{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002832","ANALYSIS_ID":"AN004625","VERSION":"1","CREATED_ON":"August 28, 2023, 2:26 pm"},

"PROJECT":{"PROJECT_TITLE":"Resource competition predicts assembly of in vitro gut bacterial communities","PROJECT_SUMMARY":"Microbiota dynamics arise from a plethora of interspecies interactions, including resource competition, cross-feeding, and pH modulation. The individual contributions of these mechanisms are challenging to untangle, especially in natural or complex laboratory environments where the landscape of resource competition is unclear. Here, we developed a framework to estimate the extent of multi-species niche overlaps by combining metabolomics data of individual species, growth measurements in pairwise spent media, and mathematical models. When applied to an in vitro model system of human gut commensals in complex media, our framework revealed that a simple model of resource competition described most pairwise interactions. By grouping metabolomic features depleted by the same set of species, we constructed a coarse-grained consumer-resource model that predicted assembly compositions to reasonable accuracy. Moreover, deviations from model predictions enabled us to identify and incorporate into the model additional interactions, including pH-mediated effects and cross-feeding, which improved model performance. In sum, our work provides an experimental and theoretical framework to dissect microbial interactions in complex in vitro environments.","INSTITUTE":"Stanford University","LAST_NAME":"DeFelice","FIRST_NAME":"Brian","ADDRESS":"1291 Welch Rd., Rm. G0821 (SIM1), Stanford CA, California, 94305, USA","EMAIL":"bcdefelice@ucdavis.edu","PHONE":"5303564485"},

"STUDY":{"STUDY_TITLE":"Resource competition predicts assembly of in vitro gut bacterial communities- HILIC","STUDY_SUMMARY":"Microbiota dynamics arise from a plethora of interspecies interactions, including resource competition, cross-feeding, and pH modulation. The individual contributions of these mechanisms are challenging to untangle, especially in natural or complex laboratory environments where the landscape of resource competition is unclear. Here, we developed a framework to estimate the extent of multi-species niche overlaps by combining metabolomics data of individual species, growth measurements in pairwise spent media, and mathematical models. When applied to an in vitro model system of human gut commensals in complex media, our framework revealed that a simple model of resource competition described most pairwise interactions. By grouping metabolomic features depleted by the same set of species, we constructed a coarse-grained consumer-resource model that predicted assembly compositions to reasonable accuracy. Moreover, deviations from model predictions enabled us to identify and incorporate into the model additional interactions, including pH-mediated effects and cross-feeding, which improved model performance. In sum, our work provides an experimental and theoretical framework to dissect microbial interactions in complex in vitro environments.","INSTITUTE":"Stanford University","LAST_NAME":"DeFelice","FIRST_NAME":"Brian","ADDRESS":"1291 Welch Rd.","EMAIL":"bcdefelice@ucdavis.edu","PHONE":"5303564485"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Bacteroides thetaiotaomicron","TAXONOMY_ID":"8188","SUBJECT_COMMENTS":"Fecal derived communities and isolates, supernatant was assayed"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0001",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 11"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0001.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0002",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 21"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0002.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0003",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 7"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0003.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0004",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 19"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0004.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0005",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 11"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0005.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0006",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 14"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0006.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0007",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 23"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0007.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0008",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 5"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0008.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0009",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 6"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0009.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0010",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 8"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0010.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0011",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 5"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0011.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0012",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 9"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0012.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0013",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0013.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0014",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 23"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0014.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0015",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 18"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0015.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0016",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 5"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0016.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0017",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0017.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0018",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 2"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0018.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0019",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 18"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0019.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0020",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 3"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0020.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0021",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 19"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0021.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0022",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 10"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0022.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0023",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 16"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0023.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0024",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 13"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0024.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0025",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 10"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0025.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0026",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 3"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0026.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0027",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0027.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0028",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 4"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0028.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0029",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 17"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0029.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0030",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 22"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0030.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0031",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 4"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0031.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0032",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 13"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0032.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0033",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 14"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0033.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0034",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 19"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0034.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0035",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 10"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0035.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0036",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 20"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0036.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0037",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 9"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0037.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0038",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 2"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0038.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0039",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 16"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0039.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0040",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 2"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0040.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0041",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 21"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0041.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0042",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 12"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0042.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0043",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 9"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0043.raw"}
},
{
"Subject ID":"-",
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"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 13"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0044.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0045",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 1"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0045.raw"}
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{
"Subject ID":"-",
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"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 1"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0046.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0047",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 17"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0047.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0048",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0048.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0049",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 20"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0049.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0050",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 16"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0050.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0051",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 22"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0051.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0052",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 18"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0052.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0053",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 1"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0053.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0054",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 15"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0054.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0055",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 11"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0055.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0056",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 14"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0056.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0057",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 7"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0057.raw"}
},
{
"Subject ID":"-",
