{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002515","ANALYSIS_ID":"AN004142","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":"Time course 2: Acetate quantification from growth of Eggerthella lenta in defined media","STUDY_TYPE":"Untargeted LC-MS","STUDY_SUMMARY":"This dataset contains targeted metabolomics analysis of carboxylic acids in supernatants from 3 strains of Eggerthella lenta grown in defined EDM1 media with varying acetate concentrations.","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":"Bacteria","SUBJECT_SPECIES":"Eggerthella lenta","TAXONOMY_ID":"84112","GENOTYPE_STRAIN":"DSM 2243, Valencia, AB8n2"},
"SUBJECT_SAMPLE_FACTORS":[
{
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"Additional sample data":{"RAW_FILE_NAME":"P1-B03.d","RAW_FILE_NAME":"P1-B03.mzML","MS_Sample":"S.B3","Replicate":"3","well":"B3","OD600":"0.142","Row":"B","Column":"3"}
},
{
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"Additional sample data":{"RAW_FILE_NAME":"P1-E02.d","RAW_FILE_NAME":"P1-E02.mzML","MS_Sample":"S.E2","Replicate":"1","well":"E2","OD600":"0.162","Row":"E","Column":"2"}
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{
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{
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{
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},
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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"Additional sample data":{"RAW_FILE_NAME":"P1-F02.d","RAW_FILE_NAME":"P1-F02.mzML","MS_Sample":"S.F2","Replicate":"1","well":"F2","OD600":"0.201","Row":"F","Column":"2"}
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{
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{
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{
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{
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},
{
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},
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},
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},
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
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},
{
"Subject ID":"-",
"Sample ID":"PooledQC_01",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"PooledQC_01.d","RAW_FILE_NAME":"PooledQC_01.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
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"Additional sample data":{"RAW_FILE_NAME":"PooledQC_02.d","RAW_FILE_NAME":"PooledQC_02.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
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"Additional sample data":{"RAW_FILE_NAME":"PooledQC_03.d","RAW_FILE_NAME":"PooledQC_03.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
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},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_02",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_02.d","RAW_FILE_NAME":"Std_mSt_02.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_03",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_03.d","RAW_FILE_NAME":"Std_mSt_03.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_04",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_04.d","RAW_FILE_NAME":"Std_mSt_04.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_05",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_05.d","RAW_FILE_NAME":"Std_mSt_05.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_06",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_06.d","RAW_FILE_NAME":"Std_mSt_06.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_07",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_07.d","RAW_FILE_NAME":"Std_mSt_07.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_08",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_08.d","RAW_FILE_NAME":"Std_mSt_08.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_09",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_09.d","RAW_FILE_NAME":"Std_mSt_09.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_10",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_10.d","RAW_FILE_NAME":"Std_mSt_10.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_11",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_11.d","RAW_FILE_NAME":"Std_mSt_11.