{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002513","ANALYSIS_ID":"AN004139","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"Systems biology illuminates the alternative metabolic niche of the human gut bacterium Eggerthella lenta","PROJECT_TYPE":"Untargeted LC-MS","PROJECT_SUMMARY":"Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem.","INSTITUTE":"University of California, San Francisco","DEPARTMENT":"Microbiology and Immunology","LABORATORY":"Peter Turnbaugh","LAST_NAME":"Noecker","FIRST_NAME":"Cecilia","ADDRESS":"513 Parnassus Ave HSW1501, San Francisco, CA 94143","EMAIL":"cecilia.noecker@ucsf.edu","PHONE":"415-502-3264","FUNDING_SOURCE":"This work was supported by the National Institutes of Health (2R01HL122593; 1R01AT011117; 1R01DK114034 to P.J.T., F32GM140808 to C.N.). P.J.T. is a Chan Zuckerberg Biohub Investigator and held an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund.","PUBLICATIONS":"https://doi.org/10.1101/2022.09.19.508335","DOI":"http://dx.doi.org/10.21228/M89B04"},

"STUDY":{"STUDY_TITLE":"Gnotobiotic mice: Metabolites in serum of germ-free mice colonized with strains of gut bacterium Eggerthella lenta","STUDY_TYPE":"Untargeted LC-MS","STUDY_SUMMARY":"This dataset contains untargeted metabolomics analysis of serum of gnotobiotic mice either colonized with different strains of Eggerthella lenta for 2 weeks, or germ-free controls.","INSTITUTE":"University of California, San Francisco","LAST_NAME":"Noecker","FIRST_NAME":"Cecilia","ADDRESS":"513 Parnassus Ave HSW1501, San Francisco, CA 94143","EMAIL":"cecilia.noecker@ucsf.edu","PHONE":"415-502-3264","SUBMIT_DATE":"2023-03-21"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J","AGE_OR_AGE_RANGE":"6-10 weeks","GENDER":"Male","ANIMAL_ANIMAL_SUPPLIER":"University of California, San Francisco Gnotobiotics core facility"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Serum_El15644_6",
"Factors":{"SampleType":"-","Group":"-"},
"Additional sample data":{"Replicate":"-","Cage":"-","RAW_FILE_NAME":"Neg_Serum_El15644_6.raw","RAW_FILE_NAME":"Pos_Serum_El15644_6.raw","RAW_FILE_NAME":"Neg_Serum_El15644_6.mzML","RAW_FILE_NAME":"Pos_Serum_El15644_6.mzML"}
},
{
"Subject ID":"14",
"Sample ID":"Serum_El15644_14",
"Factors":{"SampleType":"Serum","Group":"El15644"},
"Additional sample data":{"Replicate":"14","Cage":"7","RAW_FILE_NAME":"Neg_Serum_El15644_14.raw","RAW_FILE_NAME":"Pos_Serum_El15644_14.raw","RAW_FILE_NAME":"Neg_Serum_El15644_14.mzML","RAW_FILE_NAME":"Pos_Serum_El15644_14.mzML"}
},
{
"Subject ID":"21",
"Sample ID":"Serum_El15644_21",
"Factors":{"SampleType":"Serum","Group":"El15644"},
"Additional sample data":{"Replicate":"21","Cage":"11","RAW_FILE_NAME":"Neg_Serum_El15644_21.raw","RAW_FILE_NAME":"Pos_Serum_El15644_21.raw","RAW_FILE_NAME":"Neg_Serum_El15644_21.mzML","RAW_FILE_NAME":"Pos_Serum_El15644_21.mzML"}
},
{
"Subject ID":"22",
"Sample ID":"Serum_El15644_22",
