{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002472","ANALYSIS_ID":"AN004037","VERSION":"1","CREATED_ON":"February 10, 2023, 9:57 am"},
"PROJECT":{"PROJECT_TITLE":"Linking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation","PROJECT_TYPE":"Metabolomic profiling of human fecal and plasma samples and bacterial strains","PROJECT_SUMMARY":"Understanding the role of the gut microbiome in inflammatory and autoimmune diseases requires the identification of microbial molecular effectors and their link to host pathophysiology. Here, we present a framework to identify and characterize novel microbial metabolites in patient samples and to directly link their production to disease-associated microbes. We applied this approach to investigate the spectrum of disease severity and treatment response in ulcerative colitis (UC) using longitudinal metabolite and strain profiles combined with paired plasma profiles.","INSTITUTE":"Broad Institute of MIT and Harvard","LAST_NAME":"Xavier","FIRST_NAME":"Ramnik","ADDRESS":"415 Main Street","EMAIL":"rxavier@broadinstitute.org","PHONE":"6177147080","CONTRIBUTORS":"Melanie Schirmer, Martin Strazar, Julian Avila-Pacheco, Daniel F. Rojas-Tapias, Eric Brown, Emily Temple, Subra Kugathasan, Zach Costliow, Hera Vlamakis, Jeff Hyams, Lee Denson, Clary B. Clish, Ramnik J. Xavier"},
"STUDY":{"STUDY_TITLE":"Linking bacterial metabolites to disease-associated microbes to uncover mechanisms of host-microbial interactions in intestinal inflammation. Veillonella parvula cell and media profiling","STUDY_SUMMARY":"Understanding the role of the gut microbiome in inflammatory and autoimmune diseases requires the identification of microbial molecular effectors and their link to host pathophysiology. Here, we present a framework to identify and characterize novel microbial metabolites in patient samples and to directly link their production to disease-associated microbes. We applied this approach to investigate the spectrum of disease severity and treatment response in ulcerative colitis (UC) using longitudinal metabolite and strain profiles combined with paired plasma profiles.","INSTITUTE":"Broad Institute of MIT and Harvard","LAST_NAME":"Xavier","FIRST_NAME":"Ramnik","ADDRESS":"415 Main Street","EMAIL":"rxavier@broadinstitute.org","PHONE":"617717084"},
"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Veillonella parvula","TAXONOMY_ID":"29466"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"L_C1",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"37","RAW_FILE_NAME":"0028_XAV_VparvulaStool_CP-L_C1.raw RAW_FILE_NAME":"0028_XAV_VparvulaStool_HP-L_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L_C2",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"39","RAW_FILE_NAME":"0030_XAV_VparvulaStool_CP-L_C2.raw RAW_FILE_NAME":"0030_XAV_VparvulaStool_HP-L_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L_C3",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"35","RAW_FILE_NAME":"0026_XAV_VparvulaStool_CP-L_C3.raw RAW_FILE_NAME":"0026_XAV_VparvulaStool_HP-L_C3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_C1",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"38","RAW_FILE_NAME":"0029_XAV_VparvulaStool_CP-N_C1.raw RAW_FILE_NAME":"0029_XAV_VparvulaStool_HP-N_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_C2",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"40","RAW_FILE_NAME":"0031_XAV_VparvulaStool_CP-N_C2.raw RAW_FILE_NAME":"0031_XAV_VparvulaStool_HP-N_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_C3",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"33","RAW_FILE_NAME":"0024_XAV_VparvulaStool_CP-N_C3.raw RAW_FILE_NAME":"0024_XAV_VparvulaStool_HP-N_C3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_C1",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"41","RAW_FILE_NAME":"0032_XAV_VparvulaStool_CP-LN_C1.raw RAW_FILE_NAME":"0032_XAV_VparvulaStool_HP-LN_C1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_C2",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"34","RAW_FILE_NAME":"0025_XAV_VparvulaStool_CP-LN_C2.raw RAW_FILE_NAME":"0025_XAV_VparvulaStool_HP-LN_C2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_C3",
