and its metabolome in yaks associated with feeding regime'.
Answer: Background: Grazing yearly on pasture is a traditional practice for yaks, which cannot meet the requirements of yak products since the insufficient forage supplied in the cold season results in a long production cycle. An intensive feeding system increasing production efficiency has been selected for beef and dairy cattle. However, its impacts on yaks are less studied, and it is unclear how the rumen microbiome, rumen metabolites and the host metabolome respond to an intensive feeding system and contribute to yak growth. Here, multi-omics, including rumen metagenomics, rumen and plasma metabolomics, were performed to classify the effects and regulatory mechanisms of intensive feeding system.Results: In our results, increased growth performance and rumen volatile fatty acid (VFA) concentration were observed in yaks under the intensive feeding system compared to yaks grazing on pastures. Metagenomics of the rumen microbiome revealed that species of Clostridium and Methanobrevibacter as well as Piromyces sp. E2 and Anaeromyces robustus were increased in the rumen of intensively fed yaks, interacting and contributing to amino acid and carbohydrate metabolism. The rumen of yaks grazing on pasture had more cellulolytic microbes, such as Bacteroides and Fibrobacter species. Moreover, yaks under the intensive feeding system had lower methanogen and increased methane degradation functions, suggesting that the methane emission of these yaks may be decreased. These abundant microbiomes were correlated with the pathways of “Alanine aspartate and glutamate metabolism” and “Pyruvate metabolism”. Similar with rumen VFA results, metabolomics found that intensively fed yaks had greater concentrations of metabolites related to carbohydrates. The methyl metabolites associated with methane production were greater in the rumen of yak grazing on pasture. Additionally, these changed rumen microbiomes and their metabolites resulted in changes in plasma metabolome, finally affecting yaks’ growth.Conclusions: This study compressively classifies the mechanism that an intensive feeding system benefits yak production and reveals the importance of the rumen microbiome for host metabolism and performance. These findings evidence that an intensive feeding system could be used for the yak industry.