GNPS - Metabolomic profiles of human fecal samples in different storage conditions
Ontology highlight
ABSTRACT:
INSTRUMENT(S): maXis 4G
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Pieter Dorrestein
PROVIDER: MSV000084554 | GNPS | Thu Nov 07 14:42:00 GMT 2019
REPOSITORIES: GNPS
Similar Datasets
Project description:Data was collected on a LC-MS/MS system (c-18 column) positive mode. Data analyzing storage conditions of different storage collection devices for human fecal samples.
2019-11-07 | MSV000084554 | MassIVE
Project description:Comparison of the fecal microbiota during variable collection and storage methods
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Project description:Background and objectivesCKD is a common public health problem. Identifying biomarkers adds prognostic/diagnostic value by contributing to an understanding of CKD at the molecular level and possibly defining new drug targets. Metabolomics provides a snapshot of biochemical events at a particular time in the progression of CKD. This cross-sectional metabolomics study ascertained whether plasma metabolite profiles are significantly different in CKD stages 2, 3, and 4.Design, setting, participants, & measurementsAn analysis of plasma metabolites, using gas and liquid chromatography coupled to mass spectrometry, was conducted on 30 nondiabetic men ages 40-52 years, with 10 participants each in CKD stages 2, 3, and 4 based on their estimated GFR (calculated by the Modified Diet in Renal Disease formula). Participants were recruited in late 2008, and plasma samples were tested at Metabolon Inc and analyzed in 2012.ResultsComparison of stage 3/stage 2 identified 62 metabolites that differed (P ≤ 0.05), with 39 higher and 23 lower in stage 3 compared with stage 2; comparisons of stage 4/stage 2 identified 111 metabolites, with 66 higher and 45 lower; and comparisons of stage 4/stage 3 identified 11 metabolites, with 7 higher and 4 lower. Major differences in metabolite profiles with increasing stage of CKD were observed, including altered arginine metabolism, elevated coagulation/inflammation, impaired carboxylate anion transport, and decreased adrenal steroid hormone production.ConclusionsGlobal metabolite profiling of plasma uncovered potential biomarkers of stages of CKD. Moreover, these biomarkers provide insight into possible pathophysiologic processes that may contribute to progression of CKD.
| S-EPMC3586968 | biostudies-literature
Project description:BackgroundDiet, loss of aryl hydrocarbon receptor (AhR) expression and their modification of the gut microbiota community composition and its metabolites affect the development of colorectal cancer (CRC). However, the concordance between fecal microbiota composition and the fecal metabolome is poorly understood. Mice with specific AhR deletion (AhRKO) in intestinal epithelial cell and their wild-type littermates were fed a low-fat diet or a high-fat diet. Shifts in the fecal microbiome and metabolome associated with diet and loss of AhR expression were assessed. Microbiome and metabolome data were integrated to identify specific microbial taxa that contributed to the observed metabolite shifts.ResultsOur analysis shows that diet has a more pronounced effect on mouse fecal microbiota composition than the impact of the loss of AhR. In contrast, metabolomic analysis showed that the loss of AhR in intestinal epithelial cells had a more pronounced effect on metabolite profile compared to diet. Integration analysis of microbiome and metabolome identified unclassified Clostridiales, unclassified Desulfovibrionaceae, and Akkermansia as key contributors to the synthesis and/or utilization of tryptophan metabolites.ConclusionsAkkermansia are likely to contribute to the synthesis and/or degradation of tryptophan metabolites. Our study highlights the use of multi-omic analysis to investigate the relationship between the microbiome and metabolome and identifies possible taxa that can be targeted to manipulate the microbiome for CRC treatment.
| S-EPMC7708923 | biostudies-literature
Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 1: reproducibility of labeling: mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples. Keywords: variety among tissues
2008-04-01 | GSE7530 | GEO
Project description:Ulcerative colitis is a chronic inflammatory disease of the colon that carries a significant disease burden in children. Therefore, new therapeutic approaches are being explored to help children living with this disease. Fecal microbiota transplantation (FMT) has been successful in some children with ulcerative colitis. However, the mechanism of its therapeutic effect in this patient population is not well understood. To characterize changes in gut microbial and metabolomic profiles after FMT, we performed 16S rRNA gene sequencing, shotgun metagenomic sequencing, virome analysis and untargeted metabolomics by gas chromatography-time of flight-mass spectrometry on stool samples collected before and after FMT from four children with ulcerative colitis who responded to this treatment. Alpha diversity of the gut microbiota increased after intervention, with species richness rising from 251 (S.D. 125) to 358 (S.D. 27). In responders, the mean relative abundance of bacteria in the class Clostridia shifted toward donor levels, increasing from 33% (S.D. 11%) to 54% (S.D. 16%). Patient metabolomic and viromic profiles exhibited a similar but less pronounced shift toward donor profiles after FMT. The fecal concentrations of several metabolites were altered after FMT, correlating with clinical improvement. Larger studies using a similar multi-omics approach may suggest novel strategies for the treatment of pediatric ulcerative colitis.