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"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 21"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0058.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0059",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 22"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0059.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0060",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 8"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0060.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0061",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 4"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0061.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0062",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 15"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0062.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0063",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 12"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0063.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0064",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 15"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0064.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0065",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 3"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0065.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0066",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 8"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0066.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0067",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh timecourse experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0067.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0068",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh timecourse experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0068.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0069",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 20"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0069.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0070",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 6"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0070.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0071",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0071.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0072",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 23"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0072.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0073",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 7"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0073.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0074",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 12"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0074.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0075",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 6"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0075.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0076",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0076.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0077",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh timecourse experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0077.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_1_MSA0078",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 17"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_1_MSA0078.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0001",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0001.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0002",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0002.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0004",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0004.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0005",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0005.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0006",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0006.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0008",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0008.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0009",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0009.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0012",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0012.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0013",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0013.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0014",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0014.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0016",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0016.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0019",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0019.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0020",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0020.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0022",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0022.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0023",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0023.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0028",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0028.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0029",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0029.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0037",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0037.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0038",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0038.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0040",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0040.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0041",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0041.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0044",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0044.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0045",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0045.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0046",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0046.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0048",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0048.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0050",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0050.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Neg_2_MSA0051",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii  additional experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Neg_2_MSA0051.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0001",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 11"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0001.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0002",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 21"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0002.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0003",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 7"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0003.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0004",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 19"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0004.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0005",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 11"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0005.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0006",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 14"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0006.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0007",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 23"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0007.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0008",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 5"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0008.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0009",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 6"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0009.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0010",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 8"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0010.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0011",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 5"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0011.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0012",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 9"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0012.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0013",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0013.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0014",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 23"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0014.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0015",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 18"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0015.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0016",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 5"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0016.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0017",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0017.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0018",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 2"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0018.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0019",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 18"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0019.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0020",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 3"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0020.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0021",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 19"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0021.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0022",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 10"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0022.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0023",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 16"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0023.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0024",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 13"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0024.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0025",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 10"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0025.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0026",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 3"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0026.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0027",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0027.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0028",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 4"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0028.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0029",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 17"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0029.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0030",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 22"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0030.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0031",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 4"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0031.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0032",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 13"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0032.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0033",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 14"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0033.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0034",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 19"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0034.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0035",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 10"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0035.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0036",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 20"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0036.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0037",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 9"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0037.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0038",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 2"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0038.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0039",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 16"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0039.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0040",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 2"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0040.