LuYuxing/MetaBench huggingface dataset:
Question: Write a study description for the study titled 'Uncovering the Effects of Microorganisms and Metabolism on the Growth of Monochasma sheareri Franch. ex Maxim under Parasitic Cultivation'.
Answer: In this study, we systematically analyzed the root metabolites, root exudates and associated microbial communities of M. savatieri under both parasitic and non-parasitic conditions using metabolomics as well as 16S rRNA gene and ITS high-throughput sequencing techniques. Our research provides a theoretical foundation for the development of high-yield cultivation techniques for M. savatieri, deepening the understanding of the underlying mechanisms of parasitism.
Question: Write a study description for the study titled 'Mass spectrometry based metabolomics for in vitro systems pharmacology: Pitfalls, challenges, and computational solutions'.
Answer: INTRODUCTION: Mass spectrometry based metabolomics has become a promising complement and alternative to transcriptomics and proteomics in many fields including in vitro systems pharmacology. Despite several merits, metabolomics based on liquid chromatography mass spectrometry (LC-MS) is a developing area that is yet attached to several pitfalls and challenges. To reach a level of high reliability and robustness, these issues need to be tackled by implementation of refined experimental and computational protocols.OBJECTIVES: This study illustrates some key pitfalls in LC-MS based metabolomics and introduces an automated computational procedure to compensate for them.METHODS: Non-cancerous mammary gland derived cells were exposed to 21 chemicals from four pharmacological classes plus a set of 6 pesticides. Changes in the metabolome of cell lysates were assessed after 24h using LC-MS. A data processing pipeline was established and evaluated to handle issues including contaminants, carry over effects, intensity decay and inherent methodology variability and biases. A key component in this pipeline is a latent variable method called OOS-DA (optimal orthonormal system for discriminant analysis), being theoretically more easily motivated than PLS-DA in this context, as it is rooted in pattern classification rather than regression modeling.RESULTS: The pipeline is shown to reduce experimental variability/biases and is used to confirm that LC-MS spectra hold drug class specific information.CONCLUSIONS: LC-MS based metabolomics is a promising methodology, but comes with pitfalls and challenges. Key difficulties can be largely overcome by means of a computational procedure of the kind introduced and demonstrated here. The pipeline is freely available on www.github.com/stephanieherman/MS-data-processing.
Question: Write a study description for the study titled 'Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma'.
Answer: A discovery-based lipid profiling study of serum samples from a cohort that included patients with clear cell Renal Cell Carcinoma (ccRCC) stage I, II, III, and IV (n=112) and controls (n=52) was performed using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry and machine learning techniques. Multivariate models based on support vector machines and the LASSO variable selection method yielded two discriminant lipid panels for ccRCC detection and early diagnosis. A 16-lipid panel allowed discriminating ccRCC patients from controls with 95.7% accuracy in a training set under cross- validation, and 77.1% accuracy in an independent test set. A second model trained to discriminate early (I and II) from late (III and IV) stage ccRCC yielded a panel of 26 compounds that classified stage I patients from an independent test set with 82.1% accuracy. Thirteen species, including cholic acid, undecylenic acid, lauric acid, LPC(16:0/0:0), and PC(18:2/18:2) identified with level 1 exhibited significant lower levels in samples from ccRCC patients compared to controls. Moreover, 3α-hydroxy-5α-androstan-17-one 3-sulfate, cis-5-dodecenoic acid, arachidonic acid, cis-13-docosenoic acid, PI(16:0/18:1), PC(16:0/18:2), and PC(O-16:0/20:4) contributed to discriminate early from late ccRCC stage patients. The results are auspicious for early ccRCC diagnosis after validation of the panels in larger and different cohorts.
Question: Write a study description for the study titled 'Metabolomic responses to long-term salt stress in related Lotus species (C)'.
