Metabolon samples: Compounds were identified by comparison to Metabolon's library of authenticated reference standards (>3,300 commercially available purified compounds), based on three criteria: retention time/index (RI) within a narrow window of the proposed identification, accurate mass match within ±10 ppm, and MS/MS forward and reverse scores against authentic standard library spectra. Recurrent unknown entities identified by chromatographic and mass spectral consistency were also reported.
In-house samples: Processed spectra from Compound Discoverer 3.3 SP were searched against ChemSpider databases including BioCyc, Human Metabolome Database (HMDB), and KEGG to assign compound names. Identifications were based on accurate mass matching and, where available, MS/MS spectral matching to reference databases.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - alternating - hilic","Liquid Chromatography MS - alternating - reverse-phase"],"chromatography_protocol":["Metabolon samples: Chromatographic separation was performed on a Waters ACQUITY UPLC system using an ACQUITY UPLC BEH C18 column (100 mm × 2.1 mm, 1.7 µm particle size; 186003555; Waters, Milford, MA). Four parallel methods were used to maximize metabolite coverage: (1) acidic positive ion conditions optimized for hydrophilic compounds, eluted with water and methanol containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA); (2) acidic positive ion conditions optimized for hydrophobic compounds, eluted from the same C18 column using methanol, acetonitrile, water, 0.05% PFPA, and 0.01% FA at higher organic content; (3) basic negative ion conditions on a separate dedicated C18 column, eluted with methanol and water containing 6.5 mM ammonium bicarbonate at pH 8; and (4) negative ionization following elution from a HILIC column (Waters UPLC BEH Amide, 2.1 × 150 mm, 1.7 µm) using water and acetonitrile with 10 mM ammonium formate at pH 10.8.
In-house samples: Chromatographic separation was performed on a Vanquish Neo UHPLC system (ThermoFisher Scientific) using a SeQuant ZIC-pHILIC column (150 mm × 2.1 mm, 5 µm particle size; 150454; Sigma-Aldrich). Mobile phase A consisted of 10 mM ammonium acetate in water, pH 9.8; mobile phase B consisted of 100% methanol. All chemicals were LC-MS grade. The flow rate was 0.15 mL/min and column temperature was maintained at 25°C. Metabolites were separated over a 19-minute gradient from 90% B to 30% B. The column was washed for 5 minutes at 30% B, then re-equilibrated at 90% B for 8 minutes.
"],"publication":["Exercise-Associated Microbial Metabolites Prevent Skeletal Muscle Atrophy in Adult Mice."],"submitter_name":["Yuan Wen"],"submitter_affiliation":["University of Kentucky"],"organism_part":["not applicable","cell culture medium","blood serum","cecum","skeletal muscle"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Metabolon samples (cecal content, serum, and gastrocnemius from cecal transfer experiments): Samples were shipped to Metabolon, Inc. (Morrisville, NC) and processed using their standard Global HD4 extraction protocol. Samples were extracted with methanol under vigorous shaking for 2 min to precipitate protein and dissociate small molecules bound to protein or trapped in the precipitated protein matrix, followed by centrifugation. Recovery standards were added prior to extraction to allow assessment of extraction efficiency.
In-house samples (gastrocnemius from VEH and PAS experiments): Gastrocnemius samples (n = 6/group) were pulverized using a CryoPREP CP02 Cryogenic Dry Pulverization system (Covaris, Woburn, MA), suspended in 1 mL of extraction solution (50% HPLC-grade methanol and 1% formic acid), and homogenized with zirconium silicate beads (ZSB10; Next Advance, Inc., Troy, NY) using a Bullet Blender Gold (Next Advance, Inc.). The supernatant was filtered using Captiva EMR-Lipid cartridges (5190-1002; Agilent Technologies, Santa Clara, CA) placed on top of autosampler vials (5190-2280; Agilent Technologies). Samples were dried and concentrated using a Savant SpeedVac Integrated Vacuum Concentrator System (SPD2030; ThermoFisher Scientific) at 25°C until a complete pellet formed (~48 hrs). The pellet was resuspended in 5% acetonitrile and 0.1% formic acid, filtered through 0.22 µm filters (8160; Costar, Glendale, AZ), and stored in polymer feet autosampler inserts (5183-2088; Agilent Technologies) within autosampler vials. Pooled QC samples (created by combining equal aliquots of all experimental samples) and solvent blanks were prepared in parallel.
