LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'The influence of storage on the “chemical age” of red wines'.
Answer: Storage conditions and duration have a considerable influence on wine quality. Optimum temperature and humidity conditions may improve wine quality through ageing, while incorrect or excessively long storage leads to negative results. In order to evaluate the global effects of storage on red wine composition, 20 Sangiovese wines were stored in two different conditions (cellar or house) for a period of 2 years and analysed every 6 months. Untargeted LC-MS analysis showed various putative markers for the type and length of conservation (i.e. pigments, flavanols, pantothenic acid etc.), while targeted LC-MS confirmed and expanded these results within specific metabolic groups. The results of multivariate analysis showed that wines stored in the cellar changed little even after 2 years of storage, while wines stored in typical domestic conditions (house) developed approximately four times faster, reaching after just 6 months a composition similar to wines stored in the cellar for 2 years. The formation of several monosulfonated flavanols during the domestic ageing provided the first evidence in wine of a reaction between wine tannins - both catechins and proanthocyanidins - and the exogenous antioxidant bisulfite. Moreover, ageing under domestic conditions appeared to induce an accelerated decrease of wine pigments, while specifically promoting the formation of the pinotin A-like pigments.
Question: Write a study description for the study titled 'Acute heat stress amplifies exercise-induced metabolomic perturbations and reveals variation in circulating amino acids in endurance-trained males'.
Answer: Using untargeted metabolomics, we aimed to characterise the systemic impact of environmental heat stress during exercise. Twenty-three trained male triathletes completed a 30-min exercise test in hot (35°C) and temperate (21°C) conditions. Venous blood samples were collected immediately pre- and post-exercise, and the serum fraction was assessed via untargeted 1H-NMR metabolomics. Data were analysed via uni- and multivariate analyses to identify differences between conditions. Mean power output was higher in temperate (231 ± 36 W) versus hot (223 ± 31 W) conditions (P < 0.001). Mean heart rate (temperate, 162 ± 10 beats per min, hot, 167 ± 9 beats per min, P < 0.001), peak core temperature (Trec ), core temperature change (ΔTrec ) (P < 0.001) and peak rating of perceived exertion (P = 0.005) were higher in hot versus temperate conditions. Change in metabolite abundance following exercise revealed distinct clustering following multivariate analysis. Six metabolites increased (2-hydroxyvaleric acid, acetate, alanine, glucarate, glucose, lactate) in hot relative to temperate (P < 0.05) conditions. Leucine and lysine decreased in both conditions but to a greater extent in temperate conditions (P < 0.05). Citrate (P = 0.04) was greater in temperate conditions whilst creatinine decreased in hot conditions only (P > 0.05). Environmental heat stress increased glycolytic metabolite abundance and led to distinct alterations in the circulating amino acid availability, including increased alanine, glutamine, leucine and isoleucine. The data highlight the need for additional exercise nutrition and metabolism research, specifically focusing on protein requirements for exercise under heat stress.
Question: Write a study description for the study titled 'Multi-kingdom gut microbiota dysbiosis is associated with the development of pulmonary arterial hypertension'.
Answer: Gut microbiota dysbiosis has been implicated in pulmonary arterial hypertension (PAH). However, most studies have focused on the bacterial community and the exact role and mechanisms of multi-kingdom gut microbiota, including bacteria, archaea and fungi in PAH remains largely unclear. Idiopathic PAH (IPAH) patients exhibited distinct gut microbiota profiles with altered bacterial, archaeal and fungal compositions compared to healthy controls. Fecal microbiota transplantation (FMT) from IPAH patients or monocrotaline (MCT)-induced PAH rats to antibiotic treated rats induced PAH phenotypes, including increased right ventricular systolic pressure (RVSP) and pulmonary vascular remodeling. Conversely, FMT from normal rats to MCT-PAH rats ameliorated PAH symptoms and reversed multi-kingdom gut microbiota dysbiosis. Metabolomics revealed significant alterations in plasma metabolites. Our findings established a causal link between multi-kingdom gut microbiota dysbiosis and PAH, demonstrating the therapeutic potential of FMT in reversing PAH phenotypes. More importantly, in addition to gut bacteria, gut archaeal and fungal communities also significantly correlate with PAH pathogenesis, highlighting their indispensable role in the gut.