Answer: The legume genus Lotus includes glycophytic forage crops and other species adapted to extreme environments, such as saline soils. Understanding salt tolerance mechanisms will contribute to the discovery of new traits which may enhance the breeding efforts towards improved performance of legumes in marginal agricultural environments. Here, we used a combination of ionomic and gas chromatography-mass spectrometry (GC-MS)-based metabolite profilings of complete shoots (pooling leaves, petioles and stems) to compare the extremophile Lotus creticus, adapted to highly saline coastal regions, and two cultivated glycophytic grassland forage species, Lotus corniculatus and Lotus tenuis. L. creticus exhibited better survival after exposure to long-term lethal salinity and was more efficient at excluding Cl- from the shoots than the glycophytes. In contrast, Na+ levels were higher in the extremophile under both control and salt stress, a trait often observed in halophytes. Ionomics demonstrated a differential rearrangement of shoot nutrient levels in the extremophile upon salt exposure. Metabolite profiling showed that responses to NaCl in L. creticus shoots were globally similar to those of the glycophytes, providing little evidence for metabolic pre-adaptation to salinity. This study is the first comparing salt acclimation responses between extremophile and non-extremophile legumes, and challenges the generalization of the metabolic salt pre-adaptation hypothesis.
Question: Write a study description for the study titled 'The impact of rumen and hindgut microbiomes on the persistent productivity of dairy cows.'.
Answer: BackgroundPersistent productivity and productive lifespan determine the lifetime output of dairy cows and influence overall herd profitability. The composition and metabolic activity of the gastrointestinal microbiota of dairy cows influence persistent productivity. However, the processes by which host-microbiome crosstalk drives dairy cow persistent productivity remain unclear. Therefore, we performed an integrative comparative analysis of rumen and rectum metagenomes and metabolomes, together with serum and milk metabolomes, in long-lived dairy cows that exhibited divergent persistent productivity levels to elucidate the potential mechanisms that underpin modulation of persistent productivity by the rumen and rectum microbiota.ResultsSerum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group, but rectum fermentation parameters and rumen and rectum microbiota diversity showed no significant differences between LH and LL cows. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows’ rumen and rectum microbial interaction networks exhibited dependence on key nodes and streamlined inter-node connectivity that enhanced local functional synergy, with robustness, cohesion, and vulnerability levels similar to LL cows. The rumen Acidaminococcaceae bacterium and rectum Parabacteroides sp. exerted a positive effect on MY via microbiota-host co-metabolism of the purine metabolites guanosine and D-ribose-1-phosphate. Furthermore, the specific rumen microbiome module enhanced the levels of circulating eicosapentaenoic acid (EPA), thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively impacted MY.ConclusionsThe rumen and rectum microbiota positively influence production levels of long-lived dairy cows via microbiota and host co-metabolites of purine metabolites. Additionally, rumen microbiota improves production levels by enhancing host synthesis of EPA through the modulation of α-linolenic acid metabolism. The study reveals the potential role of rumen and rectum microbiota in regulating productivity of cows with sustained production capacity, providing insights for nutritional management strategies aimed at improving the health status and persistent production capacity of dairy cows.
Question: Write a study description for the study titled 'Regional Immunological and Microbial Characterization of Peyer's Patches in the Small Intestine of Bactrian Camels'.
Answer: Background: Our earlier research showed that Bactrian camels have a unique lymph aggregation structure that is similar to ileal Peyer's patches (PPs) and plays a role in the mucosal immunology of the digestive tract. However, Bactrian camels exhibit PPs not only in the ileum but also in all segments of the small intestine, with the colonization flora and metabolite characteristics of these PPs in these regions remaining unclear.Method: In this study, the microbiota and metabolism of 36 intestinal PPs samples, including duodenal (D-PPs), jejunal (J-PPs) and ileal PPs (I-PPs) were profiled for six Bactrian camels using 16Sr RNA gene sequencing and liquid chromatography-mass spectrometry (LC-MS). To further investigate, we utilized an enzyme-linked immunosorbent test (ELISA) to analyze the levels of IgA, IgG and IgM in the same tissues. Results: A total of 11,063 distinct microbial amplicon sequence variations (ASVs) were detected. Among these ASVs, Out of these ASVs, 108 showed significant differences between D-PPs and J-PPs, 122 ASVs showed significant differences between D-PPs and I-PPs, and 20 ASVs were found to be different between I-PPs and J-PPs. On another hand, a total of 1006 metabolites were discovered. There were 191 metabolic differentiators between D-PPs and J-PPs, 193 between D-PPs and I-PPs and 6 between I-PPs and J-PPs. Those metabolites are mostly composed of amino acids and their derivatives. They are involved in the metabolism of histidine, arginine and proline, as well as the creation of phenylalanine, tyrosine and tryptophan. Conclusions: The microflora and metabolite characteristics of D-PPs in Bactrian camel were significantly different from those of J-PPs and I-PPs, while the microflora and metabolite characteristics of J-PPs and I-PPs were similar, which was the same distribution trend of intestinal secretory antibodies. This study provides new evidence for further study of segmental regulation of gastrointestinal mucosal immunity in Bactrian camels.