"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS14386"],"author":["Yuan Wen. University of Kentucky. ywen2@uky.edu.","Benjamin Burke. University of Kentucky. benjamin.burke@uky.edu.","John McCarthy. University of Kentucky. jjmcca2@uky.edu."],"data_transformation_protocol":["Metabolon samples: Raw data were extracted, peak-identified, and QC-processed using Metabolon's proprietary hardware and software. Peaks were quantified using area-under-the-curve. For studies spanning multiple days, a data normalization step (block correction) was applied to correct for instrument inter-day tuning differences by registering medians to equal one and normalizing each data point proportionately.
In-house samples: Raw spectra were processed using Compound Discoverer 3.3 SP (ThermoFisher Scientific) for peak picking, alignment, deconvolution, and feature detection.
"],"study_factor":["Treatment"],"submitter_email":["ywen2@uky.edu"],"sample_collection_protocol":["Female C57BL/6J mice (4–12 months old) were used. Three sample types were collected: cecal contents, serum, and gastrocnemius muscle. Following the experimental protocol, mice were anesthetized via isoflurane and euthanized via cervical dislocation. Cecal contents were immediately snap-frozen in liquid nitrogen. Whole blood was collected, allowed to clot, and centrifuged at 150 × g for 15 min; the supernatant was removed and centrifuged again at 300 × g for 15 min to obtain serum. Gastrocnemius muscles were excised, weighed, and snap-frozen in liquid nitrogen. All samples were stored at −80°C until analysis. All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Kentucky.
"],"omics_type":["Metabolomics"],"study_design":["Metabolomics","Mus musculus","Muscle atrophy","not applicable","Thermo Scientific Orbitrap Exploris 240","untargeted analysis","Experimental","Process blank","Compound Discoverer","Waters ACQUITY UPLC system","Thermo Scientific Vanquish UHPLC System","Thermo Scientific Q Exactive","cell culture medium","blood serum","Quality control","cecum","skeletal muscle","Metabolon (United States)"],"curator_keywords":["Metabolomics","Mus musculus","Muscle atrophy","not applicable","Thermo Scientific Orbitrap Exploris 240","untargeted analysis","Experimental","Process blank","Compound Discoverer","Waters ACQUITY UPLC system","Thermo Scientific Vanquish UHPLC System","Thermo Scientific Q Exactive","cell culture medium","blood serum","Quality control","cecum","skeletal muscle","Metabolon (United States)"],"mass_spectrometry_protocol":["Metabolon samples: Analyses were performed on a ThermoFisher Scientific Q Exactive hybrid quadrupole-Orbitrap mass spectrometer interfaced with a heated electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at 35,000 resolution (FWHM). The MS analysis alternated between MS and data-dependent MS/MS scans using dynamic exclusion. The scan range varied slightly between methods but covered 70–1000 m/z. Methods 1 and 2 used positive ion mode; Methods 3 and 4 used negative ion mode.
In-house samples: Samples were analyzed on a ThermoFisher Scientific Orbitrap Exploris 240 mass spectrometer with a heated electrospray ionization source coupled to the Vanquish Neo UHPLC. Polarity-switching MS1-only acquisition was performed at 120,000 FWHM resolution with a scan range of 80–1200 m/z. The automatic gain control (AGC) target was set to 'Custom' at 1e6 absolute AGC value with a maximum injection time of 50 ms.
