LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Metabolic cooperation and spatiotemporal niche partitioning in a kefir microbial community; Kefir fermentation curve (FIA-MS)'.
Answer: Microbial communities often undergo intricate compositional changes yet also maintain stable coexistence of diverse species. The mechanisms underlying long-term coexistence remain unclear, as system-wide studies have been largely limited to engineered communities, ex situ adapted cultures, or synthetic assemblies. Here we show how kefir, a natural milk-fermenting community of prokaryotes and yeasts, realises stable coexistence through spatiotemporal orchestration of species and metabolite dynamics. During milk fermentation, kefir grains (a polysaccharide matrix synthesized by kefir microbes) grow in mass but remain unchanged in composition. In contrast, the milk is colonized in a sequential manner in which early members open metabolic niches for followers. Through metabolomics and large-scale mapping of inter-species interactions, we show how microbes poorly suited for milk survive in, and even dominate the community, through metabolic cooperation and uneven partitioning between grain and milk. Overall, our findings reveal how inter-species interactions partitioned in space and time lead to stable coexistence.Linked metabolomics studies:MTBLS1823 Spent-medium assay, measured untargeted (FIA-qTOF) and targeted (HILIC, LC-MS)MTBLS1830 Interaction between the kefir isolates Lactococcus lactis and Acetobacter fabarum (GC-MS)Linked cross omic data sets:Genomes of isolated kefir species are available in the NCBI database under the accession: PRJNA375758 (bioproject ID: 375758).Metatranscriptomic sequencing data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJEB37001.Genome-scale metabolic models for kefir bacteria can be found at github.com/cdanielmachado/kefir_models.
Question: Write a study description for the study titled 'System-wide analysis of short-term response to high temperature in Pinus radiata'.
Answer: Pinus radiata seedlings, the most widely planted pine species in the world, were exposed to temperatures within a range mimicking future scenarios based on current models of heat increase. The short-term heat response in P. radiata was studied in detail by exploring the metabolome, proteome and targeted transcriptome. The use of complementary mass spectrometry techniques, GC-MS and LC-Orbitrap-MS, together with novel bioinformatics tools allowed the reliable quantification of 2075 metabolites and 901 protein groups. Integrative analyses of different functional levels and plant physiological status revealed a complex molecular interaction network of positive and negative correlations between proteins and metabolites involved in short-term heat response, including three main physiological functions as: 1) A hormone subnetwork, where fatty acids, flavonoids and hormones presented a key role; 2) An oxidoreductase subnetwork, including several dehydrogenase and peroxidase proteins; and 3) A heat shock protein subnetwork, with numerous proteins that contain a HSP20 domain, all of which were overexpressed at the transcriptional level. Integrated analysis pinpointed the basic mechanisms underlying the short-term physiological reaction of P. radiata during heat response. This approach was feasible in forest species and unmasked two novel candidate biomarkers of heat resistance, PHO1 and TRANSCRIPTION FACTOR APFI, and a MITOCHONDRIAL SMALL HEAT SHOCK PROTEIN, for use in future breeding programs.Data availability:The proteomics data have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD032754.
Question: Write a study description for the study titled 'Systems acclimation to osmotic stress in zygnematophyte cells'.
Answer: Zygnematophytes are the closest algal relatives of land plants. They hold key information to infer how the earliest land plants overcame the barrage of terrestrial stressors, prime of which is osmotic stress. Here, we applied two osmotic stressors on a unicellular and a multicellular representative of zygnematophytes and studied their response over a 25-hour time course generating 130, 60 and 30 of transcriptomic, proteomic and metabolomic samples combined with photophysiology, sugar analysis, immunocytochemical glycoprotein analysis and microscopy. Our data highlight a shared protein chassis that shows divergent responses with the same outcome: successful acclimation to osmotic challenges. We establish a model of how the algal sisters of land plants can overcome a prime stressor in the terrestrial habitat and highlight components of the plant terrestrialization toolkit.
Question: Write a study description for the study titled 'Bacteroides uniformis degrades β-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis'.
Answer: The gut microbiota plays a crucial role in the onset and progression of inflammatory bowel disease (IBD). β-glucan (BG), a soluble dietary fiber widely present in oats, barley, fungi, yeast and some bacteria, has multiple bioactive properties such as mitigating intestinal inflammation; however, the underlying mechanisms remain unclear. Here, we demonstrate that BG protects against colitis by increasing the abundance of Lactobacillus johnsonii in the gut, which promotes the production of indole-3-lactic acid (ILA) to activate the aryl hydrocarbon receptor (AhR) and increase the secretion of IL-22. Interestingly, L. johnsonii can not utilize BG but requires a cross-feeding interaction with Bacteroides uniformis. B. uniformis-derived nicotinamide (NAM) via the cobB gene promotes the growth of L. johnsonii. Deletion of cobB from B. uniformis results in inefficacy in L. johnsonii growth and fighting against colitis. In support of our findings, we conducted a clinical trial of the BG intervention, which demonstrated that BG increases the abundance of B. uniformis and L. johnsonii in the human gut along with increasing ILA levels. Our findings reveal the mechanism by which BG ameliorates colitis via L. johnsonii-ILA-AhR axis and provide new insights into cross-feeding between bacteria.