"Factors":{"SampleType":"Serum","Group":"El15644"},
"Additional sample data":{"Replicate":"22","Cage":"11","RAW_FILE_NAME":"Neg_Serum_El15644_22.raw","RAW_FILE_NAME":"Pos_Serum_El15644_22.raw","RAW_FILE_NAME":"Neg_Serum_El15644_22.mzML","RAW_FILE_NAME":"Pos_Serum_El15644_22.mzML"}
},
{
"Subject ID":"23",
"Sample ID":"Serum_El15644_23",
"Factors":{"SampleType":"Serum","Group":"El15644"},
"Additional sample data":{"Replicate":"23","Cage":"11","RAW_FILE_NAME":"Neg_Serum_El15644_23.raw","RAW_FILE_NAME":"Pos_Serum_El15644_23.raw","RAW_FILE_NAME":"Neg_Serum_El15644_23.mzML","RAW_FILE_NAME":"Pos_Serum_El15644_23.mzML"}
},
{
"Subject ID":"7",
"Sample ID":"Serum_El15644_7",
"Factors":{"SampleType":"Serum","Group":"El15644"},
"Additional sample data":{"Replicate":"7","Cage":"3","RAW_FILE_NAME":"Neg_Serum_El15644_7.raw","RAW_FILE_NAME":"Pos_Serum_El15644_7.raw","RAW_FILE_NAME":"Neg_Serum_El15644_7.mzML","RAW_FILE_NAME":"Pos_Serum_El15644_7.mzML"}
},
{
"Subject ID":"12",
"Sample ID":"Serum_El2243_12",
"Factors":{"SampleType":"Serum","Group":"El2243"},
"Additional sample data":{"Replicate":"12","Cage":"6","RAW_FILE_NAME":"Neg_Serum_El2243_12.raw","RAW_FILE_NAME":"Pos_Serum_El2243_12.raw","RAW_FILE_NAME":"Neg_Serum_El2243_12.mzML","RAW_FILE_NAME":"Pos_Serum_El2243_12.mzML"}
},
{
"Subject ID":"13",
"Sample ID":"Serum_El2243_13",
"Factors":{"SampleType":"Serum","Group":"El2243"},
"Additional sample data":{"Replicate":"13","Cage":"6","RAW_FILE_NAME":"Neg_Serum_El2243_13.raw","RAW_FILE_NAME":"Pos_Serum_El2243_13.raw","RAW_FILE_NAME":"Neg_Serum_El2243_13.mzML","RAW_FILE_NAME":"Pos_Serum_El2243_13.mzML"}
},
{
"Subject ID":"24",
"Sample ID":"Serum_El2243_24",
"Factors":{"SampleType":"Serum","Group":"El2243"},
"Additional sample data":{"Replicate":"24","Cage":"12","RAW_FILE_NAME":"Neg_Serum_El2243_24.raw","RAW_FILE_NAME":"Pos_Serum_El2243_24.raw","RAW_FILE_NAME":"Neg_Serum_El2243_24.mzML","RAW_FILE_NAME":"Pos_Serum_El2243_24.mzML"}
},
{
"Subject ID":"25",
"Sample ID":"Serum_El2243_25",
"Factors":{"SampleType":"Serum","Group":"El2243"},
"Additional sample data":{"Replicate":"25","Cage":"12","RAW_FILE_NAME":"Neg_Serum_El2243_25.raw","RAW_FILE_NAME":"Pos_Serum_El2243_25.raw","RAW_FILE_NAME":"Neg_Serum_El2243_25.mzML","RAW_FILE_NAME":"Pos_Serum_El2243_25.mzML"}
},
{
"Subject ID":"4",
"Sample ID":"Serum_El2243_4",
"Factors":{"SampleType":"Serum","Group":"El2243"},
"Additional sample data":{"Replicate":"4","Cage":"2","RAW_FILE_NAME":"Neg_Serum_El2243_4.raw","RAW_FILE_NAME":"Pos_Serum_El2243_4.raw","RAW_FILE_NAME":"Neg_Serum_El2243_4.mzML","RAW_FILE_NAME":"Pos_Serum_El2243_4.mzML"}
},
{
"Subject ID":"5",
"Sample ID":"Serum_El2243_5",
"Factors":{"SampleType":"Serum","Group":"El2243"},
"Additional sample data":{"Replicate":"5","Cage":"2","RAW_FILE_NAME":"Neg_Serum_El2243_5.raw","RAW_FILE_NAME":"Pos_Serum_El2243_5.raw","RAW_FILE_NAME":"Neg_Serum_El2243_5.mzML","RAW_FILE_NAME":"Pos_Serum_El2243_5.mzML"}
},
{
"Subject ID":"18",