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0041",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 21"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0041.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0042",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 12"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0042.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0043",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 9"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0043.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0044",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 13"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0044.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0045",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 1"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0045.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0046",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 1"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0046.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0047",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 17"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0047.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0048",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0048.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0049",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 20"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0049.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0050",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 16"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0050.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0051",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 22"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0051.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0052",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 18"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0052.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0053",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 1"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0053.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0054",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 15"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0054.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0055",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 11"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0055.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0056",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 14"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0056.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0057",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 7"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0057.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0058",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 21"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0058.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0059",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 22"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0059.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0060",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 8"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0060.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0061",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 4"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0061.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0062",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 15"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0062.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0063",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 12"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0063.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0064",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 15"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0064.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0065",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 3"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0065.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0066",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 8"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0066.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0067",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh timecourse experiment"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0068",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh timecourse experiment"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0068.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0069",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 20"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0069.raw"}
},
{
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"Sample ID":"M00179_20220322_Pos_1_MSA0070",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 6"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0070.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0071",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0072",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 23"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0072.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0073",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 7"},
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{
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"Sample ID":"M00179_20220322_Pos_1_MSA0074",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 12"},
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{
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"Sample ID":"M00179_20220322_Pos_1_MSA0075",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 6"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0076",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_1_MSA0076.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_1_MSA0077",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh timecourse experiment"},
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{
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"Sample ID":"M00179_20220322_Pos_1_MSA0078",
"Factors":{"Genotype":"bacterial community","Treatment":"15-member community timepoint 17"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0001",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis  additional experiment"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0002",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis  additional experiment"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0004",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron  additional experiment"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0005",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Bacteroides thetaiotaomicron"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0006",
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0008",
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0009",
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"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_2_MSA0009.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0012",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Parabacteroides distasonis"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0013",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Bacteroides thetaiotaomicron"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0014",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Parabacteroides distasonis"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0016",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis  additional experiment"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0019",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Parabacteroides distasonis"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0020",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Parabacteroides distasonis"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0022",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_2_MSA0022.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0023",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Bacteroides thetaiotaomicron"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0028",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_2_MSA0028.raw"}
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0029",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Bacteroides thetaiotaomicron"},
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},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0037",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI-heme spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"M00179_20220322_Pos_2_MSA0037.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0038",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii  additional experiment"},
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},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0040",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Parabacteroides distasonis"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0041",
"Factors":{"Genotype":"bacterial community","Treatment":"Escherichia fergusonii-spent media spent by Bacteroides thetaiotaomicron"},
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{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0044",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron  additional experiment"},
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},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0045",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Parabacteroides distasonis"},
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},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0046",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii  additional experiment"},
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},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0048",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Bacteroides thetaiotaomicron"},
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},
{
"Subject ID":"-",
"Sample ID":"M00179_20220322_Pos_2_MSA0050",
"Factors":{"Genotype":"bacterial community","Treatment":"9-to-1 fresh BHI and Escherichia fergusonii-spent media mix spent by Bacteroides thetaiotaomicron"},
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},
{
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"Sample ID":"M00179_20220322_Pos_2_MSA0051",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii  additional experiment"},
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{
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"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0001",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Blautia producta"},
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{
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{
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},
{
"Subject ID":"-",
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{
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{
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},
{
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"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0010",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hylemonae"},
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{
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"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0011",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Parabacteroides distasonis"},
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{
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"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0012",
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{
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0014",
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},
{
"Subject ID":"-",
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0016",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides uniformis"},
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0017",
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0018",
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},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0020",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0020.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0021",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Blautia producta"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0021.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0023",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0023.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0024",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hylemonae"},
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},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0025",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0025.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0029",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hathewayi"},
