{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003000","ANALYSIS_ID":"AN004927","VERSION":"1","CREATED_ON":"December 8, 2023, 12:04 pm"},

"PROJECT":{"PROJECT_TITLE":"Effect of Antibiotic Administration on Metabolomic Radiation Biodosimetry","PROJECT_SUMMARY":"Development of novel biodosimetry assays and medical countermeasures is needed to obtain a level of radiation preparedness in the event of malicious or accidental mass exposures to ionizing radiation (IR). For biodosimetry, metabolic profiling with mass spectrometry (MS) platforms has identified several small molecules in easily accessible biofluids that are promising for dose reconstruction. As our microbiome has profound effects on biofluid metabolite composition, it is of interest how variation in the host microbiome may affect metabolomics based biodosimetry. Here, we chemically ‘knocked out’ the microbiome of male and female C57BL/6 mice (Abx mice) and then irradiated (0, 3, or 8 Gy) them to determine the role of the host microbiome on biofluid radiation signatures (3 d serum).","INSTITUTE":"Georgetown University","LAST_NAME":"Pannkuk","FIRST_NAME":"Evan","ADDRESS":"3970 Reservoir Rd, NW New Research Build, washington dc, District of Columbia, 20057, USA","EMAIL":"elp44@georgetown.edu","PHONE":"2026875650"},

"STUDY":{"STUDY_TITLE":"Effects of Microbiome Depletion on Radiation Biodosimetry Metabolomics","STUDY_SUMMARY":"Development of novel biodosimetry assays and medical countermeasures is needed to obtain a level of radiation preparedness in the event of malicious or accidental mass exposures to ionizing radiation (IR). For biodosimetry, metabolic profiling with mass spectrometry (MS) platforms has identified several small molecules in easily accessible biofluids that are promising for dose reconstruction. As our microbiome has profound effects on biofluid metabolite composition, it is of interest how variation in the host microbiome may affect metabolomics based biodosimetry. Here, we chemically ‘knocked out’ the microbiome of male and female C57BL/6 mice (Abx mice) and then irradiated (0, 3, or 8 Gy) them to determine the role of the host microbiome on biofluid radiation signatures (3 d serum).","INSTITUTE":"Georgetown University","LAST_NAME":"Pannkuk","FIRST_NAME":"Evan","ADDRESS":"3970 Reservoir Rd, NW New Research Build, washington dc, District of Columbia, 20057, USA","EMAIL":"elp44@georgetown.edu","PHONE":"2026875650"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENDER":"Male and female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"wo_3Gy",
"Sample ID":"7588M",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_09","RAW_FILE_NAME":"NEG_09"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7579M",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_10","RAW_FILE_NAME":"NEG_10"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7634F",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_11","RAW_FILE_NAME":"NEG_11"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7636F",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_12","RAW_FILE_NAME":"NEG_12"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7614F",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_13","RAW_FILE_NAME":"NEG_13"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7628F",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_14","RAW_FILE_NAME":"NEG_14"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7635F",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_15","RAW_FILE_NAME":"NEG_15"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7642F",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_16","RAW_FILE_NAME":"NEG_16"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7650F",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_17","RAW_FILE_NAME":"NEG_17"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7639F",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_22","RAW_FILE_NAME":"NEG_22"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7589M",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_23","RAW_FILE_NAME":"NEG_23"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7594M",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_24","RAW_FILE_NAME":"NEG_24"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7582M",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_25","RAW_FILE_NAME":"NEG_25"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7632F",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_26","RAW_FILE_NAME":"NEG_26"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7600M",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_27","RAW_FILE_NAME":"NEG_27"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7626F",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_28","RAW_FILE_NAME":"NEG_28"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7637F",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_29","RAW_FILE_NAME":"NEG_29"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7596M",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_30","RAW_FILE_NAME":"NEG_30"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7595M",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_31","RAW_FILE_NAME":"NEG_31"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7631F",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_36","RAW_FILE_NAME":"NEG_36"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7607M",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_37","RAW_FILE_NAME":"NEG_37"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7616F",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_38","RAW_FILE_NAME":"NEG_38"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7581M",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_39","RAW_FILE_NAME":"NEG_39"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7604M",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_40","RAW_FILE_NAME":"NEG_40"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7633F",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_41","RAW_FILE_NAME":"NEG_41"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7640F",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_42","RAW_FILE_NAME":"NEG_42"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7608M",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_43","RAW_FILE_NAME":"NEG_43"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7643F",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_44","RAW_FILE_NAME":"NEG_44"}
},
{
"Subject ID":"wo_3Gy",
"Sample ID":"7623F",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_45","RAW_FILE_NAME":"NEG_45"}
},
{
"Subject ID":"wo_3Gy",
"Sample ID":"7625F",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_50","RAW_FILE_NAME":"NEG_50"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7641F",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_51","RAW_FILE_NAME":"NEG_51"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7603M",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_52","RAW_FILE_NAME":"NEG_52"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7644F",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_53","RAW_FILE_NAME":"NEG_53"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7592M",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_54","RAW_FILE_NAME":"NEG_54"}
},
{
"Subject ID":"wo_3Gy",
"Sample ID":"7586M",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_55","RAW_FILE_NAME":"NEG_55"}
},
{
"Subject ID":"wo_3Gy",
"Sample ID":"7622F",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_56","RAW_FILE_NAME":"NEG_56"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7630F",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_57","RAW_FILE_NAME":"NEG_57"}
},
{
"Subject ID":"wo_3Gy",
"Sample ID":"7587M",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_58","RAW_FILE_NAME":"NEG_58"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7599M",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_59","RAW_FILE_NAME":"NEG_59"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7619F",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_64","RAW_FILE_NAME":"NEG_64"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7605M",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_65","RAW_FILE_NAME":"NEG_65"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7638F",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_66","RAW_FILE_NAME":"NEG_66"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7583M",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_67","RAW_FILE_NAME":"NEG_67"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7591M",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_68","RAW_FILE_NAME":"NEG_68"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7627F",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_69","RAW_FILE_NAME":"NEG_69"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7618F",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_70","RAW_FILE_NAME":"NEG_70"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7602M",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_71","RAW_FILE_NAME":"NEG_71"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7598M",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_72","RAW_FILE_NAME":"NEG_72"}
},
{
"Subject ID":"wo_0Gy",
"Sample ID":"7617F",
"Factors":{"Antibiotics":"wo","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_73","RAW_FILE_NAME":"NEG_73"}
},
{
"Subject ID":"w_8Gy",
"Sample ID":"7606M",
"Factors":{"Antibiotics":"w","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_78","RAW_FILE_NAME":"NEG_78"}
},
{
"Subject ID":"w_0Gy",
"Sample ID":"7597M",
"Factors":{"Antibiotics":"w","Irradiation":"0Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_79","RAW_FILE_NAME":"NEG_79"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7590M",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_80","RAW_FILE_NAME":"NEG_80"}
},
{
"Subject ID":"wo_3Gy",
"Sample ID":"7621F",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_81","RAW_FILE_NAME":"NEG_81"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7629F",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_82","RAW_FILE_NAME":"NEG_82"}
},
{
"Subject ID":"w_3Gy",
"Sample ID":"7601M",
"Factors":{"Antibiotics":"w","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_83","RAW_FILE_NAME":"NEG_83"}
},
{
"Subject ID":"wo_3Gy",
"Sample ID":"7585M",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_84","RAW_FILE_NAME":"NEG_84"}
},
{
"Subject ID":"wo_8Gy",
"Sample ID":"7593M",
"Factors":{"Antibiotics":"wo","Irradiation":"8Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_85","RAW_FILE_NAME":"NEG_85"}
},
{
"Subject ID":"wo_3Gy",
"Sample ID":"7624F",
"Factors":{"Antibiotics":"wo","Irradiation":"3Gy"},
"Additional sample data":{"RAW_FILE_NAME":"POS_86","RAW_FILE_NAME":"NEG_86"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"On day 3, mice were euthanized by CO2 inhalation, blood was collected by cardiac puncture, and tissues were collected. Tissues were flash frozen. Serum samples were prepared using BD Microtainer Tube (REF 365967) with ~100 µL of whole blood added to each tube, kept at room temperature for 30 min, then spun at 1300× g at 4 °C for 10 min. All tissues and biofluids were stored at −80 °C until analysis.","SAMPLE_TYPE":"Blood (serum)"},