"Sample ID":"Serum_ElAB12n2_18",
"Factors":{"SampleType":"Serum","Group":"ElAB12n2"},
"Additional sample data":{"Replicate":"18","Cage":"9","RAW_FILE_NAME":"Neg_Serum_ElAB12n2_18.raw","RAW_FILE_NAME":"Pos_Serum_ElAB12n2_18.raw","RAW_FILE_NAME":"Neg_Serum_ElAB12n2_18.mzML","RAW_FILE_NAME":"Pos_Serum_ElAB12n2_18.mzML"}
},
{
"Subject ID":"28",
"Sample ID":"Serum_ElAB12n2_28",
"Factors":{"SampleType":"Serum","Group":"ElAB12n2"},
"Additional sample data":{"Replicate":"28","Cage":"14","RAW_FILE_NAME":"Neg_Serum_ElAB12n2_28.raw","RAW_FILE_NAME":"Pos_Serum_ElAB12n2_28.raw","RAW_FILE_NAME":"Neg_Serum_ElAB12n2_28.mzML","RAW_FILE_NAME":"Pos_Serum_ElAB12n2_28.mzML"}
},
{
"Subject ID":"29",
"Sample ID":"Serum_ElAB12n2_29",
"Factors":{"SampleType":"Serum","Group":"ElAB12n2"},
"Additional sample data":{"Replicate":"29","Cage":"14","RAW_FILE_NAME":"Neg_Serum_ElAB12n2_29.raw","RAW_FILE_NAME":"Pos_Serum_ElAB12n2_29.raw","RAW_FILE_NAME":"Neg_Serum_ElAB12n2_29.mzML","RAW_FILE_NAME":"Pos_Serum_ElAB12n2_29.mzML"}
},
{
"Subject ID":"30",
"Sample ID":"Serum_ElAB12n2_30",
"Factors":{"SampleType":"Serum","Group":"ElAB12n2"},
"Additional sample data":{"Replicate":"30","Cage":"14","RAW_FILE_NAME":"Neg_Serum_ElAB12n2_30.raw","RAW_FILE_NAME":"Pos_Serum_ElAB12n2_30.raw","RAW_FILE_NAME":"Neg_Serum_ElAB12n2_30.mzML","RAW_FILE_NAME":"Pos_Serum_ElAB12n2_30.mzML"}
},
{
"Subject ID":"1",
"Sample ID":"Serum_GF_1",
"Factors":{"SampleType":"Serum","Group":"GF"},
"Additional sample data":{"Replicate":"1","Cage":"1","RAW_FILE_NAME":"Neg_Serum_GF_1.raw","RAW_FILE_NAME":"Pos_Serum_GF_1.raw","RAW_FILE_NAME":"Neg_Serum_GF_1.mzML","RAW_FILE_NAME":"Pos_Serum_GF_1.mzML"}
},
{
"Subject ID":"2",
"Sample ID":"Serum_GF_2",
"Factors":{"SampleType":"Serum","Group":"GF"},
"Additional sample data":{"Replicate":"2","Cage":"1","RAW_FILE_NAME":"Neg_Serum_GF_2.raw","RAW_FILE_NAME":"Pos_Serum_GF_2.raw","RAW_FILE_NAME":"Neg_Serum_GF_2.mzML","RAW_FILE_NAME":"Pos_Serum_GF_2.mzML"}
},
{
"Subject ID":"26",
"Sample ID":"Serum_GF_26",
"Factors":{"SampleType":"Serum","Group":"GF"},
"Additional sample data":{"Replicate":"26","Cage":"13","RAW_FILE_NAME":"Neg_Serum_GF_26.raw","RAW_FILE_NAME":"Pos_Serum_GF_26.raw","RAW_FILE_NAME":"Neg_Serum_GF_26.mzML","RAW_FILE_NAME":"Pos_Serum_GF_26.mzML"}
},
{
"Subject ID":"27",
"Sample ID":"Serum_GF_27",
"Factors":{"SampleType":"Serum","Group":"GF"},
"Additional sample data":{"Replicate":"27","Cage":"15","RAW_FILE_NAME":"Neg_Serum_GF_27.raw","RAW_FILE_NAME":"Pos_Serum_GF_27.raw","RAW_FILE_NAME":"Neg_Serum_GF_27.mzML","RAW_FILE_NAME":"Pos_Serum_GF_27.mzML"}
},
{
"Subject ID":"3",
"Sample ID":"Serum_GF_3",
"Factors":{"SampleType":"Serum","Group":"GF"},