Question: Write a study description for the study titled 'Impact of in vitro hormone treatments on the bibenzyl production of Radula complanata (Targeted metabolomics)'.
Answer: Bibenzyls are a specialized metabolite class found throughout the plant kingdom. One of the most prolific producers of bibenzyls are liverworts, specifically plants of the Radula genera. These plants possess an incredible diversity of bibenzyls, prenylated bibenzyls and a few (bis)bibenzyls, several of which have medicinal properties, including perrottetinene, an analog of tetrahydrocannabinol from cannabis. To provide insight into the bibenzyls’ biosynthesis in planta, exogenous phytohormones were applied to in vitro grown Radula complanata and bibenzyl metabolite production was monitored with targeted and untargeted metabolomics. The targeted metabolomic analysis of six prenylated bibenzyls revealed that production of these metabolites was largely reduced when plants were treated with abscisic acid (AA), salicylic acid (SA), 1-naphthaleneacetic acid (NAA) or 6-benzylaminopurine (BAP). The reduction of these metabolites in the BAP and NAA treatment suggests that prenylated bibenzyl production is negatively correlated with vegetative plant growth. The reduction of bibenzyls at low AA and SA concentrations and mild increase at higher AA and SA concentrations suggest that their production is regulated by these stress hormones. In addition, six other bibenzyl metabolites were tentatively identified from the untargeted analysis. These results provide insight into the influence of phytohormones on the bioactive bibenzyl content of R. complanata.Targeted metabolomics is reported in the current study MTBLS4321.Untargeted metabolomics is reported in MTBLS3563.
Question: Write a study description for the study titled 'First evidence of sexual reproduction in a widespread protist parasite infecting marine dinoflagellates'.
Answer: While most parasites primarily reproduce asexually, they can transition to sexual reproduction to promote genetic diversity and maintain their infectiousness. Nonetheless, documentation of sexual reproduction is seldom observed in most parasitic species. In this study, we demonstrate the existence of specialized spores dedicated to sexual reproduction in the marine protist parasite Amoebophrya, which parasitizes planktonic dinoflagellates. These sexual spores exhibit distinct characteristics compared to infective spores, including larger size, unique swimming behavior, shorter lifespan, distinct metabolite production, and an inability to infect a new host. Transcriptome analysis of these spores, isolated through cytometry, reveals a significant expression of genes associated with meiosis and DNA replication, highlighting their involvement in sexual reproduction. The production of these sexual spores exhibits intergenerational variability and remains unaffected by host populations, including factors such as density, age, and the initial host-parasite ratio. Strikingly, a given infected host cell generates one of the two spore types, indicating a predetermined mechanism that is activated before release from the host. Through implementing a decision-support hierarchical model, we identify the density of infective spores before infection, both within the culture prepared for the inoculum (n-1 generation) and within the inoculum itself, as critical explanatory variables for understanding sexual spore production. We suggest that a density-dependent signal, operating among infective free-living spores of one generation, may induce sexual reproduction during the host infection, producing sexual spores in the subsequent generation.
Question: Write a study description for the study titled 'Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis'.
