LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Narrow-spectrum resource-utilizing bacteria drive the stability of synthetic communities through enhancing metabolic interactions'.
Answer: The importance of synthetic microbial communities in agriculture is increasingly being recognized, but methods for constructing targeted synthetic communities using existing microbial resources remain limited. In this study, six plant beneficial bacterial strains with distinct capacities for utilizing rhizosphere resources and functions of nitrogen fixation, phosphate solubilization, indoleacetic acid synthesis, and siderophore production were selected to construct stable and multifunctional communities for promoting plant growth. Metabolic modeling revealed a negative correlation between resource utilization width and community stability: that is, narrow-spectrum resource-utilizing strains enhanced metabolic interaction potential and reduced metabolic resource overlap, thereby increasing the stability of the community. Comprehensive validation, including large-scale simulations, metabolite supplementation, cross-feeding, and in situ experiments, consistently confirmed the central roles of the narrow-spectrum resource-utilizing strains, Cellulosimicrobium cellulans E and Pseudomonas stutzeri G, which formed metabolic interaction networks via the secretion of asparagine, vitamin B12, isoleucine, and their precursors or derivatives. Two synthetic multifunctional communities, SynCom4 and SynCom5, demonstrated high stability in the tomato rhizosphere and led to an increase in plant dry weight by over 80%. Our study elucidates the link between resource utilization width and community stability, providing a rational basis for the construction of stable, multifunctional microbial communities for specific habitats.
Question: Write a study description for the study titled 'Intestinal accumulation of microbiota-produced succinate caused by loss of microRNAs leads to diarrhea in weanling piglets'.
Answer: Diarrheal disease is a common health problem with complex causality. Although diarrhea is accompanied by disturbances in microbial diversity, how gut microbes are involved in the occurrence of diarrhea remains largely unknown. Here, using a pig model of post-weaning stress-induced diarrhea, we aim to elucidate and enrich the mechanistic basis of diarrhea. We found significant alterations in fecal microbiome, their metabolites, and microRNAs levels in piglets with diarrhea. Specifically, loss of ssc-miRNA-425-5p and ssc-miRNA-423-3p, which inhibit the gene expression of fumarate reductase (frd) in Prevotella genus, caused succinate accumulation in piglets, which resulted in diarrhea. Single-cell RNA sequencing indicated impaired epithelial function and increased immune response in the colon of piglet with diarrhea. Notably, the accumulated succinate increased colonic fluid secretion by regulating transepithelial Cl-secretion in the epithelial cells. Meanwhile, succinate promoted colonic inflammatory responses by activating MyD88-dependent TLR4 signaling in the macrophages. Overall, our findings expand the mechanistic basis of diarrhea and suggest that colonic accumulation of microbiota-produced succinate caused by loss of miRNAs leads to diarrhea in weanling piglets.
Question: Write a study description for the study titled 'Uncovering the secrets of monoculture yield decline: Trade-offs between leaf and root chemical and physical defence traits in a grasslands experiment'.
Answer: Plant monocultures growing for extended periods face severe losses of productivity. This phenomenon, known as 'yield decline', is often caused by the accumulation of above- and below-ground plant antagonists. The effectiveness of plant defences against antagonists might help explain differences in yield decline among species. Using a trait-based approach, we studied the role of 20 physical and chemical defence traits of leaves and fine roots on yield decline of 4- and 18-year-old monocultures of 27 grassland species. We hypothesized that yield decline is lower for species with high defences, that root defences are better predictors of yield decline than leaf defences, and that in roots, physical defences better predict yield decline than chemical defences, while the reverse is true for leaves. We additionally hypothesized that the relationship between defences and yield decline increase with time and that species increasing the expression of defence traits after long-term monoculture growth would suffer less yield decline. We summarized leaf and fine root defence traits using principal component analysis and analysed the relationship between the most informative components as well as their temporal changes and monoculture yield decline. The significant predictors of yield decline were traits related to the so-called collaboration gradient of the root economics space (specific root length and root diameter) as well as their temporal changes and traits related to the leaf physical vs chemical defence trade-off (leaf dry matter, silicon and cellulose content, toughness and phytochemical diversity). We were unable to unequivocally identify the mechanisms relating the effect of those traits to yield decline as they could mediate plant responses to several stressor such as antagonist nutrient depletion and drought. Further studies are needed to differentiate between these alternative mechanisms and gain a comprehensive understanding of the drivers behind the impact of root and leaf defence traits on yield decline.
Question: Write a study description for the study titled 'Serum metabolomic profiles associated with postmenopausal hormone use'.