Question: Write a study description for the study titled 'Seagrass excretes sugars to their rhizosphere making them the sweet spots in the sea (Sediment porewater; GC-MS assay)'.
Answer: Seagrasses are one of the most efficient natural sinks of carbon dioxide (CO2) on Earth. Despite covering less than 0.1% of coastal regions, they have the capacity to bury up to 10% of marine organic matter and can bury the same amount of carbon 35 times faster than tropical rainforests. On land, the soil’s ability to sequestrate carbon is intimately linked to microbial metabolism. Despite the growing attention to the link between plant production, microbial communities, and the carbon cycle in terrestrial ecosystems, these processes remain enigmatic in the sea. Here, we show that seagrasses excrete organic sugars, namely in the form of sucrose, into their rhizospheres. Surprisingly, the microbial communities living underneath meadows do not fully use this sugar stock in their metabolism. Instead, sucrose piles up in the sediments to mM concentrations underneath multiple types of seagrass meadows. Sediment incubation experiments show that microbial communities living underneath a meadow use sucrose at low metabolic rates. Our metagenomic analyses revealed that the distinct community of microorganisms occurring underneath meadows is limited in their ability to degrade simple sugars, which allows these compounds to persist in the environment over relatively long periods of time. Our findings reveal how seagrasses form blue carbon stocks despite the relatively small area they occupy. Unfortunately, anthropogenic disturbances are threatening the long-term persistence of seagrass meadows. Given that these sediments contain a large stock of sugars that heterotopic bacteria can degrade, it is even more important to protect these ecosystems from degradation.GC-MS assay of Sediment porewater is reported in the current study MTBLS1610GC-MS assay of Seawater sediment is reported in MTBLS1570GC-MS assay of Plant tissues is reported in MTBLS1579MALDI-MSI assay of Plant roots is reported in the MTBLS1746
Question: Write a study description for the study titled 'Ionic homeostasis, carbohydrate metabolism, and oxidative balance underlie wild soybean resistance to low potassium stress'.
Answer: The scarcity of potassium resources in farmland soils poses a major challenge to global food security. Wild soybean (Glycine soja), a valuable wild germplasm related to cultivated soybeans, is known for its high-stress resistance and adaptability. This study comprehensively compares two wild soybean ecotypes in terms of growth parameters, photosynthetic physiology, mineral ions and metabolite contents, and gene expression, aiming to clarify the regulatory mechanisms of low potassium stress tolerance in wild soybean seedlings' leaves. Results show that in barren-tolerant wild soybean (GS2), genes involved in potassium ion transport were significantly upregulated. This promotes potassium absorption and transport, maintaining a high K⁺ concentration and K⁺/Na⁺ ratio. Carbohydrate synthesis is enhanced in GS2, with increased sucrose and raffinose accumulation and a more active tricarboxylic acid (TCA) cycle. GS2 also strengthens the ascorbic acid-glutathione (ASA-GSH) cycle, along with promoting salicylic acid and 4-aminobutyric acid GABA synthesis, which boosts antioxidant capacity and reactive oxygen species (ROS) scavenging, maintaining oxidative balance. Under low potassium stress, GS2 accumulates unsaturated fatty acids, enhancing cell-membrane fluidity and providing a stress-resistant structural barrier. Overall, this study provides a basis for developing high-quality wild soybean resources and exploring genes for low potassium stress tolerance, which could contribute to improving cultivated soybeans' adaptability to potassium-deficient soils and ensuring global food production stability.
Question: Write a study description for the study titled 'Multiomic profiling of iron-deficient infant monkeys reveals alterations in neurologically important biochemicals in serum and cerebrospinal fluid before the onset of anemia'.