"],"additional_accession":[]},"is_claimable":false,"name":"Exercise-Associated Microbial Metabolites Prevent Skeletal Muscle Atrophy in Adult Mice","description":"We previously reported that skeletal muscle adaptation to regular exercise requires a healthy gut microbiome, contributing to growing evidence that some exercise benefits are mediated by microbiome-derived metabolites. Here, to identify such exercise-associated microbial metabolites, we transfer cecal contents from exercise-trained donor mice into exercise-naïve recipient mice undergoing unilateral hindlimb immobilization. Recipients of cecal material from exercise-trained donors exhibit less muscle atrophy compared with those receiving transfers from sedentary donors. Untargeted metabolomics reveal metabolites enriched in cecal content, serum, and muscle of recipients from exercise-trained donors, consistent with microbial origin. Oral administration of two such metabolites (pipecolic acid and succinate) attenuates muscle atrophy and preserves muscle function in exercise-naïve mice, potentially by enhancing cellular energy status and translational capacity. These findings further define the gut microbiome-skeletal muscle axis and provide evidence that exercise-associated microbial metabolites serve as a novel class of exercise mimetics for treating conditions responsive to physical activity.","dates":{"publication":"2026-05-27","submission":"2026-04-27"},"accession":"MTBLS14386","cross_references":{"HMDB":["HMDB0000227","HMDB0001301","HMDB0001414","HMDB0001257","HMDB0011599","HMDB0000699","HMDB0004705","HMDB0011616","HMDB0011691","HMDB0011629","HMDB0011640","HMDB0000208","HMDB0000715","HMDB0060282","HMDB0000355","HMDB0000440","HMDB0000807","HMDB0000619","HMDB0000020","HMDB0000157","HMDB0000132","HMDB0004704","HMDB0006270,HMDB0000673","HMDB0000232","HMDB0001325","HMDB0002064","HMDB0001015","HMDB0000045","HMDB0000101","HMDB0001209","HMDB0001043","HMDB0000517","HMDB0000191","HMDB0000669","HMDB0000755","HMDB0000205","HMDB0000056","HMDB0001008","HMDB0000030","HMDB0000254","HMDB0000442,HMDB0000357,HMDB0000011","HMDB0000067","HMDB0001565","HMDB0000562","HMDB0000078","HMDB0000192","HMDB0000095","HMDB0001401","HMDB0000252","HMDB0001202","HMDB0000626","HMDB0000269","HMDB0001248","HMDB0000134","HMDB0011737","HMDB0000625","HMDB0000661","HMDB0000123","HMDB0000138","HMDB0000128","HMDB0001397","HMDB0000085","HMDB0000870","HMDB0000177","HMDB0000195","HMDB0000211","HMDB0000213","HMDB0000172","HMDB0000510","HMDB0002757","HMDB0000904","HMDB0000687","HMDB0000761","HMDB0003405","HMDB0031518,HMDB0000156,HMDB0000744","HMDB0000696","HMDB0000202","HMDB0003502","HMDB0000220","HMDB0001406","HMDB0000827","HMDB0000214","HMDB0000226","HMDB0003229","HMDB0000159","HMDB0001429","HMDB0004610","HMDB0000162,HMDB0003411","HMDB0000190","HMDB0001545","HMDB0000305","HMDB0000244","HMDB0001895","HMDB0000187","HMDB0000259","HMDB0000251","HMDB0000806","HMDB0002666","HMDB0000296","HMDB0000012","HMDB0000301","HMDB0000148","HMDB0000641","HMDB0000167","HMDB0000929","HMDB0000883","HMDB0001488","HMDB0001431","HMDB0000122","HMDB0000050","HMDB0000043","HMDB0000574","HMDB0000169","HMDB0000092","HMDB0000161","HMDB0000158","HMDB0000691","HMDB0000