Answer: Natural variation can be extremely useful in unraveling the determinants of phenotypic trait evolution but has rarely been analyzed with unbiased metabolic profiling to understand how its effects are organized at the level of biochemical pathways. Native populations of Nicotiana attenuata, a wild tobacco species, have been shown to be highly genetically diverse for traits important for their interactions with insects. To resolve the chemodiversity existing in these populations, we developed a metabolomics and computational pipeline to annotate leaf metabolic responses to Manduca sexta herbivory. We selected seeds from 43 accessions of different populations from the southwestern United States—including the well-characterized Utah 30th generation inbred accession—and grew 183 plants in the glasshouse for standardized herbivory elicitation. Metabolic profiles were generated from elicited leaves of each plant using a high-throughput ultra HPLC (UHPLC)-quadrupole TOFMS (qTOFMS) method, processed to systematically infer covariation patterns among biochemically related metabolites, as well as unknown ones, and finally assembled to map natural variation. Navigating this map revealed metabolic branch-specific variations that surprisingly only partly overlapped with jasmonate accumulation polymorphisms and deviated from canonical jasmonate signaling. Fragmentation analysis via indiscriminant tandem mass spectrometry (idMS/MS) was conducted with 10 accessions that spanned a large proportion of the variance found in the complete accession dataset, and compound spectra were computationally assembled into spectral similarity networks. The biological information captured by this networking approach facilitates the mining of the mass spectral data of unknowns with high natural variation, as demonstrated by the annotation of a strongly herbivory-inducible phenolic derivative, and can guide pathway analysis.
Question: Write a study description for the study titled 'Gallbladder microbial species and host bile acids biosynthesis linked to cholesterol gallstone comparing to pigment individuals'.
Answer: Gallstones are crystalline deposits in the gallbladder that are traditionally classified as cholesterol, pigment or mixed stones based on their composition. Microbiota and host metabolism variances among the different types of gallstones remain largely unclear. Here, the bile and gallstone microbial species spectra of 29 subjects with gallstone disease (GSD, 24 cholesterol and 5 pigment) were revealed by type IIB restriction site-associated DNA microbiome sequencing (2bRAD-M). Among them (21 subjects: 18 cholesterol and 3 pigment), plasma samples were subjected to liquid chromatography-mass spectrometry (LC-MS) untargeted metabolomics. The microbiome yielded 896 species comprising 882 bacteria, 13 fungi, and 1 archaeon. Microbial profiling revealed significant enrichment of Cutibacterium acnes and Microbacterium sp005774735 in gallstone and Agrobacterium pusense and Enterovirga sp013044135 in the bile of cholesterol GSD subjects. The metabolome revealed 2296 metabolites, in which malvidin 3-(6''-malonylglucoside), 2-Methylpropyl glucosinolate and ergothioneine were markedly enriched in cholesterol GSD subjects. Metabolite set enrichment analysis (MSEA) demonstrated enriched bile acids biosynthesis in individuals with cholesterol GSD. Overall, the multi-omics analysis revealed that microbiota and host metabolism interaction perturbations differ depending on the disease type. Perturbed gallstone type-related microbiota may contribute to unbalanced bile acids metabolism in the gallbladder and host, representing a potential early diagnostic marker and therapeutic target for GSD.
Question: Write a study description for the study titled 'Metabolomics to elucidate the effects of novel sustainable feed additives in the feed of farmed salmon (HoloFood Trial A - seaweed-dose response)'.
Answer: Testing the effect of blue mussel ensilage as a novel cost-efficient protein feed source for Atlantic salmon feed. Fermentation of novel raw materials for fish feed is a new practice with little prior experience of direct relevance to aquaculture and fish farming. In Trial A, an alternative marine compound is included in the feed, which is based on seaweed. In the trial were multiple inclusion levels used to investigate the effect of seaweed inclusion in an aquaculture setting.HoloFood Trial A - seaweed-dose response is reported in the current study MTBLS4381.HoloFood Trial B - blue mussel-dose response is reported in MTBLS4382.HoloFood Trial C - blue mussel ensilage-dose response is reported in MTBLS4384.HoloFood Trial D - fermented seaweed open water-dose response is reported in MTBLS6733.HoloFood Trial 1/2/3 is reported in MTBLS6988.Linked cross omic data sets:Nucleic acid data associated with this study are available in the European Nucleotide Archive (ENA): accession number PRJEB43192.Metagenomic data associated with this study are available from MGnify under the Super Study 'holofood'.