Answer: The effects of iron deficiency (ID) during infancy extend beyond the hematologic compartment and include short- and long-term adverse effects on many tissues including the brain. However, sensitive biomarkers of iron-dependent brain health are lacking in humans. To determine whether serum and cerebrospinal fluid (CSF) biomarkers of ID-induced metabolic dysfunction are concordant in the pre/early anemic stage of ID before anemia in a nonhuman primate model of infantile iron deficiency anemia (IDA). ID (n = 7), rhesus infants at 4 mo (pre-anemic period) and 6 mo of age (anemic) were examined. Hematological, metabolomic and proteomic profiles were generated via HPLC/MS at both time points to discriminate serum biomarkers of ID-induced brain metabolic dysfunction. We identified 227 metabolites and 205 proteins in serum. Abnormalities indicating altered liver function, lipid dysregulation and increased acute phase reactants were present in ID. In CSF, we measured 210 metabolites and 1560 proteins with changes in ID infants indicative of metabolomic and proteomic differences indexing disrupted synaptogenesis. Systemic and CSF proteomic and metabolomic changes were present and concurrent in the pre-anemic and anemic periods. Multiomic serum and CSF profiling uncovered pathways disrupted by ID in both the pre-anemic and anemic stages of infantile IDA, including evidence for hepatic dysfunction and activation of acute phase response. Parallel changes observed in serum and CSF potentially provide measurable serum biomarkers of ID that reflect at-risk brain processes prior to progression to clinical anemia.Data availability:The proteomics data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD028275.
Question: Write a study description for the study titled 'Sequential lipidomic, metabolomic, and proteomic analyses of serum, liver, and heart tissue specimens from peroxisomal biogenesis factor 11α knockout mice'.
Answer: Peroxisomes are versatile single membrane-enclosed cytoplasmic organelles, involved in reactive oxygen species (ROS) and lipid metabolism and diverse other metabolic processes. Peroxisomal disorders result from mutations in Pex genes-encoded proteins named peroxins (PEX proteins) and single peroxisomal enzyme deficiencies. The PEX11 protein family (α, β, and γ isoforms) plays an important role in peroxisomal proliferation and fission. However, their specific functions and the metabolic impact caused by their deficiencies have not been precisely characterized. To understand the systemic molecular alterations caused by peroxisomal defects, here we utilized untreated peroxisomal biogenesis factor 11α knockout (Pex11α KO) mouse model and performed serial relative-quantitative lipidomic, metabolomic, and proteomic analyses of serum, liver, and heart tissue homogenates. We demonstrated significant specific changes in the abundances of multiple lipid species, polar metabolites, and proteins and dysregulated metabolic pathways in distinct biological specimens of the Pex11α KO adult mice in comparison to the wild type (WT) controls. Overall, the present study reports comprehensive semi-quantitative molecular omics information of the Pex11α KO mice, which might serve in the future as a reference for a better understanding of the roles of Pex11α and underlying pathophysiological mechanisms of peroxisomal biogenesis disorders.
Question: Write a study description for the study titled 'LC-MS based plant metabolic profiles of thirteen grassland species grown in diverse neighbourhoods'.
Answer: In plants, secondary metabolite profiles provide a unique opportunity to explore seasonal variation and responses to the environment. These include both abiotic and biotic factors. In field experiments, such stress factors occur in combination. This variation alters the plant metabolic profiles in yet uninvestigated ways. This data set contains trait and mass spectrometry data of thirteen grassland species collected at four time points in the growing season in 2017. We collected above-ground vegetative material of seven grass and six herb species that were grown in plant communities with different levels of diversity in the Jena Experiment. For each sample, we recorded visible traits and acquired shoot metabolic profiles on a UPLC-ESI-Qq-TOF-MS. We performed the raw data pre-processing in Galaxy-W4M and prepared the data for statistical analysis in R by applying missing data imputation, batch correction, and validity checks on the features. This comprehensive data set provides the opportunity to investigate environmental dynamics across diverse neighbourhoods that are reflected in the metabolomic profile.
Question: Write a study description for the study titled 'Unraveling the metabolic effects of benzophenone-3 on the endosymbiotic dinoflagellate Cladocopium goreaui'.