Question: Write a study description for the study titled 'Lactation-related metabolic mechanism investigated based on mammary gland metabolomics and 4 biofluids’ metabolomics relationships in dairy cows'.
Answer: BACKGROUND: Lactation is extremely important for dairy cows; however, the understanding of the underlying metabolic mechanisms is very limited. This study was conducted to investigate the inherent metabolic patterns during lactation using the overall biofluid metabolomics and the metabolic differences from non-lactation periods, as determined using partial tissue-metabolomics. We analyzed the metabolomic profiles of four biofluids (rumen fluid, serum, milk and urine) and their relationships in six mid-lactation Holstein cows and compared their mammary gland (MG) metabolomic profiles with those of six non-lactating cows by using gas chromatography-time of flight/mass spectrometry. RESULTS: In total, 33 metabolites were shared among the four biofluids, and 274 metabolites were identified in the MG tissues. The sub-clusters of the hierarchical clustering analysis revealed that the rumen fluid and serum metabolomics profiles were grouped together and highly correlated but were separate from those for milk. Urine had the most different profile compared to the other three biofluids. Creatine was identified as the most different metabolite among the four biofluids (VIP=1.537). Five metabolic pathways, including gluconeogenesis, pyruvate metabolism, the tricarboxylic acid cycle (TCA cycle), glycerolipid metabolism, and aspartate metabolism, showed the most functional enrichment among the four biofluids (false discovery rate<0.05, fold enrichment >2). Clear discriminations were observed in the MG metabolomics profiles between the lactating and non-lactating cows, with 54 metabolites having a significantly higher abundance (P<0.05, VIP>1) in the lactation group. Lactobionic acid, citric acid, orotic acid and oxamide were extracted by the S-plot as potential biomarkers of the metabolic difference between lactation and non-lactation. The TCA cycle, glyoxylate and dicarboxylate metabolism, glutamate metabolism and glycine metabolism were determined to be pathways that were significantly impacted (P<0.01, impact value >0.1) in the lactation group. Among them, the TCA cycle was the most up-regulated pathway (P<0.0001), with 7 of the 10 related metabolites increased in the MG tissues of the lactating cows. CONCLUSIONS: The overall biofluid and MG tissue metabolic mechanisms in the lactating cows were interpreted in this study. Our findings are the first to provide an integrated insight and a better understanding of the metabolic mechanism of lactation, which is beneficial for developing regulated strategies to improve the metabolic status of lactating dairy cows.
Question: Write a study description for the study titled 'Evaluation of sample preparation methods for NMR-based metabolomics of cow milk'.
Answer: The quality of milk metabolome analyzed by nuclear magnetic resonance (NMR) is greatly influenced by the way samples are prepared. Although this analytical method is increasingly used to study milk metabolites, a thorough examination of available sample preparation protocols for milk has not been reported yet. We evaluated the performance of eight milk preparation methods namely (1) raw milk without any processing; (2) skimmed milk; (3) ultrafiltered milk; (4) skimming followed by ultrafiltration; (5) ultracentrifuged milk; (6) methanol; (7) dichloromethane; and (8) methanol/dichloromethane, in terms of spectra quality, repeatability, signal-to-noise ratio, extraction efficiency and yield criteria. A pooled sample of milk was used for all protocols. Skimming, ultracentrifugation and unprocessed milk protocols showed poor NMR spectra quality. Protocols involving multiple steps, namely methanol/dichloromethane extraction, and skimming followed by ultrafiltration produced inadequate results for signal-to-noise ratio parameter. Methanol and skimming associated to ultrafiltration provided good repeatability results compared to the other protocols. Chemical-based sample preparation protocols, particularly methanol, showed more efficient metabolite extraction compared to physical preparation methods. When considering all evaluation parameters, the methanol extraction protocol proved to be the best method. As a proof of utility, methanol protocol was then applied to milk samples from dairy cows fed a diet with or without a feed additive, showing a clear separation between the two groups of cows.
Question: Write a study description for the study titled 'Positional Enrichment by Proton Analysis (PEPA): a One-Dimensional 1H-NMR Approach for 13C Stable Isotope Tracer Studies in Metabolomics'.