"Factors":{"Matrix":"Cell","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"36","RAW_FILE_NAME":"0027_XAV_VparvulaStool_CP-LN_C3.raw RAW_FILE_NAME":"0027_XAV_VparvulaStool_HP-LN_C3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L_SM1",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"14","RAW_FILE_NAME":"0010_XAV_VparvulaStool_CP-L_SM1.raw RAW_FILE_NAME":"0010_XAV_VparvulaStool_HP-L_SM1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L_SM2",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"13","RAW_FILE_NAME":"0009_XAV_VparvulaStool_CP-L_SM2.raw RAW_FILE_NAME":"0009_XAV_VparvulaStool_HP-L_SM2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L_SM3",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"15","RAW_FILE_NAME":"0011_XAV_VparvulaStool_CP-L_SM3.raw RAW_FILE_NAME":"0011_XAV_VparvulaStool_HP-L_SM3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_SM1",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"6","RAW_FILE_NAME":"0002_XAV_VparvulaStool_CP-N_SM1.raw RAW_FILE_NAME":"0002_XAV_VparvulaStool_HP-N_SM1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_SM2",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"21","RAW_FILE_NAME":"0017_XAV_VparvulaStool_CP-N_SM2.raw RAW_FILE_NAME":"0017_XAV_VparvulaStool_HP-N_SM2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_SM3",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"19","RAW_FILE_NAME":"0015_XAV_VparvulaStool_CP-N_SM3.raw RAW_FILE_NAME":"0015_XAV_VparvulaStool_HP-N_SM3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_SM1",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"9","RAW_FILE_NAME":"0005_XAV_VparvulaStool_CP-LN_SM1.raw RAW_FILE_NAME":"0005_XAV_VparvulaStool_HP-LN_SM1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_SM2",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"10","RAW_FILE_NAME":"0006_XAV_VparvulaStool_CP-LN_SM2.raw RAW_FILE_NAME":"0006_XAV_VparvulaStool_HP-LN_SM2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_SM3",
"Factors":{"Matrix":"Spent Media","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"16","RAW_FILE_NAME":"0012_XAV_VparvulaStool_CP-LN_SM3.raw RAW_FILE_NAME":"0012_XAV_VparvulaStool_HP-LN_SM3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L_UM1",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"11","RAW_FILE_NAME":"0007_XAV_VparvulaStool_CP-L_UM1.raw RAW_FILE_NAME":"0007_XAV_VparvulaStool_HP-L_UM1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L_UM2",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"18","RAW_FILE_NAME":"0014_XAV_VparvulaStool_CP-L_UM2.raw RAW_FILE_NAME":"0014_XAV_VparvulaStool_HP-L_UM2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L_UM3",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Lactate"},
"Additional sample data":{"Injection Order":"5","RAW_FILE_NAME":"0001_XAV_VparvulaStool_CP-L_UM3.raw RAW_FILE_NAME":"0001_XAV_VparvulaStool_HP-L_UM3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_UM1",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"20","RAW_FILE_NAME":"0016_XAV_VparvulaStool_CP-N_UM1.raw RAW_FILE_NAME":"0016_XAV_VparvulaStool_HP-N_UM1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_UM2",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"22","RAW_FILE_NAME":"0018_XAV_VparvulaStool_CP-N_UM2.raw RAW_FILE_NAME":"0018_XAV_VparvulaStool_HP-N_UM2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N_UM3",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Nitrate"},
"Additional sample data":{"Injection Order":"7","RAW_FILE_NAME":"0003_XAV_VparvulaStool_CP-N_UM3.raw RAW_FILE_NAME":"0003_XAV_VparvulaStool_HP-N_UM3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_UM1",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"12","RAW_FILE_NAME":"0008_XAV_VparvulaStool_CP-LN_UM1.raw RAW_FILE_NAME":"0008_XAV_VparvulaStool_HP-LN_UM1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_UM2",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"8","RAW_FILE_NAME":"0004_XAV_VparvulaStool_CP-LN_UM2.raw RAW_FILE_NAME":"0004_XAV_VparvulaStool_HP-LN_UM2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"LN_UM3",
"Factors":{"Matrix":"Unspent Media","Sample Type":"Experiment","Tretment":"Lactate+Nitrate"},
"Additional sample data":{"Injection Order":"17","RAW_FILE_NAME":"0013_XAV_VparvulaStool_CP-LN_UM3.raw RAW_FILE_NAME":"0013_XAV_VparvulaStool_HP-LN_UM3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"C_100",
"Factors":{"Matrix":"Cell_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0035_XAV_VparvulaStool_CP-C_100.raw RAW_FILE_NAME":"0035_XAV_VparvulaStool_HP-C_100.raw"}
},
{
"Subject ID":"-",
"Sample ID":"C_20",
"Factors":{"Matrix":"Cell_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0034_XAV_VparvulaStool_CP-C_20.raw RAW_FILE_NAME":"0034_XAV_VparvulaStool_HP-C_20.raw"}
},
{
"Subject ID":"-",
"Sample ID":"C_40",
"Factors":{"Matrix":"Cell_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0037_XAV_VparvulaStool_CP-C_40.raw RAW_FILE_NAME":"0037_XAV_VparvulaStool_HP-C_40.raw"}
},
{
"Subject ID":"-",
"Sample ID":"C_60",
"Factors":{"Matrix":"Cell_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0036_XAV_VparvulaStool_CP-C_60.raw RAW_FILE_NAME":"0036_XAV_VparvulaStool_HP-C_60.raw"}
},
{
"Subject ID":"-",
"Sample ID":"C_80",
"Factors":{"Matrix":"Cell_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0033_XAV_VparvulaStool_CP-C_80.raw RAW_FILE_NAME":"0033_XAV_VparvulaStool_HP-C_80.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SM_100",
"Factors":{"Matrix":"Media_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0021_XAV_VparvulaStool_CP-SM_100.raw RAW_FILE_NAME":"0021_XAV_VparvulaStool_HP-SM_100.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SM_20",