Answer: As a well-known pseudo-persistent environmental pollutant, oxybenzone (BP-3) and its related organic ultraviolet (UV) filters have been verified to directly contribute to the increasing mortality rate of coral reefs. Previous studies have revealed the potential role of symbiotic Symbiodiniaceae in protecting corals from the toxic effects of UV filters. However, the detailed protection mechanism(s) have not been explained. Here, the impacts of BP-3 on the symbiotic Symbiodiniaceae Cladocopium goreaui were explored. C. goreaui cells exhibited distinct cell growth at different BP-3 doses, with increasing growth at the lower concentration (2 mg/L) and rapid death at a higher concentration (20 mg/L). Furthermore, C. goreaui cells showed a significant BP-3 uptake at the lower BP-3 concentration. BP-3 absorbing cells exhibited elevated photosynthetic efficiency, and decreased cellular carbon and nitrogen contents. Besides, the derivatives of BP-3 and aromatic amino acid metabolism highly responded to BP-3 absorption and biodegradation. Our physiological and metabolic results reveal that the symbiotic Symbiodiniaceae could resist the toxicity of a range of BP-3 through promoting cell division, photosynthesis and reprogramming amino acid metabolism. This study provides novel insights into the influences of organic UV filters to coral reef ecosystems, which urgently needs increasing attention and management.
Question: Write a study description for the study titled 'Cryogenic OrbiSIMS Localizes Semi-Volatile Molecules in Biological Tissues'.
Answer: OrbiSIMS is a recently developed instrument for label-free imaging of chemicals with micron spatial resolution and high mass resolution. We report a cryogenic workflow for OrbiSIMS (Cryo-OrbiSIMS) that improves chemical detection of lipids and other biomolecules in tissues. Cryo-OrbiSIMS boosts ionization yield and decreases ion-beam induced fragmentation, greatly improving the detection of biomolecules such as triacylglycerides. It also increases chemical coverage to include molecules with intermediate or high vapor pressures, such as free fatty acids and semi-volatile organic compounds (SVOCs). We find that Cryo-OrbiSIMS reveals the hitherto unknown localization patterns of SVOCs with high spatial and chemical resolution in diverse plant, animal and human tissues. We also show that Cryo-OrbiSIMS can be combined with genetic analysis to identify enzymes regulating SVOC metabolism. Cryo-OrbiSIMS is applicable to high resolution imaging of a wide variety of non-volatile and semi-volatile molecules across many areas of biomedicine.
Question: Write a study description for the study titled 'Regulation impact of Duolang sheep-sourced Ligilactobacillus salivarius on rumen microbiome homeostasis and host metabolism in Hu sheep'.
Answer: Background: Hu sheep, renowned for their prolificacy and economic value, have been introduced to Xinjiang for intensive farming operations. However, their suboptimal adaptation to local harsh environments limits growth efficiency and health management. In contrast, Duolang sheep, an indigenous Xinjiang breed, exhibit exceptional environmental resilience, largely attributed to their unique rumen microbiome enriched with fiber-degrading bacteria, which enhance roughage utilization and stress tolerance. To address Hu sheep’s adaptive challenges, this study applies Ligilactobacillus salivarius KS1018, a probiotic strain isolated from Duolang sheep, to Hu sheep, investigating its role in improving rumen microbial homeostasis, metabolic adaptation, and physiological resilience under Xinjiang’s environmental conditions.Results: Thirty-two male Hu lambs were allocated into four groups: Control (C) and three treatment groups receiving daily doses of 0.5×109 CFU/d (low-dose group, LLS, 1.0×109 CFU/d (medium-dose group, MLS), or 1.5×109 CFU/d (high-dose group, HLS) for 56 days. Although growth performance did not reveal significant enhancement, supplementation with the high dose of L. salivarius KS1018 (HLS group) significantly reduced ruminal NH3-N (p < 0.05) and increased total VFAs (p = 0.043), alongside elevated serum triglycerides (p = 0.021) and β-hydroxybutyrate (p < 0.05), indicating enhanced nitrogen utilization and ketogenesis. Rumen metabolomics revealed dose-dependent metabolic shifts: group HLS prioritized oxidative phosphorylation and pyrimidine metabolism (p < 0.001), while group MLS upregulated branched-chain amino acid biosynthesis (p < 0.01). Procrustes analysis confirmed strong microbiome-metabolome coordination (M2 = 0.56, p = 0.001), linking Lachnospira and Negativicutes enrichment to VFA production and redox homeostasis. Group HLS exhibited a decline in ruminal pH, suggesting a potential risk of subacute acidosis at higher doses.Conclusions: L. salivarius KS1018 optimizes rumen metabolism through microbial-host crosstalk, improving nitrogen efficiency and stress resilience in Hu sheep. The strain promoted ketogenesis and oxidative phosphorylation pathways, which alleviated oxidative stress and enhanced immune function under environmental challenges. Notably, the arid-adaptive genetic traits likely contribute to stabilizing rumen microbial networks, mimicking the superior roughage utilization capacity of its native Duolang sheep host. Our findings highlight the potential of L. salivarius KS1018 as a metabolic modulator in ruminant nutrition, redefining its role beyond traditional growth-centric applications.