Answer: INTRODUCTION: Postmenopausal hormone use is linked to several health outcomes and the risk associated with some may differ depending on whether estrogen is used alone or in combination with progestin.OBJECTIVE: Metabolomic analyses of postmenopausal hormone use and differences between hormone regimes was carried out to identify metabolites associated with each type of hormone treatment.METHODS: Untargeted metabolomics analysis was carried out on serum from 1,336 women enrolled in the Cancer Prevention II Nutrition Cohort. Levels of 781 named metabolites were compared between 667 nonusers with 332 estrogen-only and with 337 estrogen plus progestin users using linear regression. Metabolite levels were also compared between estrogen-only and estrogen plus progestin users.RESULTS: Compared to nonusers, 276 metabolites were statistically significantly (P<6.40 x 10-5) associated with estrogen-only use and 222 were associated with estrogen plus progestin use. The metabolites associated with both types of hormones included numerous lipids, acyl carnitines, and amino acids as well as the thyroid hormone thyroxine and the oncometabolite fumarate. The 65 metabolites that differed significantly between estrogen-only and estrogen plus progestin users included 19 steroids and 12 lipids that contained the bioactive fatty acid arachidonic acid.CONCLUSIONS: These findings suggest that postmenopausal hormone use influences metabolic pathways linked to a variety of cellular processes, including the regulation of metabolism and stress responses, energy production, and inflammation. The differential association of numerous lipids that could influence cellular signaling suggests that differences in signal transduction may contribute to the disparate risks for some diseases between estrogen-only and estrogen plus progestin users.
Question: Write a study description for the study titled 'Stable isotope-resolved metabolomics of WT, GYG1 KO, and GYG2 KO human embryonic stem cells using 13C-labeled glucose and palmitate'.
Answer: Proper regulation of glycogen metabolism is fundamental to cellular energy homeostasis, and its disruption is associated with various metabolic disorders, including glycogen storage diseases (GSDs) and potentially diabetes. Despite glycogen’s role as an essential energy reservoir, the mechanisms governing its synthesis and structural diversity across tissues remain unclear. Here, we uncover the distinct physiological roles of the human glycogenins GYG1 and GYG2 in glycogen synthesis. Through cellular models, structural biology, and biochemical analyses, we demonstrate that, unlike GYG1, GYG2 exhibits minimal autoglycosylation activity and acts as a suppressor of glycogen formation. Together, these two glycogenins coordinate glycogen synthase activity and influence glycogen assembly in a cell-type-dependent manner. Importantly, these glycogenins modulate glucose metabolic pathways, thereby ensuring cellular glucose homeostasis. These findings address longstanding questions in glycogen metabolism and establish both GYG1 and GYG2 as critical regulators of glycogen synthesis and breakdown in human, providing insights with potential therapeutic implications for treating GSDs and metabolic diseases.
Question: Write a study description for the study titled 'Maternal regulation of biliary disease in neonates via gut microbial metabolites'.
Answer: Maternal seeding of the microbiome in neonates promotes a long-lasting biological footprint, but how it impacts disease susceptibility in early life remains unknown. We hypothesized that feeding butyrate to pregnant mice influences the newborn’s susceptibility to biliary atresia, a severe cholangiopathy of neonates. Here, we show that butyrate administration to mothers renders newborn mice resistant to inflammation and injury of bile ducts and improves survival. The prevention of hepatic immune cell activation and survival trait is linked to fecal signatures of Bacteroidetes and Clostridia and increases glutamate/glutamine and hypoxanthine in stool metabolites of newborn mice. In human neonates with biliary atresia, the fecal microbiome signature of these bacteria is under-represented, with suppression of glutamate/glutamine and increased hypoxanthine pathways. The direct administration of butyrate or glutamine to newborn mice attenuates the disease phenotype, but only glutamine renders bile duct epithelial cells resistant to cytotoxicity by natural killer cells. Thus, maternal intake of butyrate influences the fecal microbial population and metabolites in newborn mice and the phenotypic expression of experimental biliary atresia, with glutamine promoting survival of bile duct epithelial cells.
Question: Write a study description for the study titled 'The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis'.
Answer: BACKGROUND: Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant root constituents Praeruptorin (A-E), are the active constituents of the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and, thus, the development of better breeding strategies.RESULTS: The authors assembled a telomere-to-telomere genome by combining PacBio HiFi, ONT ultra- long and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes and genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced two WGD events like the ones in the Apiaceae family. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins' spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins.CONCLUSIONS: The authors obtained a T2T genome for P. praeruptorum, which provides molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.
Question: Write a study description for the study titled 'Hyocholic acid species as novel biomarkers for metabolic disorders'.