Answer: A novel metabolomics approach for NMR-based stable isotope tracer studies called PEPA is presented, and its performance validated using human cancer cells. PEPA detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of 13C-satellite peaks using 1D-1H-NMR spectra. In comparison with 13C-NMR, TOCSY and HSQC, PEPA improves sensitivity, accelerates the elucidation of 13C positions in labeled metabolites and the quantification of the percentage of stable isotope enrichment. Altogether, PEPA provides a novel framework for extending the high-throughput of 1H-NMR metabolic profiling to stable isotope tracing in metabolomics, facilitating and complementing the information derived from 2D-NMR experiments and expanding the range of isotopically enriched metabolites detected in cellular extracts. The study also contains data, subjected to this technique, pertaining to exonuclease domain like 2 (EXD2), a nuclear encoded gene that we have found is targeted to the mitochondria and is critical for normal metabolism.
Question: Write a study description for the study titled '3D Imaging and metabolomic profiling reveal higher neuroactive kavalactone contents in lateral roots and crown root peels of Piper methysticum (kava)'.
Answer: BACKGROUND: Kava is an important neuroactive medicinal plant. While kava has a large global consumer footprint for its clinical and recreational use, factors related to its use lack standardization and the tissue-specific metabolite profile of its neuroactive constituents is not well understood.RESULTS: Here we characterized the metabolomic profile and spatio-temporal characteristics of tissues from the roots and stems using cross-platform metabolomics and a 3D imaging approach. Gas chromatography–mass spectrometry and liquid chromatography–mass spectrometry revealed the highest content of kavalactones in crown root peels and lateral roots. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) imaging revealed a unique tissue-specific presence of each target kavalactone. X-ray micro-computed tomography analysis demonstrated that lateral roots have morphological characteristics suitable for synthesis of the highest content of kavalactones.CONCLUSIONS: These results provide mechanistic insights into the social and clinical practice of the use of only peeled roots by linking specific tissue characteristics to concentrations of neuroactive compounds.
Question: Write a study description for the study titled 'Sponges With Microbial Symbionts Transform Dissolved Organic Matter and Take Up Organohalides (2019 collection assay)'.
Answer: Seawater dissolved organic matter (DOM) is a large reservoir of carbon composed of a complex and poorly characterized mixture of molecules. Sponges have long been known to consume dissolved organic carbon (DOC) from this mixture, but the role of microbial sponge symbionts in this process is complex, and the molecules involved remain largely unknown. In order to better understand how sponge processing changes seawater DOM, we used untargeted metabolomics to characterize DOM in samples of incurrent and excurrent seawater taken from sponges on the fore-reef off Carrie Bow Cay, Belize, over 2 years. We collected samples from three sponge species each with either high or low microbial abundance (HMA, LMA) to explore the relationship between symbiont abundance and DOM alterations. Analyses revealed that sponges took up metabolites and changed the composition of seawater DOM, but only for the three HMA species, and none of the LMA species, implicating microbial symbionts in this uptake. Using a new mass spectra classification tool, we found that putative compositions of features depleted in the excurrent samples of HMA sponges were similar in both years and were dominated by organic acids and derivatives (74%) and organic nitrogen compounds (19%). Interestingly, HMA sponges also took up halogenated compounds (containing chlorine or bromine), providing evidence of a previously unknown mechanism of halide cycling. The metabolites taken up by HMA sponges may be used as a food source or as building blocks of chemical defenses, selective advantages that may have guided the evolution of microbial symbioses in sponges.2019 collection assay is reported in the current study MTBLS22002018 collection assay is reported in MTBLS2199
Question: Write a study description for the study titled 'Multi-omics analyses of serum metabolome and gut microbiome reveal shifted metabolites associated with gut microbial dysbiosis in Guillain-Barre syndrome'.