Question: Write a study description for the study titled 'An Expanded Database of High-Resolution MS/MS Spectra for Lichen Derived Natural Products'.
Answer: The history of lichen compound identification has long relied on techniques such as spot tests and TLC, which have been surpassed in sensitivity and accuracy by modern metabolomic techniques such as high-resolution MS/MS. In 2019, Olivier-Jimenez et al. released the Lichen DataBase (LDB), a library containing the Q-TOF MS/MS spectra of 251 metabolites on the GNPS and MetaboLights platforms, that has been widely used for the identification of lichen-derived unknowns. To increase the compound coverage, we have generated the Orbitrap MS/MS spectra of a further 534 lichen-derived compounds from the metabolite library of Jack Elix, housed at the CANB herbarium (Canberra, Australia). This included 399 unique metabolites that are not in the LDB, bringing the total number combined to 650. Technical validation was achieved by investigating the compounds in three Australian lichen extracts using the Library Search and Molecular Networking tools on the GNPS platform. This update provides a much larger database for lichen compound identification, which we envisage will allow refining of the chemotaxonomy framework and contribute to compound discovery.
Question: Write a study description for the study titled 'Cross-feeding and co-degradation within a bacterial consortium dominated by challenging-to-cultivate Leucobacter sp. HA-1 enhances sulfonamides degradation'.
Answer: Background: The use of sulfonamides (SAs) caused residual pollution in the environment. Bacteria play an important role in the degradation of sulfonamide antibiotics, and microbial consortium offers advantages over single bacterium. However, the complex degradation process and interaction mechanisms within such consortiums still poorly understood. Results: Here, a consortium named ACJ, consisting of Leucobacter sp. HA-1, Bacillus sp. HC-1 and Gordonia sp. HAEJ-1, obtained from activated sludge of pharmaceutical plants, was identified as capable of degrading various SAs. Several papers failed to get the pure culture of Leucobacter sp. in the degradation of SAs, here we successfully obtained the Leucobacter sp. HA-1 pure culture involved in the degradation of SAs with the growth factors provided by strain HC-1 or HAEJ-1. Strain HA-1 was responsible for the initial attack of sulfonamide molecules resulting in the release of 2-aminoquinoxaline (2-AQ) and trihydroxybenzene (HHQ), which were further degraded and used for growth by strain HAEJ-1. Genomic, metabolomic and transcriptomic analyses revealed genes associated with nucleotide repair, ABC transporters, quorum sensing, TCA cycle and cell cycle in strain HA-1 were up-regulated during co-culture compared without the other two strains, which indicated that HA-1 utilized certain factors from strain HC-1 or HAEJ-1 for growth. Conclusion: These results revealed that there was a bidirectional ecological relationship of cross-feeding and co-degradation among consortium ACJ. In summary, this study provides new insights into the mechanisms of microbial consortium interaction and co-degradation in antibiotic-contaminated environments.