767","HMDB0000243","HMDB0000300","HMDB0000098","HMDB0000089","HMDB0029942","HMDB0000288","HMDB0000273","HMDB0000235","HMDB0000660","HMDB0003213","HMDB0000034","HMDB0000630","HMDB0000262","HMDB0002259","HMDB0000772","HMDB0002212","HMDB0000163","HMDB0000283","HMDB0000168","HMDB0011761","HMDB0000666","HMDB0000258","HMDB0000239","HMDB0000826","HMDB0000725","HMDB0000462","HMDB0000107","HMDB0000292","HMDB0000663","HMDB0000267","HMDB0002243","HMDB0000271","HMDB0000210","HMDB0000070","HMDB0002894","HMDB0000139,HMDB0006372","HMDB0000026","HMDB0011756","HMDB0011745","HMDB0011757","HMDB0002068","HMDB0000054","HMDB0000303","HMDB0000133","HMDB0011741","HMDB0001893","HMDB0001890","HMDB0000828","HMDB0000766","HMDB0003681","HMDB0002166","HMDB0000518","HMDB0000094","HMDB0000306","HMDB0000289","HMDB0000946","HMDB0000892","HMDB0002088","HMDB0011738","HMDB0000707","HMDB0000039","HMDB0000230","HMDB0012275","HMDB0000489","HMDB01104","HMDB0000064","HMDB0005060","HMDB0029151","HMDB0062549","HMDB0003331","HMDB0001227","HMDB0000131","HMDB0000097","HMDB0001123","HMDB0011171","HMDB0011718","HMDB04950","HMDB0000754","HMDB0002100","HMDB0004949","HMDB0005320","HMDB0009784","HMDB0007973","HMDB0001348","HMDB0007972","HMDB0004950","HMDB0000468","HMDB0000951","HMDB0000036","HMDB0000896","HMDB0000784","HMDB0001999","HMDB0001844","HMDB0031193","HMDB0000622","HMDB0000062","HMDB0001870","HMDB0000764","HMDB0000209","HMDB0000714","HMDB0000881","HMDB0000893","HMDB0000491","HMDB0002005","HMDB0000362","HMDB0003464","HMDB0000857","HMDB0001432","HMDB0001370","HMDB0000014","HMDB0000071","HMDB0001520","HMDB0000127","HMDB0000126","HMDB0002320","HMDB0000684","HMDB0000086","HMDB0001262","HMDB0001138","HMDB0060493","HMDB0000241","HMDB0000299","HMDB0000402","HMDB00631","HMDB0003072","HMDB0000152","HMDB0001336","HMDB0003355","HMDB0000719","HMDB0000671","HMDB0000682","HMDB0000905","HMDB0028854","HMDB0000594","HMDB0000695","HMDB0002712","HMDB0004948","HMDB0010163","HMDB0010570","HMDB0240261","HMDB0000564","HMDB0002183","HMDB0007869","HMDB0000814","HMDB0000665,HMDB00746,HMDB0000624","HMDB0000176","HMDB0006024","HMDB0000779,HMDB0000563","HMDB0000222","HMDB0000812","HMDB0000734","HMDB0000201","HMDB0000731","HMDB0004437","HMDB0002329","HMDB0000500","HMDB0000448","HMDB0032616","HMDB0002545","HMDB0001964","HMDB0002670","HMDB0000937","HMDB0011567","HMDB0002124","HMDB0000019","HMDB0011537","HMDB0028818","HMDB0000721","HMDB0010734","HMDB0011538","HMDB0032538","HMDB0001842","HMDB0000867","HMDB0000878","HMDB0062620,HMDB0000943","HMDB0000565","HMDB0000852","HMDB0000197","HMDB0011568","HMDB0002649","HMDB0011533","HMDB0001132","HMDB00502","HMDB0000391","HMDB0000415","HMDB0000467","HMDB00400","HMDB0002302","HMDB0000875","HMDB0000623","HMDB0061715","HMDB0000866","HMDB0000017","HMDB0029068","HMDB0011172","HMDB0000325","HMDB0000350","HMDB0000321","HMDB0002261","HMDB0006528,HMDB0001976","HMDB0061714","HMDB0002226","HMDB0000898","HMDB0002024","HMDB0002820","HMDB0000792","HMDB0002902","HMDB0003312","HMDB0003217","HMDB0005781","HMDB0004157","HMDB0006547","HMDB0000932","HMDB0006029","HMDB0013713","HMDB0000512","HMDB0006028","HMDB0000759","HMDB0003869","HMDB0010382","HMDB0004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