Metabolites were identified using an in-house R program and BiotreeDB version 3.0 by matching retention time, precursor ion mass-to-charge ratio and MS/MS spectra. Identification confidence was annotated according to the Metabolomics Standards Initiative criteria. Level 1 metabolites were matched to authentic standards using MS1, MS/MS and retention time; Level 2 metabolites were matched to public spectral databases using MS1 and MS/MS information; Level 3 metabolites were annotated using theoretical databases based on MS1, MS/MS and predicted retention time; and unmatched features were classified as Level 4 unknown compounds.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - hilic","Liquid Chromatography MS - positive - reverse-phase","Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["Chromatographic separation was performed using a Thermo Scientific Vanquish UHPLC system. For polar metabolite analysis, a Waters ACQUITY UPLC BEH Amide column (2.1 mm × 100 mm, 1.7 μm) was used. Mobile phase A was water containing 25 mmol/L ammonium acetate and 25 mmol/L ammonium hydroxide, and mobile phase B was acetonitrile. For non-polar metabolite analysis, a Phenomenex Kinetex C18 column (2.1 mm × 100 mm, 2.6 μm) was used. Mobile phase A was water containing 0.01% acetic acid, and mobile phase B was isopropanol and acetonitrile at a volume ratio of 1:1. For both chromatographic systems, the autosampler temperature was maintained at 4°C and the injection volume was 2 μL.
"],"publication":["Vitamin D deficiency disrupts a host–microbiota bile acid axis in aged mice to drive Faecalibaculum rodentium expansion and intestinal epithelial barrier dysfunction."],"submitter_name":["Xin Feng"],"submitter_affiliation":["College of Food Science and Nutritional Engineering, China Agricultural University"],"organism_part":["feces"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Approximately 25 mg of each fecal sample was weighed into a microcentrifuge tube under low-temperature conditions. Two homogenization beads and 500 μL of extraction solvent containing isotope-labelled internal standards were added. The extraction solvent consisted of methanol, acetonitrile and water at a volume ratio of 2:2:1. Samples were vortexed for 30 s, homogenized at 35 Hz for 4 min and sonicated in an ice-water bath for 5 min. The homogenization and sonication procedure was repeated three times. The samples were then incubated at -40°C for 1 h. Subsequently, 300 μL of the extract was transferred to a 96-well filtration plate and filtered under positive pressure at 6 psi for 180 s. The filtrates were collected for LC-MS analysis. A pooled quality-control sample was prepared by combining equal aliquots of the supernatants from all experimental samples.
"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15279"],"author":["Wenbiao Shi. Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University. wenbiao.shi@cau.edu.cn.","Xin Feng. College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China. No. 17 Qinghua East Road, Haidian District, Beijing 100083, China. 15961877791@163.com."],"data_transformation_protocol":["The acquired mass spectrometry data were converted to the mzXML format using ProteoWizard version 3.0.24054. Feature detection, extraction, alignment and integration were performed using an in-house R program based on XCMS. Features were filtered using relative standard deviation-based de-noising and missing-value filtering. Features with excessive missing values were removed, and the remaining missing values were imputed using one-half of the minimum detected value. Peak areas were normalized using the total ion current normalization method.
"],"study_factor":["Experimental group"],"submitter_email":["15961877791@163.com"],"sample_collection_protocol":["Fecal samples were collected individually from male C57BL/6J mice that were initially 18 months old and received a 16-week dietary intervention. The Aged group was fed a vitamin D-sufficient diet containing 1,000 IU/kg vitamin D3, whereas the Aged+VDD group was fed a vitamin D-deficient diet containing 0 IU/kg vitamin D3. Both diets contained 1% calcium and 0.7% phosphorus. Following collection, the fecal samples were stored at -80°C until metabolomic analysis.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Vanquish UHPLC System","ultra-performance liquid chromatography-mass spectrometry","Metabolomics","Mus musculus","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","Aging","experimental blank","targeted metabolite profiling","feces","untargeted metabolite profiling"],"curator_keywords":["Thermo Scientific Vanquish UHPLC System","ultra-performance liquid chromatography-mass spectrometry","Metabolomics","Mus musculus","untargeted analysis","Thermo Scientific Orbitrap Exploris 120","Aging","experimental blank","targeted metabolite profiling","feces","untargeted metabolite profiling"],"mass_spectrometry_protocol":["Mass spectrometric data were acquired using a Thermo Scientific Orbitrap Exploris 120 mass spectrometer controlled by Xcalibur software version 4.4. Electrospray ionization was operated separately in positive and negative ion modes over an m/z range of 70-1050. The sheath gas flow rate was 50 Arb, the auxiliary gas flow rate was 15 Arb and the capillary temperature was 320°C. The full MS resolution was 60,000 and the MS/MS resolution was 15,000. Stepped normalized collision energies of 20, 30 and 40 were used. The spray voltage was 3.8 kV in positive ion mode and -3.4 kV in negative ion mode.
"],"additional_accession":[]},"is_claimable":false,"name":"Vitamin D deficiency disrupts a host–microbiota bile acid axis in aged mice to drive Faecalibaculum rodentium expansion and intestinal epithelial barrier dysfunction","description":"This study investigated how vitamin D deficiency alters the fecal metabolome and bile acid metabolism in mice and evaluated the contribution of Faecalibaculum rodentium bile salt hydrolase activity to intestinal epithelial barrier dysfunction. Two complementary mouse experiments were included. In the first experiment, 18-month-old male C57BL/6J mice were fed either a vitamin D-sufficient diet containing 1,000 IU/kg vitamin D3 or a vitamin D-deficient diet containing 0 IU/kg vitamin D3 for 16 weeks. Fecal samples from the aged vitamin D-sufficient and vitamin D-deficient groups were analyzed by untargeted UHPLC-MS/MS metabolomics to characterize vitamin D deficiency-associated metabolic changes. In the second experiment, antibiotic-treated male C57BL/6J mice were assigned to control, Faecalibaculum rodentium gavage, or Faecalibaculum rodentium plus the gut-restricted bile salt hydrolase inhibitor GR-7 groups. Fecal bile acids were analyzed using targeted UPLC-MRM-MS/MS in negative ion mode to determine whether Faecalibaculum rodentium-induced bile acid remodeling was dependent on microbial bile salt hydrolase activity. Together, these datasets characterize a vitamin D–microbiota–bile acid axis associated with intestinal epithelial barrier dysfunction.","dates":{"publication":"2026-08-07","submission":"2026-08-07"},"accession":"MTBLS15279","cross_references":{}}