Answer: Hyocholic acid (HCA) is a major bile acid (BA) species in the BA pool of pigs, a species known for its exceptional resistance to spontaneous development of diabetic phenotypes. HCA and its derivatives are also present in human blood and urine. We investigate whether human HCA profiles can predict the development of metabolic disorders. We find in the first cohort (n = 1107) that both obesity and diabetes are associated with lower serum concentrations of HCA species. A separate cohort study (n = 91) validates this finding and further reveals that individuals with pre-diabetes are associated with lower levels of HCA species in feces. Serum HCA levels increase in the patients after gastric bypass surgery (n = 38) and can predict the remission of diabetes two years after surgery. The results are replicated in two independent, prospective cohorts (n = 132 and n = 207), where serum HCA species are found to be strong predictors for metabolic disorders in 5 and 10 years, respectively. These findings underscore the association of HCA species with diabetes, and demonstrate the feasibility of using HCA profiles to assess the future risk of developing metabolic abnormalities.
Question: Write a study description for the study titled 'Comparative label-free lipidomic analysis of Mycobacterium tuberculosis during dormancy and reactivation'.
Answer: Mycobacterium tuberculosis employs several strategies to combat and adapt to adverse conditions encountered inside the host. The non-replicative dormant state of the bacterium is linked to drug resistance and slower response to anti-tubercular therapy. It is known that alterations in lipid content allow dormant bacteria to acclimatize to cellular stress. Employing comparative lipidomic analysis we profiled the changes in lipid metabolism in M. tuberculosis using a modified Wayne's model of hypoxia-induced dormancy. Further we subjected the dormant bacteria to resuscitation, and analyzed their lipidomes until the lipid profile was similar to that of normoxially grown bacteria. An enhanced degradation of cell wall-associated and cytoplasmic lipids during dormancy, and their gradual restoration during reactivation, were clearly evident. This study throws light on distinct lipid metabolic patterns that M. tuberculosis undergoes to maintain its cellular energetics during dormancy and reactivation.
Question: Write a study description for the study titled 'Volatilomic insight of head and neck cancer via the effects observed on saliva metabolites'.
Answer: Head and neck cancer (HNC) is a heterogeneous malignant disease with distinct global distribution. Metabolic adaptations of HNC are significantly gaining clinical interests nowadays. Here, we investigated effects of HNC on differential expression of volatile metabolites in human saliva. We applied headspace solid phase microextraction coupled with gas chromatography-mass spectrometry analysis of saliva samples collected from 59 human subjects (HNC - 32, Control - 27). We identified and quantified 48 volatile organic metabolites (VOMs) and observed profound effects of HNC on these metabolites. These effects were VOM specific and significantly differed in the biologically comparable healthy controls. HNC induced changes in salivary VOM composition were well attributed to in vivo metabolic effects. A panel of 15 VOMs with variable importance in projection (VIP) score >1, false discovery rate (FDR) corrected p-value < 0.05 and log2 fold change (log2 FC) value of ≥0.58/≤-0.58 were regarded as discriminatory metabolites of pathophysiological importance. Afterwards, receiver operator characteristic curve (ROC) projected certain VOMs viz., 1,4-dichlorobenzene, 1,2-decanediol, 2,5-bis1,1-dimethylethylphenol and E-3-decen-2-ol with profound metabolic effects of HNC and highest class segregation potential. Moreover, metabolic pathways analysis portrayed several dysregulated pathways in HNC, which enhanced our basic understanding on salivary VOM changes. Our observations could redefine several known/already investigated systemic phenomenons (e.g. biochemical pathways). These findings will inspire further research in this direction and may open unconventional avenues for non-invasive monitoring of HNC and its therapy in the future.
Question: Write a study description for the study titled 'Metabolomic alterations in invasive ductal carcinoma of breast: A comprehensive metabolomic study using tissue and serum samples'.
Answer: Invasive ductal carcinoma (IDC) is the most common type of breast cancer and the leading cause of breast cancer related mortality. In the present study, metabolomic profiles of 72 tissue samples and 146 serum samples were analysed using targeted liquid chromatography multiple reaction monitoring mass spectrometry (LC-MRM/MS) and untargeted gas chromatography mass spectrometry (GC-MS) approaches. Combination of univariate and multivariate statistical treatment identified significant alterations of 42 and 32 metabolites in tissue and serum samples of IDC respectively when compared to control. A decent interconnection of metabolomic changes was observed between tissue and serum, indicating a bi-directional interaction of metabolites in IDC. Additionally, 8 tissue metabolites and 9 serum metabolites showed progressive change from control to benign to IDC suggesting their possible role in malignant transformation. We have identified a panel of three metabolites viz. tryptophan, tyrosine, and creatine in tissue and serum, which could be useful in screening of IDC subjects from both control and benign. The metabolomic alterations in IDC showed perturbations in purine and pyrimidine metabolism, amino sugar metabolism, amino acid metabolism, fatty acid biosynthesis etc. Comprehensively, this study provides valuable insights into metabolic adaptations of IDC, which can help to identify diagnostic markers as well as potential therapeutic targets.