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_mSt_12",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_mSt_12.d","RAW_FILE_NAME":"Std_mSt_12.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_01",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_01.d","RAW_FILE_NAME":"Std_PBSSt_01.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_02",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_02.d","RAW_FILE_NAME":"Std_PBSSt_02.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_03",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_03.d","RAW_FILE_NAME":"Std_PBSSt_03.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_04",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_04.d","RAW_FILE_NAME":"Std_PBSSt_04.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_05",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_05.d","RAW_FILE_NAME":"Std_PBSSt_05.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_06",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_06.d","RAW_FILE_NAME":"Std_PBSSt_06.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_07",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_07.d","RAW_FILE_NAME":"Std_PBSSt_07.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_08",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_08.d","RAW_FILE_NAME":"Std_PBSSt_08.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_09",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_09.d","RAW_FILE_NAME":"Std_PBSSt_09.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_10",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_10.d","RAW_FILE_NAME":"Std_PBSSt_10.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_11",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_11.d","RAW_FILE_NAME":"Std_PBSSt_11.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"Std_PBSSt_12",
"Factors":{"Strain":"-","AcetateConc":"-","TimePoint":"-","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"Std_PBSSt_12.d","RAW_FILE_NAME":"Std_PBSSt_12.mzML","MS_Sample":"-","Replicate":"-","well":"-","OD600":"-","Row":"-","Column":"-"}
},
{
"Subject ID":"-",
"Sample ID":"P1-E01",
"Factors":{"Strain":"c","AcetateConc":"0","TimePoint":"TP4","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-E01.d","RAW_FILE_NAME":"P1-E01.mzML","MS_Sample":"S.E1","Replicate":"1","well":"E1","OD600":"-","Row":"E","Column":"1"}
},
{
"Subject ID":"-",
"Sample ID":"P1-E04",
"Factors":{"Strain":"c","AcetateConc":"0","TimePoint":"TP4","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-E04.d","RAW_FILE_NAME":"P1-E04.mzML","MS_Sample":"S.E4","Replicate":"2","well":"E4","OD600":"-","Row":"E","Column":"4"}
},
{
"Subject ID":"-",
"Sample ID":"P1-E06",
"Factors":{"Strain":"c","AcetateConc":"0","TimePoint":"TP7","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-E06.d","RAW_FILE_NAME":"P1-E06.mzML","MS_Sample":"S.E6","Replicate":"1","well":"E6","OD600":"-","Row":"E","Column":"6"}
},
{
"Subject ID":"-",
"Sample ID":"P1-E08",
"Factors":{"Strain":"c","AcetateConc":"0","TimePoint":"TP7","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-E08.d","RAW_FILE_NAME":"P1-E08.mzML","MS_Sample":"S.E8","Replicate":"2","well":"E8","OD600":"-","Row":"E","Column":"8"}
},
{
"Subject ID":"-",
"Sample ID":"P1-C01",
"Factors":{"Strain":"c","AcetateConc":"10","TimePoint":"TP4","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-C01.d","RAW_FILE_NAME":"P1-C01.mzML","MS_Sample":"S.C1","Replicate":"1","well":"C1","OD600":"-","Row":"C","Column":"1"}
},
{
"Subject ID":"-",
"Sample ID":"P1-C04",
"Factors":{"Strain":"c","AcetateConc":"10","TimePoint":"TP4","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-C04.d","RAW_FILE_NAME":"P1-C04.mzML","MS_Sample":"S.C4","Replicate":"2","well":"C4","OD600":"-","Row":"C","Column":"4"}
},
{
"Subject ID":"-",
"Sample ID":"P1-C06",
"Factors":{"Strain":"c","AcetateConc":"10","TimePoint":"TP7","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-C06.d","RAW_FILE_NAME":"P1-C06.mzML","MS_Sample":"S.C6","Replicate":"1","well":"C6","OD600":"-","Row":"C","Column":"6"}
},
{
"Subject ID":"-",
"Sample ID":"P1-C08",
"Factors":{"Strain":"c","AcetateConc":"10","TimePoint":"TP7","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-C08.d","RAW_FILE_NAME":"P1-C08.mzML","MS_Sample":"S.C8","Replicate":"2","well":"C8","OD600":"-","Row":"C","Column":"8"}
