Three-tier quality control was performed on the XCMS output data: 1) In the metabolite annotation stage, structural identification was performed via matching against a standard spectral library; 2) In the data cleaning stage, null value filtering (removing ion peaks with > 50% missing values), KNN algorithm-based imputation of missing values, and RSD filtering (retaining feature peaks with a relative standard deviation ≤ 50%) were performed; 3) The resulting high-quality dataset was used for multivariate statistical analysis. This processing workflow effectively reduces the impact of technical variability on metabolomics analysis.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - positive - hilic","Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["Analysis was performed using an UHPLC (1290 Infinity LC, Agilent Technologies) coupled to a quadrupole time-of-flight (AB Sciex TripleTOF 6600) in Shanghai Applied Protein Technology Co., Ltd. Three samples in each group were used for analysis.
The chromatographic conditions were set as follows. In both electrospray ionization (ESI) positive and negative modes, the mobile phase contained A = 25 mM ammonium acetate and 25 mM ammonium hydroxide in water and B= acetonitrile. The gradient was 85% B for 1 min and was linearly reduced to 65% in 11 min, and then was reduced to 40% in 0.1 min and kept for 4 min, and then increased to 95% in 0.1 min, with a 5 min re-equilibration period employed. Samples were injected via an automatic sampler at 4 ℃, with a 2 μL injection volume and a flow rate of 0.5 mL/min.
"],"publication":["Dietary Bacillus coagulans supplementation improves liver health and modulates hepatic metabolic profiles in juvenile fourfinger threadfin (Eleutheronema tetradactylum)."],"submitter_name":["Nuo Chen"],"submitter_affiliation":["Guangdong Ocean University"],"organism_part":["intestine"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["After thawing slowly at 4 ℃, approximately 100 mg of liver tissue was sectioned on dry ice and transferred into a 2 mL Eppendorf tube. For metabolite extraction, 1 mL of pre-chilled mixed solvent (methanol: acetonitrile: water in a 2:2:1 volume ratio) was added. The samples were homogenized using an MP-type homogenizer (set program parameters to 24 cycles × 2, at a speed of 6.0 m/s, with each cycle lasting 20 seconds, repeated 3 times).
After grinding, the samples underwent two 30-minute cycles of low-temperature ultrasonic treatment, were allowed to settle at -20 ℃ for 60 minutes, and then centrifuged for 15 minutes (14,000 g, 4 ℃). The supernatant was collected and aliquoted into 900 μL/tube. The samples were vacuum freeze-dried, and the resulted powder was stored at -80 ℃ for subsequent analysis. Prior to mass spectrometry analysis, 100 μL of resuspension solution (acetonitrile: water in a 1:1 volume ratio) was added to the sample powder, and thoroughly vortexed.
Quality control (QC) samples prepared by mixing equal volumes of all test samples, were used to assess the condition of the instrument as well as the equilibration and stability of the chromatography-mass spectrometry system throughout the entire experimental process.
"],"organism":["Eleutheronema tetradactylum"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15455"],"author":["Jing Li. Guangdong Ocean University. lijing2025@gdou.edu.cn.","Nuo Chen. Guangdong Ocean University. chenn659@stu.gdou.edu.cn.","Zhongliang Wang. Guangdong Ocean University. wangzl@gdou.edu.cn."],"data_transformation_protocol":["The raw instrument data was converted to the MzML standard format using ProteoWizard software (version 3.0.6428), followed by chromatographic peak alignment, retention time correction, and peak area integration via the XCMS online platform (version 3.7.1). XCMS parameters were set as follows: the centWave algorithm was used with a mass deviation tolerance of 10 ppm during the peak detection stage, a peak width range of 10-60 scan points, and a signal intensity pre-filtering threshold of 10-100. During the peak grouping stage, the bandwidth was set to 5, the mass window to 0.025, and the minimum presence ratio to 0.5.
Juvenile E. tetradactylum were purchased from a local commercial fish company. The feed was purchased from Weifang Santong Biological Engineering Co., Ltd. (Weifang, China), with guaranteed nutritional composition of crude protein (content ≥ 55%), crude fat (content ≥ 8%), crude fiber (content ≤ 3%), and crude ash (content ≤ 16%). The B. coagulans T-21 strain was supplied by Kunming Aikete Biotechnology Co., Ltd. (Kunming, China).