| S-EPMC6454419 | biostudies-literature
Project description:Background/aimsBoth fecal immunochemical test (FIT) and fecal calprotectin (Fcal) results are useful biomarkers for ulcerative colitis (UC). However, the situations in which each marker should be used are largely unknown.MethodsA total of 110 colonoscopy intervals of UC patients were assessed, and correlations between changes in colonoscopic findings and changes in the two aforementioned fecal markers were examined.ResultsAmong patients with mucosal healing (MH) and negative FIT or Fcal results at the initial colonoscopy, FIT and Fcal findings exhibited accuracies of 93% (38/41) and 79% (26/33), respectively, for predicting the results of the subsequent examination. Among the 24 patients who showed endoscopic activity at the precedent colonoscopy and MH at the subsequent examination, positive-to-negative conversion of FIT and Fcal findings at the subsequent examination was observed in 92% (12/13) and 62% (8/13) of patients, respectively. Among the 43 patients who showed endoscopic activity at both the precedent and subsequent examinations, Fcal findings reflected the change in endoscopic activity better than FIT results (r=0.59, p＜0.0001 vs r=0.30, p=0.054).ConclusionsThe FIT is useful for confirming MH and the occurrence of relapse. In contrast, Fcal is useful for monitoring the mucosal status of patients with active inflammation.
| S-EPMC5832338 | biostudies-literature
Project description:Flavor is a critical factor in apple quality. To better understand apple flavor, this study aimed to identify the relationships between sensory attributes and the chemical composition (volatiles and non-volatiles) of apples using a combined metabolomic and sensory evaluation. Sensory results showed the positive (apple, fruity, pineapple, sweetness, sourness) and negative (cucumber) flavor attributes of apples. A metabolomic analysis with statistical correlations revealed significant metabolites related to the flavor attributes of apples. Volatile esters (e.g., hexyl acetate and 2-methylbutyl acetate for apple and fruity notes) and non-volatile sugars and acids (total sugars, tartaric acid, and malic acid for balanced sweet and tart flavors) were associated with the apple flavor preferred by consumers. Some aldehydes and alcohols (e.g., (E)-2-nonenal) contributed to a negative hedonic perception (cucumber). The collected information demonstrated the roles of key chemical compounds in apple flavor quality, and may be applicable to quality control.
| S-EPMC10053392 | biostudies-literature
Project description:Twenty-eight subjects were selected for the study from among celiac disease patients regularly followed at the Medical Clinic of the University of Sassari. Celiac disease (CD) was diagnosed according to international guidelines. Patients were divided into two groups of 14 subjects based on the presence or absence of additional autoimmune diseases. Only autoimmune diseases confirmed by a specialist's certification were considered for the study. Further inclusion criteria included a body mass index (BMI) between 18 and 25 kg/m², a gluten-free diet (GFD) duration of one year or more, and an age between 18 and 60 years. Exclusion criteria were: (i) use of antibiotics, probiotics, or prebiotics in the 3 months prior to enrollment; (ii) a vegetarian or vegan diet; (iii) a history of malignancy, pregnancy, alcohol abuse, or drug addiction. Following a clinical evaluation, each patient provided a fecal sample. Additionally, three questionnaires were collected concerning: i) anamnestic and anthropometric data, ii) gastrointestinal symptoms, and iii) dietary habits and lifestyle.
2025-10-16 | PXD069517 | Pride
Project description:BackgroundThe gut microbiota (GM) constitutes a critical factor in the maintenance of physiological homeostasis. Numerous studies have empirically demonstrated that the GM is closely associated with the onset and progression of osteoporosis (OP). Nevertheless, the characteristics of the GM and its metabolites related to different forms of OP are poorly understood. In the present study, we examined the changes in the GM and its metabolites associated with various types of OP as well as the correlations among them.MethodsWe simultaneously established rat postmenopausal, disuse-induced, and glucocorticoid-induced OP models. We used micro-CT and histological analyses to observe bone microstructure, three-point bending tests to measure bone strength, and enzyme-linked immunosorbent assay (ELISA) to evaluate the biochemical markers of bone turnover in the three rat OP models and the control. We applied 16s rDNA to analyze GM abundance and employed untargeted metabolomics to identify fecal metabolites in all four treatment groups. We implemented multi-omics methods to explore the relationships among OP, the GM, and its metabolites.ResultsThe 16S rDNA sequencing revealed that both the abundance and alterations of the GM significantly differed among the OP groups. In the postmenopausal OP model, the bacterial genera g__Bacteroidetes_unclassified, g__Firmicutes_unclassified, and g__Eggerthella had changed. In the disuse-induced and glucocorticoid-induced OP models, g__Akkermansia and g__Rothia changed, respectively. Untargeted metabolomics disclosed that the GM-derived metabolites significantly differed among the OP types. However, a Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that it was mainly metabolites implicated in lipid and amino acid metabolism that were altered in all cases. An association analysis indicated that the histidine metabolism intermediate 4-(β-acetylaminoethyl) imidazole was common to all OP forms and was strongly correlated with all bone metabolism-related bacterial genera. Hence, 4-(β-acetylaminoethyl) imidazole might play a vital role in OP onset and progression.ConclusionsThe present work revealed the alterations in the GM and its metabolites that are associated with OP. It also disclosed the changes in the GM that are characteristic of each type of OP. Future research should endeavor to determine the causal and regulatory effects of the GM and the metabolites typical of each form of OP.
| S-EPMC10866450 | biostudies-literature