},
{
"Subject ID":"-",
"Sample ID":"P1-E12",
"Factors":{"Strain":"c","AcetateConc":"10","TimePoint":"TP8","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-E12.d","RAW_FILE_NAME":"P1-E12.mzML","MS_Sample":"S.H11","Replicate":"2","well":"H11","OD600":"-","Row":"H","Column":"11"}
},
{
"Subject ID":"-",
"Sample ID":"P1-G11",
"Factors":{"Strain":"c","AcetateConc":"10","TimePoint":"TP8","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-G11.d","RAW_FILE_NAME":"P1-G11.mzML","MS_Sample":"S.G11","Replicate":"1","well":"G11","OD600":"-","Row":"G","Column":"11"}
},
{
"Subject ID":"-",
"Sample ID":"P1-A01",
"Factors":{"Strain":"c","AcetateConc":"1","TimePoint":"TP4","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-A01.d","RAW_FILE_NAME":"P1-A01.mzML","MS_Sample":"S.A1","Replicate":"1","well":"A1","OD600":"-","Row":"A","Column":"1"}
},
{
"Subject ID":"-",
"Sample ID":"P1-A04",
"Factors":{"Strain":"c","AcetateConc":"1","TimePoint":"TP4","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-A04.d","RAW_FILE_NAME":"P1-A04.mzML","MS_Sample":"S.A4","Replicate":"2","well":"A4","OD600":"-","Row":"A","Column":"4"}
},
{
"Subject ID":"-",
"Sample ID":"P1-A06",
"Factors":{"Strain":"c","AcetateConc":"1","TimePoint":"TP7","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-A06.d","RAW_FILE_NAME":"P1-A06.mzML","MS_Sample":"S.A6","Replicate":"1","well":"A6","OD600":"-","Row":"A","Column":"6"}
},
{
"Subject ID":"-",
"Sample ID":"P1-A08",
"Factors":{"Strain":"c","AcetateConc":"1","TimePoint":"TP7","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-A08.d","RAW_FILE_NAME":"P1-A08.mzML","MS_Sample":"S.A8","Replicate":"2","well":"A8","OD600":"-","Row":"A","Column":"8"}
},
{
"Subject ID":"-",
"Sample ID":"P1-D12",
"Factors":{"Strain":"c","AcetateConc":"1","TimePoint":"TP8","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-D12.d","RAW_FILE_NAME":"P1-D12.mzML","MS_Sample":"S.H10","Replicate":"2","well":"H10","OD600":"-","Row":"H","Column":"10"}
},
{
"Subject ID":"-",
"Sample ID":"P1-G10",
"Factors":{"Strain":"c","AcetateConc":"1","TimePoint":"TP8","Time":"-"},
"Additional sample data":{"RAW_FILE_NAME":"P1-G10.d","RAW_FILE_NAME":"P1-G10.mzML","MS_Sample":"S.G10","Replicate":"1","well":"G10","OD600":"-","Row":"G","Column":"10"}
},
{
"Subject ID":"-",
"Sample ID":"P1-A03",
"Factors":{"Strain":"Val","AcetateConc":"0","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-A03.d","RAW_FILE_NAME":"P1-A03.mzML","MS_Sample":"S.A3","Replicate":"3","well":"A3","OD600":"0.096","Row":"A","Column":"3"}
},
{
"Subject ID":"-",
"Sample ID":"P1-F01",
"Factors":{"Strain":"Val","AcetateConc":"0","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-F01.d","RAW_FILE_NAME":"P1-F01.mzML","MS_Sample":"S.F1","Replicate":"1","well":"F1","OD600":"0.116","Row":"F","Column":"1"}
},
{
"Subject ID":"-",
"Sample ID":"P1-F04",
"Factors":{"Strain":"Val","AcetateConc":"0","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-F04.d","RAW_FILE_NAME":"P1-F04.mzML","MS_Sample":"S.F4","Replicate":"2","well":"F4","OD600":"0.13","Row":"F","Column":"4"}
},
{
"Subject ID":"-",
"Sample ID":"P1-D03",
"Factors":{"Strain":"Val","AcetateConc":"0","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-D03.d","RAW_FILE_NAME":"P1-D03.mzML","MS_Sample":"S.D3","Replicate":"3","well":"D3","OD600":"0.176","Row":"D","Column":"3"}
},
{
"Subject ID":"-",
"Sample ID":"P1-F06",
"Factors":{"Strain":"Val","AcetateConc":"0","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-F06.d","RAW_FILE_NAME":"P1-F06.mzML","MS_Sample":"S.F6","Replicate":"1","well":"F6","OD600":"0.249","Row":"F","Column":"6"}
},
{
"Subject ID":"-",
"Sample ID":"P1-F08",
"Factors":{"Strain":"Val","AcetateConc":"0","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-F08.d","RAW_FILE_NAME":"P1-F08.mzML","MS_Sample":"S.F8","Replicate":"2","well":"F8","OD600":"0.26","Row":"F","Column":"8"}
},
{
"Subject ID":"-",
"Sample ID":"P1-D01",
"Factors":{"Strain":"Val","AcetateConc":"10","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-D01.d","RAW_FILE_NAME":"P1-D01.mzML","MS_Sample":"S.D1","Replicate":"1","well":"D1","OD600":"0.175","Row":"D","Column":"1"}
},
{
"Subject ID":"-",
"Sample ID":"P1-D04",