"Factors":{"Matrix":"Media_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0020_XAV_VparvulaStool_CP-SM_20.raw RAW_FILE_NAME":"0020_XAV_VparvulaStool_HP-SM_20.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SM_40",
"Factors":{"Matrix":"Media_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0023_XAV_VparvulaStool_CP-SM_40.raw RAW_FILE_NAME":"0023_XAV_VparvulaStool_HP-SM_40.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SM_60",
"Factors":{"Matrix":"Media_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0022_XAV_VparvulaStool_CP-SM_60.raw RAW_FILE_NAME":"0022_XAV_VparvulaStool_HP-SM_60.raw"}
},
{
"Subject ID":"-",
"Sample ID":"SM_80",
"Factors":{"Matrix":"Media_pool","Sample Type":"QC_Titration","Tretment":"-"},
"Additional sample data":{"Injection Order":"-","RAW_FILE_NAME":"0019_XAV_VparvulaStool_CP-SM_80.raw RAW_FILE_NAME":"0019_XAV_VparvulaStool_HP-SM_80.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The strain Veillonella parvula SKV38 xdh::cat*. Briefly, V. parvula was grown on SK agar (composition: yeast extract 10 gL-1, casitone 10 gL-1, NaCl 2 gL-1, K2HPO4 0.4 gL-1) supplemented with either DL-lactate (50 mM lactate), potassium nitrate (40 mM KNO3), or both, incubated under anaerobic conditions at 37ºC overnight and then inoculated into the respective liquid media in biological triplicates. Cells and supernatants were harvested at mid-exponential phase (OD600=0.3), after centrifugation at 10,000g for 5 min. Both cell pellets and resulting supernatants were stored at -80C until processing for metabolite extraction and metabolomic analysis. A titration of cell pools and media pools was conducted (10,20,40,60,80,100%) and used to filter the data based on the correlation of the abundance of detected features with","SAMPLE_TYPE":"Bacterial cells"},
"TREATMENT":{"TREATMENT_SUMMARY":"The strain was first streaked on an agar plate with SK media (composition: yeast extract 10 gL-1, casitone 10 gL-1, NaCl 2 gL-1, K2HPO4 0.4 gL-1) supplemented with 50 mM lactate and 40 mM KNO3 (SKLN medium) and antibiotics if required. From this agar plate, a single colony was selected and inoculated in 5mL SKLN media and grown for 24 hours. Next, overnight cells from this inoculum were grown using a 1/50 inoculum of the overnight culture, on either SK, SK + 50 mM lactate (SKL), SK + 40 mM nitrate (SKN), and SKLN."},
"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Bacterial metabolites were profiled using the HILIC-pos and C8-pos methods for mapping Veillonella metabolites present in human stool. Bacterial samples were prepared as follows: mid-exponential Veillonella cultures (OD600 = 0.3-0.4) were harvested by centrifugation at 20,000g at 4°C for 1 minute, supernatants (spent media) were aliquoted, while cell pellets were resuspended in ice-cold PBS. Cells were then spun twice at 20,000g for 1 minute and all PBS supernatant removed and discarded. Cell pellet weights were estimated and all the samples harvested were stored at -80°C until metabolite profiling was conducted. For cells profiled in the C8-pos, cell pellets were resuspended in 20 µL of H2O and metabolites extracted using 380 µL of isopropanol containing 1,2-didodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids; Alabaster, AL), 10 ul of media was extracted using 190 µL of isopropanol containing internal standards. Extracts were incubated at room temperature in the dark before centrifugation (10 min, 9,000 x g, Room Temperature). For cells profiled in the HILIC-pos mode, cell pellets were resuspended in 20 µL of H2O and metabolites extracted using180 µL HILIC extraction solution with internal standards (valine-d8, Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA), while 10 µL of media was extracted with 90 µL of extraction solution. Extracts were cleared by centrifugation (10 min, 9,000 x g, 4C) prior to analysis."},
"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Shimadzu Nexera X2","COLUMN_NAME":"Waters Atlantis HILIC (150 x 2 mm, 3 μm)","SOLVENT_A":"100% water; 10 mM ammonium formate; 0.1% formic acid","SOLVENT_B":"100% acetonitrile; 0.1% formic acid","FLOW_GRADIENT":"Isocratically with 5% mobile phase A for 1 minute followed by a linear gradient to 40% mobile phase B over 10 minutes","FLOW_RATE":"250 µL/min","COLUMN_TEMPERATURE":"30C"},
"ANALYSIS":{"ANALYSIS_TYPE":"MS"},
"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Raw data were processed using TraceFinder 3.3 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were confirmed using authentic reference standards or reference samples.","MS_RESULTS_FILE":"ST002472_AN004037_Results.txt UNITS:Abundance Has m/z:Yes Has RT:Yes RT units:Minutes"},
"MS_METABOLITE_DATA":{
"Units":"Abundance",
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}
}