"Additional sample data":{"Replicate":"3","Cage":"1","RAW_FILE_NAME":"Neg_Serum_GF_3.raw","RAW_FILE_NAME":"Pos_Serum_GF_3.raw","RAW_FILE_NAME":"Neg_Serum_GF_3.mzML","RAW_FILE_NAME":"Pos_Serum_GF_3.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Sample collection was performed as described in doi.org/10.1016/j.chom.2021.11.001 . Briefly, C57BL/6J mice (males, ages 4-8 weeks) were obtained from the University of California, San Francisco Gnotobiotics core facility (gnotobiotics.ucsf.edu) and housed in Iso positive cages (Tecniplast). Mice were colonized via oral gavage with E. lenta monocultures (109 CFU/mL, 200 μl gavage, n=6 E. lenta DSM 2243, n=5 E. lenta DSM 15644, n=4 E. lenta AB12n2) or control media (n=5 GF). Colonization was confirmed via anaerobic culturing and/or qPCR for an E. lenta specific marker (elnmrk1) [10,26]. Mice were colonized for 2 weeks prior to sacrifice and sample collection. Serum samples were collected.","SAMPLE_TYPE":"Blood (serum)","COLLECTION_FREQUENCY":"single time point (2 weeks after colonization)","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Mice were colonized via oral gavage with E. lenta monocultures (109 CFU/mL, 200 μl gavage, n=6 E. lenta DSM 2243, n=5 E. lenta DSM 15644, n=4 E. lenta AB12n2) or control media (n=5 GF). Colonization was confirmed via anaerobic culturing and/or qPCR for an E. lenta specific marker (elnmrk1). Mice were colonized for 2 weeks prior to sacrifice and sample collection. Samples were collected of ileal, cecal, and colonic contents, as well as serum."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Serum samples were first thawed on wet ice. 20 μL of serum was extracted with 4 volumes of methanol, containing stable isotope labeled internal standards. Samples were homogenized by vortexing for 20 seconds and placed in a -20oC for 1 hour to maximize protein precipitation. After freezer incubation, samples were centrifuged at 4oC at 18,407 rcf for 5 minutes. Supernatant was removed and dried under vacuum via centrivap (Labconco Corp.). Dried samples were then resuspended in 30 μL of 80% acetonitrile in water containing exogenous standard CUDA at 60 ng/mL. Samples were maintained at 4oC prior to prompt analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Samples, pools, and blanks were promptly added to a Thermo Vanquish Autosampler at 4°C in a Vanquish UHPLC (Thermo Fisher Scientific, Waltham, MA). Chromatographic separation was performed using an ACQUITY Bridged Ethylene Hybrid (BEH) Amide column 2.1 x 150 mm, 1.7-micron particle size, (Waters Corp. Milford, MA), using chromatographic conditions published elsewhere (HILIC method described in the Supplementary Methods of doi.org/10.1038/s41586-021-03707-9).","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)","COLUMN_TEMPERATURE":"40","FLOW_GRADIENT":"The gradient profile was held at 100% B for 2 minutes, from 100% B to 70% B in 5 minutes, holding at 70% B for 0.7 minute, from 70% B to 40% B for 1.3 minutes, holding at 40% B for 0.5 minutes, from 40% B to 30% B for 0.75 minutes, before returning to 100% B for 2.5 minutes and holding at 100% B for 4 minutes.","FLOW_RATE":"400 μL per