"Factors":{"Strain":"Val","AcetateConc":"10","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-D04.d","RAW_FILE_NAME":"P1-D04.mzML","MS_Sample":"S.D4","Replicate":"2","well":"D4","OD600":"0.179","Row":"D","Column":"4"}
},
{
"Subject ID":"-",
"Sample ID":"P1-G04",
"Factors":{"Strain":"Val","AcetateConc":"10","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-G04.d","RAW_FILE_NAME":"P1-G04.mzML","MS_Sample":"S.G4","Replicate":"3","well":"G4","OD600":"0.213","Row":"G","Column":"4"}
},
{
"Subject ID":"-",
"Sample ID":"P1-D06",
"Factors":{"Strain":"Val","AcetateConc":"10","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-D06.d","RAW_FILE_NAME":"P1-D06.mzML","MS_Sample":"S.D6","Replicate":"1","well":"D6","OD600":"0.693","Row":"D","Column":"6"}
},
{
"Subject ID":"-",
"Sample ID":"P1-D08",
"Factors":{"Strain":"Val","AcetateConc":"10","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-D08.d","RAW_FILE_NAME":"P1-D08.mzML","MS_Sample":"S.D8","Replicate":"2","well":"D8","OD600":"0.689","Row":"D","Column":"8"}
},
{
"Subject ID":"-",
"Sample ID":"P1-G06",
"Factors":{"Strain":"Val","AcetateConc":"10","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-G06.d","RAW_FILE_NAME":"P1-G06.mzML","MS_Sample":"S.G6","Replicate":"3","well":"G6","OD600":"0.795","Row":"G","Column":"6"}
},
{
"Subject ID":"-",
"Sample ID":"P1-B01",
"Factors":{"Strain":"Val","AcetateConc":"1","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-B01.d","RAW_FILE_NAME":"P1-B01.mzML","MS_Sample":"S.B1","Replicate":"1","well":"B1","OD600":"0.174","Row":"B","Column":"1"}
},
{
"Subject ID":"-",
"Sample ID":"P1-B04",
"Factors":{"Strain":"Val","AcetateConc":"1","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-B04.d","RAW_FILE_NAME":"P1-B04.mzML","MS_Sample":"S.B4","Replicate":"2","well":"B4","OD600":"0.193","Row":"B","Column":"4"}
},
{
"Subject ID":"-",
"Sample ID":"P1-G01",
"Factors":{"Strain":"Val","AcetateConc":"1","TimePoint":"TP4","Time":"28.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-G01.d","RAW_FILE_NAME":"P1-G01.mzML","MS_Sample":"S.G1","Replicate":"3","well":"G1","OD600":"0.204","Row":"G","Column":"1"}
},
{
"Subject ID":"-",
"Sample ID":"P1-B06",
"Factors":{"Strain":"Val","AcetateConc":"1","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-B06.d","RAW_FILE_NAME":"P1-B06.mzML","MS_Sample":"S.B6","Replicate":"1","well":"B6","OD600":"0.628","Row":"B","Column":"6"}
},
{
"Subject ID":"-",
"Sample ID":"P1-B08",
"Factors":{"Strain":"Val","AcetateConc":"1","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-B08.d","RAW_FILE_NAME":"P1-B08.mzML","MS_Sample":"S.B8","Replicate":"2","well":"B8","OD600":"0.765","Row":"B","Column":"8"}
},
{
"Subject ID":"-",
"Sample ID":"P1-G08",
"Factors":{"Strain":"Val","AcetateConc":"1","TimePoint":"TP7","Time":"47.5"},
"Additional sample data":{"RAW_FILE_NAME":"P1-G08.d","RAW_FILE_NAME":"P1-G08.mzML","MS_Sample":"S.G8","Replicate":"3","well":"G8","OD600":"0.778","Row":"G","Column":"8"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Time course experiments were conducted in tubes in the anaerobic chamber in a 37°C incubator. For all metabolomics experiments, three independent culture replicates were included for each condition, with an equal number of uninoculated control tubes. Starter cultures and inocula were prepared as described above for growth assays. 5mLs of defined media was added to VWR glass culture tubes (53283-800) with screw caps. The PBS-washed inoculum was added to culture tubes to obtain an approximate starting OD600 of 0.001. A preliminary growth assay was conducted to define time points spanning the exponential growth phase in the tested conditions. At each time point, OD600 measurements of all inoculated tubes were first measured using a Hach DR1900 spectrophotometer, with a paired control tube to normalize for the background. 100 μL from each tube were then transferred into a 96-well microplate, which was sealed and removed from the anaerobic chamber. Plates were centrifuged at 1,928 rcf at 4°C for 8 minutes, after which supernatants were collected into fresh polypropylene tubes or plates, sealed, and flash-frozen in liquid nitrogen.","SAMPLE_TYPE":"Bacterial culture supernatant","COLLECTION_FREQUENCY":"at time points specified in study design table over 64 hours (full growth phase)","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"For growth and metabolomics experiments, glycerol stocks of the 3 E. lenta strains were first streaked on BHI+ agar plates and incubated at 37°C for 2-3 days. Individual colonies were inoculated into 3-4 mL liquid BHI+ and incubated at 37°C for 40-48 hours, or until approximately early stationary phase. Culture optical density (600 nm wavelength absorbance, OD600) was measured using a Hach DR1900 spectrophotometer. 