Question: Write a study description for the study titled 'Cell-based and multi-omics profiling reveal dynamic metabolic repurposing of mitochondria to drive developmental progression of Trypanosoma brucei'.
Answer: Mitochondrial metabolic remodeling is a hallmark of the Trypanosoma brucei digenetic life cycle since the insect stage utilizes the cost-effective oxidative phosphorylation to generate ATP, while bloodstream cells switch to less energetically efficient aerobic glycolysis. Due to difficulties in acquiring enough parasites from the tsetse fly vector for biochemical analysis, the dynamics of the parasite´s mitochondrial metabolic rewiring in the vector have remained obscure. Here, we took advantage of in vitro-induced differentiation to follow changes at the RNA, protein and metabolite levels. This multi-omics and cell-based profiling showed an immediate redirection of electron flow from the cytochrome mediated pathway to a mitochondrial alternative oxidase, an increase in proline consumption and its oxidation, elevated activity of complex II and certain TCA cycle enzymes, which led to mitochondrial inner membrane hyperpolarization and increased ROS levels in both mitochondrion and cytosol. Interestingly, these ROS molecules acted as signaling molecules driving developmental progression since exogenous expression of catalase, a ROS scavenger, halted the in vitro-induced cell differentiation. Our results provide insights into the mechanisms of the parasite´s mitochondrial rewiring and reinforce the emerging concept that mitochondria act as signaling organelles through release of ROS to drive cellular differentiation.Data availability:RNA-SeqProteomic data associated with this study are available in the PRIDE repository: accession number PXD016370.
Question: Write a study description for the study titled 'Metabolomics-derived marker metabolites to characterize Phaeocystis pouchetii in natural plankton communities'.
Answer: Phaeocystis pouchetii (Hariot) Lagerheim, 1893 regularly dominates phytoplankton blooms in the Arctic. Through zooplankton grazing and microbial activity, it is considered to be a key resource for the entire marine food web but the actual relevance of biomass transfer to higher trophic levels is still under discussion. Cell physiology and algal nutritional state are suggested to be major factors controlling the observed variability in zooplankton grazing. However, no data have so far yielded insights into the metabolic state of Phaeocystis populations that would allow testing this hypothesis. Therefore, endometabolic markers of different growth phases were determined in laboratory batch cultures using comparative metabolomics and quantified in different phytoplankton blooms in the field. Metabolites, produced during exponential, early and late stationary growth of P. pouchetii were profiled using gas chromatography-mass spectrometry. Then, metabolites were characterized that correlate with the growth phases using multivariate statistical analysis. Free amino acids characterized exponential growth, whereas the early stationary phase was correlated with sugar alcohols, mono- and disaccharides. In the late stationary phase free fatty acids, sterols and terpenes increased. These marker metabolites were then traced in Phaeocystis blooms during a cruise in the Barents Sea and North Norwegian fjords. About 50 endometabolites of P. pouchetii were detected in natural phytoplankton communities. Their relative abundances at Phaeocystis-dominated stations differed from diatom-dominated stations. Mannitol, scyllo- inositol, 24-methylcholesta-5,22-dien-3β-ol, and several free fatty acids were characteristic for Phaeocystis-dominated blooms. Distinct metabolic profiles were detected in the nutrient- depleted community in the inner Porsangerfjord (<0.5 μM NO3-, <0.1 μM PO4-), with high relative amounts of free mono- and disaccharides indicative for a limited culture. This study, therefore, shows how variable physiology of phytoplankton can alter the metabolic landscape of entire plankton communities.
Question: Write a study description for the study titled 'Essential omega-3 fatty acids tune microglial phagocytosis of synaptic elements in the developing brain'.
Answer: Omega-3 fatty acids (n-3 polyunsaturated fatty acids; n-3 PUFAs) are essential for the functional maturation of the brain. Westernization of dietary habits in both developed and developing countries is accompanied by a progressive reduction in dietary intake of n-3 PUFAs. Low maternal intake of n-3 PUFAs has been linked to neurodevelopmental diseases in epidemiological studies, but the mechanisms by which a n-3 PUFA dietary imbalance affects CNS development are poorly understood. Active microglial engulfment of synaptic elements is an important process for normal brain development and altered synapse refinement is a hallmark of several neurodevelopmental disorders. Here, we identify a molecular mechanism for detrimental effects of low maternal n-3 PUFA intake on hippocampal development. Our results show that maternal dietary n-3 PUFA deficiency increases microglial phagocytosis of synaptic elements in the developing hippocampus, partly through the activation of 12/15- lipoxygenase (LOX)/12-HETE signaling, which alters neuronal morphology and affects cognition in the postnatal offspring. While women of child bearing age are at higher risk of dietary n-3 PUFA deficiency, these findings provide new insights into the mechanisms linking maternal nutrition to neurodevelopmental disorders.