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},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0030",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0030.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0031",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium clostridioforme"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0031.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0032",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM fresh"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0032.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0033",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides fragilis"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0033.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0034",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0034.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0035",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Flavonifractor plautii"},
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},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0036",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hathewayi"},
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},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0037",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0037.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0038",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium clostridioforme"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0038.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0040",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides fragilis"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0040.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0043",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Escherichia fergusonii"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0043.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0045",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0045.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0046",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus hirae"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0046.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0047",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0047.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0048",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0048.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0051",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Escherichia fergusonii"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0051.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0052",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus faecalis"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0052.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0053",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0053.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0054",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM fresh"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0054.raw"}
},
{
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"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0055",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165H_20220125_Neg_1_MSA0055.raw"}
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{
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus faecalis"},
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{
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"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0057",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides uniformis"},
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{
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hathewayi"},
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Neg_1_MSA0060",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium scindens"},
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{
"Subject ID":"-",
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium clostridioforme"},
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{
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides fragilis"},
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{
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Blautia producta"},
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{
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"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0001",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Blautia producta"},
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{
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{
"Subject ID":"-",
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0005",
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0006",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Escherichia fergusonii"},
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{
"Subject ID":"-",
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0010",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hylemonae"},
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{
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"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0011",
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{
"Subject ID":"-",
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{
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium scindens"},
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{
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{
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{
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{
"Subject ID":"-",
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{
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{
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"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0020",
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{
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{
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{
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{
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"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0025",
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{
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{
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{
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{
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{
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides fragilis"},
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{
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{
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{
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{
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"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0037",
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{
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{
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{
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{
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{
"Subject ID":"-",
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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":"-",
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hathewayi"},
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{
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"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0060",
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{
"Subject ID":"-",
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},
{
"Subject ID":"-",
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"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides fragilis"},
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{
"Subject ID":"-",
"Sample ID":"metaboproj_165H_20220125_Pos_1_MSA0063",
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},
{
"Subject ID":"-",
"Sample ID":"Pos_1''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus hirae"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_1''.raw"}
},
{
"Subject ID":"-",
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},
{
"Subject ID":"-",
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},
{
"Subject ID":"-",
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"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_2''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_2''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii"},
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},
{
"Subject ID":"-",
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"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii"},
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},
{
"Subject ID":"-",
"Sample ID":"Pos_3''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_3''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_3''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_3''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_3''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_3''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_4''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_4''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_4''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_4''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_4''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_4''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_5''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium clostridioforme"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_5''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_5''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium clostridioforme"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_5''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_5''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium clostridioforme"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_5''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_6''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Blautia producta"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_6''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_6''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Blautia producta"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_6''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_6''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Blautia producta"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_6''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_7''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium scindens"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_7''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_7''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium scindens"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_7''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_7''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium scindens"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_7''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_8''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_8''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_8''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_8''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_8''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_8''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_9''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_9''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_9''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_9''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_9''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_9''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_10''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecalis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_10''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_10''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecalis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_10''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_10''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecalis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_10''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_11''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hathewayi"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_11''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_11''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hathewayi"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_11''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_11''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hathewayi"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_11''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_12''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides fragilis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_12''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_12''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides fragilis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_12''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_12''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides fragilis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_12''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_13''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_13''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_13''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_13''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_13''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_13''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_14''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides uniformis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_14''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_14''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides uniformis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_14''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_14''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides uniformis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_14''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_15''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_15''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_15''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_15''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_15''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_15''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_BHICONTROL(labeled16'')",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_BHICONTROL(labeled16'').raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_BHICONTROL(labeled16'')_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_BHICONTROL(labeled16'')_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Pos_BHICONTROL(labeled16'')_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh"},