B. coagulans T-21 strain was inoculated into MRS broth for enrichment culture. After 48 hours, the culture was centrifuged to collect the pellet, which was washed three times with sterile phosphate-buffered saline (PBS) and finally resuspended in PBS to 1 × 10^9 CFU/ml. The cultured B. coagulans was serially diluted and evenly sprayed onto the feed surface to a concentration of 1 × 10^8CFU/g. After dehydration, the feed was stored at -20 ℃ for future use.
Prior to the trial, 420 juvenile E. tetradactylum, healthy and uniform in size, were randomly divided into two groups which contained three replicates with 70 juveniles in each replicate, and acclimated in the tanks for 1 week. In the formal experiment with a span of 8 weeks, the juvenile fish in the control group were regularly fed three times each day at 8:00, 12:00 and 17:00, while fish in the B. coagulans group were fed the B. coagulans supplemented diet. Water quality was monitored regularly to ensure the following parameters: temperature at 27-29.5 ℃, salinity at 27-30, dissolved oxygen above 6 mg/L, pH 7.8-8.0, and ammonia nitrogen below 0.3 mg/L. The experiment was conducted in an indoor recirculating aquaculture system with filtered seawater.
After the feeding trial, the juvenile fish were randomly selected from each tank and sampled. The intestine was collected and frozen in liquid nitrogen, and stored at -80 ℃.
"],"omics_type":["Metabolomics"],"study_design":["Metabolomics","Probiotics","intestine","untargeted analysis","experimental blank","Eleutheronema tetradactylum","Agilent 1290 Infinity LC","AB SCIEX TripleTOF 6600","Agilent 1290 Infinity UHPLC","Bacillus coagulans","hepatic metabolism"],"curator_keywords":["Metabolomics","Probiotics","intestine","untargeted analysis","experimental blank","Eleutheronema tetradactylum","Agilent 1290 Infinity LC","AB SCIEX TripleTOF 6600","Agilent 1290 Infinity UHPLC","Bacillus coagulans","hepatic metabolism"],"mass_spectrometry_protocol":["Mass spectrometry analysis was performed using ESI source with the following parameters: Ion Source Gas 1 (Gas1) and Ion Source Gas 2 (Gas2) both set to 60 psi, Curtain Gas (CUR) at 30 psi, ion source temperature at 600 ℃, and ion spray voltage (ISVF) at ± 5500 V (dual-mode scanning for both positive and negative ions). The time-of-flight mass spectrometry (TOF MS) scan range was m/z 60-1000 Da and accumulation time was 0.20 s/spectrum, while the secondary mass spectrometry scan ranged m/z 25-1000 Da with an accumulation time of 0.05 s/spectrum. Secondary mass spectrometry data were acquired under information-dependent acquisition (IDA) mode, set to high-sensitivity mode, with a declustering potential (DP) of ± 60 V and a collision energy of 35 ± 15 eV. Dynamic exclusion was enabled to exclude isotope peaks within 4 Da, monitoring 10 candidate per cycle. QC samples were inserted into the analysis queue in random order to monitor instrument status and data reliability.
"],"additional_accession":[]},"is_claimable":false,"name":"Bacillus coagulans enhances fillet nutritional quality and alters intestinal metabolic profiles of juvenile Eleutheronema tetradactylum","description":"This study evaluated the effects of dietary Bacillus coagulans supplementation on muscle nutritional quality and intestinal metabolomics in juvenile four-finger threadfin (Eleutheronema tetradactylum). A total of 420 healthy juveniles were randomly assigned to a control group or a B. coagulans supplemented group (1×10^8 CFU/g feed) and reared in an indoor recirculating seawater system for 8 weeks. Results showed that crude protein content in muscle was significantly increased in the B. coagulans group, while moisture, crude lipid, and ash remained unchanged. Amino acid analysis revealed significant or extremely significant increases in alanine, serine, threonine, and methionine. All detected saturated, monounsaturated, and polyunsaturated fatty acids (including DHA, EPA, palmitic acid, and oleic acid) were highly significantly elevated. Untargeted intestinal metabolomics (LC-MS/MS) combined with OPLS-DA revealed distinct metabolic profiles between groups, with 43 differential metabolites identified under positive and negative ion modes, most of which were upregulated in the B. coagulans group. KEGG pathway enrichment indicated that these metabolites were mainly involved in amino acid metabolism, lipid metabolism, and unsaturated fatty acid biosynthesis. Collectively, dietary B. coagulans improved muscle protein and fatty acid composition and modulates intestinal metabolic pathways in juvenile E. tetradactylum, highlighting its potential as a beneficial probiotic additive in aquaculture feeds.
","dates":{"publication":"2026-08-25","submission":"2026-08-25"},"accession":"MTBLS15455","cross_references":{}}