1 mL samples of BHI starter cultures were then centrifuged at 1,568 rcf for 4 minutes in a microcentrifuge (ThermoScientific mySpin 12) in the anaerobic chamber and resuspended in 1 mL sterile phosphate-buffered saline (PBS). The resulting suspension was vortexed and diluted to an approximate OD600 of 0.1, and used as inoculum into defined experimental conditions. Varying media conditions were prepared separately and all allowed to fully reduce in the anaerobic chamber prior to inoculation."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Samples (20 μL) were first mixed with an internal standard solution (30 μL; 1 mM phenylpropionate-d9) in a V-bottomed, poly(propylene), 96-well plate, and extracted by mixing with 3 sample volumes of extraction solution (75% acetonitrile:25% methanol). The plate was covered with a lid and centrifuged at 5,000 rcf for 15 min at 4 °C. Supernatant was collected for derivatization before subjecting to LC–MS analysis. Samples were processed using a derivatization method targeting compounds containing a free carboxylic acid. Extracted samples were mixed with 3-nitrophenylhydrazine (NPH; 200 mM in 50% acetonitrile) and N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide (120 mM in 6% pyridine) at a 2:1:1 ratio. The plate was sealed with a plastic sealing mat (Thermo Fisher Scientific, #AB-0566) and incubated at 40 °C, 600 rpm in a thermomixer for 60 min to derivatize the carboxylate-containing compounds. The reaction mixture was quenched with 0.02% formic acid in 10% acetonitrile:water before LC–MS."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Samples were injected via refrigerated autosampler into mobile phase and chromatographically separated by an Agilent 1290 Infinity II UPLC and detected using an Agilent 6545XT Q-TOF (quadrupole time of flight) mass spectrometer equipped with a dual jet stream electrospray ionization source, operating under extended dynamic range (1,700 m/z). Chromatographic separation was performed using an ACQUITY Bridged Ethylene Hybrid (BEH) C18 column 2.1 x 100 mm, 1.7-micron particle size, (Waters Corp. Milford, MA), using chromatographic conditions published elsewhere (Supplementary Table S26 of https://doi.org/10.1038/s41564-022-01109-9).","INSTRUMENT_NAME":"Agilent 1290 Infinity II","COLUMN_NAME":"Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)","COLUMN_TEMPERATURE":"50","FLOW_GRADIENT":"See","FLOW_RATE":"300 μL per minute","SOLVENT_A":"0.1% formic acid in water","SOLVENT_B":"0.1% formic acid in methanol","CHROMATOGRAPHY_TYPE":"Unspecified"},

"ANALYSIS":{"LABORATORY_NAME":"Dylan Dodd, Stanford","ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Agilent 6545 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","MS_COMMENTS":"Samples were injected via refrigerated autosampler into mobile phase and chromatographically separated by an Agilent 1290 Infinity II UPLC and detected using an Agilent 6545XT Q-TOF (quadrupole time of flight) mass spectrometer equipped with a dual jet stream electrospray ionization source, operating under extended dynamic range (1,700 m/z). MS1 spectra were collected in centroid mode, and peak assignments in samples were made based on comparisons of retention times and accurate masses from authentic standards using MassHunter Quantitative Analysis v.10.0 software from Agilent Technologies. Acetate was quantified from calibration curves constructed with acetate-d4 as a standard using isotope-dilution MS with phenylpropionate-d9 as the internal standard. Calibration curves were performed in a modified base form of EDM1 lacking amino acids and other carboxylic acids. A background level of 1.05mM of acetate was subtracted to obtain the final quantities.","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"mM",

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