"Additional sample data":{"RAW_FILE_NAME":"Pos_BHICONTROL(labeled16'')_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_1''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus hirae"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_1''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_1''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus hirae"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_1''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_1''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus hirae"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_1''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_2''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_2''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_2''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_2''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_2''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Escherichia fergusonii"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_2''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_3''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_3''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_3''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_3''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_3''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_3''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_4''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_4''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_4''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_4''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_4''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_4''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_5''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium clostridioforme"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_5''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_5''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium clostridioforme"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_5''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_5''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium clostridioforme"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_5''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_6''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Blautia producta"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_6''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_6''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Blautia producta"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_6''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_6''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Blautia producta"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_6''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_7''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium scindens"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_7''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_7''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium scindens"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_7''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_7''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium scindens"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_7''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_8''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_8''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_8''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_8''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_8''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_8''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_9''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_9''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_9''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_9''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_9''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_9''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_10''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecalis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_10''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_10''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecalis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_10''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_10''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Enterococcus faecalis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_10''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_11''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hathewayi"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_11''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_11''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hathewayi"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_11''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_11''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Clostridium hathewayi"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_11''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_12''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides fragilis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_12''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_12''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides fragilis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_12''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_12''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides fragilis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_12''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_13''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_13''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_13''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_13''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_13''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_13''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_14''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides uniformis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_14''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_14''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides uniformis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_14''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_14''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Bacteroides uniformis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_14''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_15''",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_15''.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_15''_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_15''_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_15''_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_15''_r2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_BHICONTROL(labeled16'')",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_BHICONTROL(labeled16'').raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_BHICONTROL(labeled16'')_r1",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_BHICONTROL(labeled16'')_r1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Neg_BHICONTROL(labeled16'')_r2",
"Factors":{"Genotype":"bacterial community","Treatment":"BHI fresh"},
"Additional sample data":{"RAW_FILE_NAME":"Neg_BHICONTROL(labeled16'')_r2.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Isolates were obtained via plating of in vitro communities –, derived from culturing fecal samples from humanized mice –, on agar plates made with various complex media and frozen as glycerol stocks, as previously described (Cell Host & Microbe (2022). https://doi.org/https://doi.org/10.1016/j.chom.2021.12.008, https://www.biorxiv.org/content/10.1101/2023.01.13.523996v1) Frozen stocks were streaked onto BHI-blood agar plates (5% defibrinated horse blood in 1.5% w/v agar). Resulting colonies were inoculated into 3 mL of Brain Heart Infusion (BHI) (BD #2237500) or modified Gifu Anaerobic Medium (mGAM) (HyServe #05433) in test tubes. All culturing was performed at 37 °C without shaking in an anaerobic chamber (Coy). To minimize potential physiological changes from freeze-thaw cycles and changes in growth medium, cultures were diluted 1:200 every 48 h for 3 passages before growth or metabolomics measurements. After the first passage, subsequent passages were performed in 96-well polystyrene plates (Greiner Bio-One #655161) filled with 200 μL of growth medium.","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Many combinations of bacterial isolates were assayed. details can be found in the publicly available preprint here: https://www.biorxiv.org/content/10.1101/2022.05.30.494065v1.abstract"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Spent media were collected as described above and immediately stored at -80 °C. Samples were thawed only once, immediately before LC-MS/MS. Thawed samples were kept on ice, each sample was homogenized by pipetting prior to dispensing. Two 20-µL aliquots of supernatant were removed from each sample well and dispensed into two shallow 96-well polypropylene plates, maintained on ice. Additionally, 5 µL were removed from each sample and combined into a homogenous pool; this pool was dispensed in 20-µL aliquots and prepared in parallel with samples. These pooled samples were used for in-run quality control, injected at predefined intervals over the course of analysis to ensure consistent instrument performance over time. Samples were analyzed using two complementary chromatography methods: reversed phase (C18) and hydrophilic interaction chromatography (HILIC). HILIC data include in this study, C18 data can be found uploaded in a separate study. All samples were analyzed by positive and negative mode electrospray ionization (ESI+, ESI-). Sample analysis order was randomized to minimize potential bias in data acquisition. Procedural blanks were prepared by extracting 20 µL of water in place of bacterial supernatant. Procedural blanks were inserted throughout the run as additional quality control."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Bacterial supernatant were analyzed via hydrophilic interaction liquid chromatography (HILIC) coupled to a Thermo Q-Exactive HF high resolution mass spectrometer. Each sample was analyzed in both positive and negative ionization modes (ESI+, ESI-) via subsequent injections. 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 (https://www.nature.com/articles/s41587-020-0531-2) and queried against a combination of our in-house MS2 library (https://www.nature.com/articles/s41586-021-03707-9) and MassBank of North America, the largest freely available spectral repository (https://doi.org/10.1002/mas.21535). Annotations were scored using guidelines from the metabolomics standards initiative (https://www.nature.com/articles/nbt0807-846b). 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.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)","SOLVENT_A":"Water + 10mM ammonium formate + 0.125% formic acid","SOLVENT_B":"95% acetonitrile + 10mM ammonium formate + 0.125% formic acid","FLOW_GRADIENT":"Gradient elution was performed from 100% (B) at 0–2 min to 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min, isocratic until 16.75 min with a column flow of","FLOW_RATE":"0.4 mL/min.","COLUMN_TEMPERATURE":"45C"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","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.","MS_RESULTS_FILE":"ST002832_AN004625_Results.txt UNITS:counts, height Has m/z:Yes Has RT:Yes RT units:Minutes"},

"MS_METABOLITE_DATA":{
"Units":"Peak height",

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}

}