Question: Write a study description for the study titled 'Using an NMR metabolomics approach to investigate the pathogenicity of amyloid-beta and alpha-synuclein'.
Answer: INTRODUCTION: The pathogenicity at differing points along the aggregation pathway of many fibril-forming proteins associated with neurodegenerative diseases is unclear. Understanding the effect of different aggregation states of these proteins on cellular processes is essential to enhance understanding of diseases and provide future options for diagnosis and therapeutic intervention.  OBJECTIVES:To establish a robust method to probe the metabolic changes of neuronal cells and use it to monitor cellular response to challenge with three amyloidogenic proteins associated with neurodegenerative diseases in different aggregation states.  METHOD: Neuroblastoma SH-SY5Y cells were employed to design a robust routine system to perform a statistically rigorous NMR metabolomics study into cellular effects of sub-toxic levels of alpha-synuclein, amyloid-beta 40 and amyloid-beta 42 in monomeric, oligomeric and fibrillar conformations.  RESULTS: This investigation developed a rigorous model to monitor intracellular metabolic profiles of neuronal cells through combination of existing methods. This model revealed eight key metabolites that are altered when neuroblastoma cells are challenged with proteins in different aggregation states. Metabolic pathways associated with lipid metabolism, neurotransmission and adaptation to oxidative stress and inflammation are the predominant contributors to the cellular variance and intracellular metabolite levels. The observed metabolite changes for monomer and oligomer challenge may represent cellular effort to counteract the pathogenicity of the challenge, whereas fibrillar challenge is indicative of system shutdown. This implies that although markers of stress are more prevalent under oligomeric challenge the fibrillar response suggests a more toxic environment.  CONCLUSION: This approach is applicable to any cell type that can be cultured in a laboratory (primary or cell line) as a method of investigating how protein challenge affects signalling pathways, providing additional understanding as to the role of protein aggregation in neurodegenerative disease initiation and progression.
Question: Write a study description for the study titled '2E,4E-decadienoic acid, a novel anti-oomycete agent from co-culture of Bacillus subtilis and Trichoderma asperellum'.
Answer: Phytophthora nicotianae is an oomycete pathogen of global significance threatening many important crops. It is mainly controlled by chemosynthetic fungicides, which endangers ecosystem and human health; thus, there is an urgent need to explore alternatives for these fungicides. In this study, a new anti-oomycete aliphatic compound was obtained through co-culture of Bacillus subtilis and Trichoderma asperellum. The action mode of this natural product on P. nicotianae was preliminarily explored by using transcriptome, metabolome and physiological index detection.
Question: Write a study description for the study titled 'Metabolic Biomarkers of Ageing in C57BL/6J Wild-Type and Flavin-Containing Monooxygenase 5 (FMO5)-Knockout Mice'.
Answer: It was recently demonstrated in mice that knockout of the flavin-containing monooxygenase 5 gene, Fmo5, slows metabolic ageing via pleiotropic effects. We have now used an NMR-based metabonomics approach to study the effects of ageing directly on the metabolic profiles of urine and plasma from male, wild-type C57BL/6J and Fmo5−/− (FMO5 KO) mice back-crossed onto the C57BL/6J background. The aim of this study was to identify metabolic signatures that are associated with ageing in both these mouse lines and to characterize the age-related differences in the metabolite profiles between the FMO5 KO mice and their wild-type counterparts at equivalent time points. We identified a range of age-related biomarkers in both urine and plasma. Some metabolites, including urinary 6-hydroxy-6-methylheptan-3-one (6H6MH3O), a mouse sex pheromone, showed similar patterns of changes with age, regardless of genetic background. Others, however, were altered only in the FMO5 KO, or only in the wild-type mice, indicating the impact of genetic modifications on mouse ageing. Elevated concentrations of urinary taurine represent a distinctive, ageing-related change observed only in wild-type mice.