minute","SOLVENT_A":"100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3","SOLVENT_B":"95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate","CHROMATOGRAPHY_TYPE":"HILIC"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2 selection of metabolites from our in-house ‘local’ library, when additional scan bandwidth was available MS2 was collected in a data-dependent manner. Mass range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was collected, loop count was 4, isolation window was 1.5 Da. Metabolomics data was processed using MS-DIAL v4.60. Features were excluded from analysis if peak height was not at least 5-fold greater in one or more samples compared to the procedural blank average.","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"relative ion counts",

"Data":[{"Metabolite":"10-Hydroxydecanoic acid","Serum_El15644_14":"5489177.0000","Serum_El15644_21":"5716856.0000","Serum_El15644_22":"6123948.0000","Serum_El15644_23":"5527376.0000","Serum_El15644_7":"4956270.0000","Serum_El2243_12":"5072149.0000","Serum_El2243_13":"5312469.0000","Serum_El2243_24":"7534054.0000","Serum_El2243_25":"5641622.0000","Serum_El2243_4":"4929676.0000","Serum_El2243_5":"5410162.0000","Serum_ElAB12n2_18":"7075422.0000","Serum_ElAB12n2_28":"5195730.0000","Serum_ElAB12n2_29":"7028816.0000","Serum_ElAB12n2_30":"7284012.0000","Serum_GF_1":"4445224.0000","Serum_GF_2":"3417229.0000","Serum_GF_26":"3213286.0000","Serum_GF_27":"3998295.0000","Serum_GF_3":"4342339.0000"},{"Metabolite":"1_2_4-Trihydroxybenzene","Serum_El15644_14":"804862.0000","Serum_El15644_21":"491044.0000","Serum_El15644_22":"451990.0000","Serum_El15644_23":"380614.0000","Serum_El15644_7":"752327.0000","Serum_El2243_12":"318030.0000","Serum_El2243_13":"238979.0000","Serum_El2243_24":"488150.0000","Serum_El2243_25":"383288.0000","Serum_El2243_4":"467419.0000","Serum_El2243_5":"1071243.0000","Serum_ElAB12n2_18":"434747.0000","Serum_ElAB12n2_28":"498491.0000","Serum_ElAB12n2_29":"268901.0000","Serum_ElAB12n2_30":"443523.0000","Serum_GF_1":"446709.0000","Serum_GF_2":"281411.0000","Serum_GF_26":"182256.0000","Serum_GF_27":"327650.0000","Serum_GF_3":"270196.0000"},{"Metabolite":"12S-HETE","Serum_El15644_14":"162135728.0000","Serum_El15644_21":"152677664.0000","Serum_El15644_22":"166057888.0000","Serum_El15644_23":"135974672.0000","Serum_El15644_7":"213954288.0000","Serum_El2243_12":"146206080.0000","Serum_El2243_13":"206663136.0000","Serum_El2243_24":"187122656.0000","Serum_El2243_25":"179645904.0000","Serum_El2243_4":"166836688.0000","Serum_El2243_5":"206578704.0000","Serum_ElAB12n2_18":"207090720.0000","Serum_ElAB12n2_28":"138797680.0000","Serum_ElAB12n2_29":"137997680.0000","Serum_ElAB12n2_30":"136109632.0000","Serum_GF_1":"167073632.0000","Serum_GF_2":"163416608.0000","Serum_GF_26":"142731376.0000","Serum_GF_27":"107060336.0000","Serum_GF_3":"154430816.0000"},{"Metabolite":"1_3-Cyclohexanedicarboxylic 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}