Answer: Objective: Guillain barre syndrome (GBS) is a rare immune-mediated inflammatory disease of the complex peripheral nervous system. Long-term “silent infection” caused by changes in intestinal flora is potentially a contributing factor for immune-mediated inflammatory diseases, but the causative link between GBS and intestinal flora remains unclear. The present study aimed to characterize gut microbiome structure and estimate its association with the serum metabolic profile and in GBS. Methods: Untargeted metabolomics profiling of serum, using liquid chromatography-mass spectrometry, and metagenomics sequencing of stool samples from a cohort of GBS and non-GBS subjects were performed to evaluate serum metabolic profiles and gut microbiome structure in GBS subjects relative to healthy controls. Pearson’s correlation analysis was used to estimate the correlations between the gut microbial abundance and serum metabolic profile. Results: For intestinal microflora, Ligilactobacillus_salivarius, Klebsiella pneumonia, Enterocloster bolteae and Methanobrevibacter smithii were notably more abundant in GBS subjects, while Bacteroides sp., Roseburia hominis, and Paraprevotella xylaniphila decreased significantly. Metabolome data revealed that the gamma-aminobutyric acid (GABA) and secondary cholic acid metabolism were perturbed in GBS. GABA increased significantly, while secondary cholic acids as methyl deoxycholate, glycodeoxycholic acid, glycolithocholic acid, taurolithocholic acid and coprocholic acid, decreased significantly in GBS versus non-GBS controls. Metagenome data also revealed that GABA biosynthesis pathway was enriched, while secondary cholic acid metabolism pathways were decreased in gut microbes in GBS subjects. Correlation analysis revealed that changes in GABA were associated with altered gut microbes, such as Enterococcus species, Ligilactobacillus salivarius, Enterocloster bolteae and Methanobrevibacter smithii, and changes in secondary cholic acids were positively correlated with Bacteroides species and Roseburia species.Conclusion: The well-known opportunistic pathogenic Klebsiella pneumonia and other special gut microbes significantly enriched in GBS. GABA and secondary cholic acid metabolism were significantly disturbed in GBS subjects and might be affected by the dysbiosis of gut microbial flora. These findings suggest that GABA may be a promising biomarker for the diagnosis of GBS and that modulation of gut microbiota might impact the clinical course of GBS.
Question: Write a study description for the study titled 'Marine metabolomics: measurement of metabolites in seawater by gas chromatography mass spectrometry'.
Answer: One of the major bottlenecks in describing marine ecosystems is characterizing the metabolome of seawater, as salt prevents metabolite analysis. We present SeaMet, a method that can detect hundreds of metabolites in less than one ml of seawater and quantifies them down to nano-molar levels using gas chromatography-mass spectrometry. Our method provides a major advance in marine metabolomics by enabling the unbiased analysis of primary metabolites across saltwater habitats.  Solid phase extraction is reported in the current study MTBLS849. Method development is reported in MTBLS826. The effect of salt and water on metabolite detection is reported in MTBLS839. Cell culture sampling is reported in MTBLS843. Environmental sampling is reported in MTBLS844. Method quantification is reported in MTBLS848.  Linked Studies: MTBLS826 MTBLS839 MTBLS843 MTBLS844 MTBLS848
Question: Write a study description for the study titled 'The plasticity of the grapevine berry transcriptome'.
Answer: Vitis vinifera cultivar Corvina clone 48 berries were harvested from different vineyards, each located in one of the three most important wine production macro-areas of the Verona region: Bardolino, Valpolicella and Soave, on the basis of the site geographical coordinates. For each of the selected vineyards, specific environmental conditions (altitude and type of soil) and farming and agricultural practices used (training system, rows facing direction, planting layout, vineyard age and rootstock type) were recorded. Vineyards were selected in order to maximize differences in locations and in microenvironmental and farming conditions. Berries were harvested at three different developmental stages: véraison, mid-ripening and harvest; each sample was collected in three biological replicates, to cover the whole vineyard variability. The same sampling procedure had been repeated over three consecutive vintages (2006, 2007 and 2008).
Question: Write a study description for the study titled 'Novel Minor Groove Binders cure animal African trypanosomiasis in an in vivo mouse model'.
Answer: Animal African trypanosomiasis (AAT) is a significant socioeconomic burden for sub-Saharan Africa because of its huge impact on livestock health. Existing therapies including those based on minor groove binders (MGBs), such as the diamidines, which have been used for decades, have now lost efficacy in some places because of the emergence of resistant parasites. Consequently, the need for new chemotherapies is urgent. Here, we describe a structurally distinct class of MGBs, Strathclyde MGBs (S-MGBs), which display excellent in vitro activities against the principal causative organisms of AAT: Trypanosoma congolense, and Trypanosoma vivax. We also show the cure of T. congolense-infected mice by a number of these compounds. In particular, we identify S-MGB-234, compound 7, as curative by using two applications of 50 mg/kg intraperitoneally. Crucially, we demonstrate that S-MGBs do not show cross-resistance with the current diamidine drugs and are not internalized via the transporters used by diamidines. This study demonstrates that S-MGBs have significant potential as novel therapeutic agents for AAT.
Question: Write a study description for the study titled 'Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders'.
Answer: Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small-intestinal microbial diversity and small-intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.
Question: Write a study description for the study titled 'Composition of the marine exometabolome is more stable than the functionally redundant microbial community in the oligotrophic North Atlantic'.
Answer: Untargeted features from the Bermuda Atlantic Time-series Study (BATS) site collected during the time period spanning 2016 to 2019. Metabolites were sampled from surface seawater to 1000 m deep and throughout the year. Dissolved organic matter extracts were analyzed in positive and negative ion mode with an ultra-high performance liquid chromatography system (Vanquish UHPLC, Thermo Scientific) coupled with an Orbitrap Fusion Lumos Tribid mass spectrometer.