"TREATMENT":{"TREATMENT_SUMMARY":"We used 8 week old male and female C57BL/6 mice that were purchased from Charles River Laboratories (Frederick, MD) and were assigned to sham, 3 Gy, or 8 Gy cohorts. A control group (Abx-con) did not receive antibiotics in drinking water and a treatment group (Abx) received broad-spectrum antibiotics (n=10 per group, half male half female) (S1 Fig). Mice were provided with deionized water ad libitum either with or without the antibiotic cocktail (enrofloxacin [0.575 mg/ml] and ampicillin [1 mg/ml]) for 8 days prior to irradiation [24]. Mice were irradiated in an acrylic, 12-slot mouse pie cage (MPC-1, Braintree Scientific, Braintree, MA) on top of a specimen turntable (XD1905-0000, Precision X-Ray Inc, Branford, CT) and 0, 3 or 8 Gy X-ray irradiated (1.67 Gy/min; X-Rad 320, Precision X-Ray Inc.; filter, 0.75 mm tin/ 0.25 mm copper/1.5 mm aluminum). For Abx-con mice, spot urines (>100 µL) were collected 1 d prior to irradiation and at 1 and 3 d post-irradiation (fecal samples collected 1 d prior to irradiation and at 3 d post-irradiation)."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"On day 3, mice were euthanized by CO2 inhalation, blood was collected by cardiac puncture, and tissues were collected. Tissues were flash frozen. Serum samples were prepared using BD Microtainer Tube (REF 365967) with ~100 µL of whole blood added to each tube, kept at room temperature for 30 min, then spun at 1300× g at 4 °C for 10 min. All tissues and biofluids were stored at −80 °C until analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The LC and MS conditions for serum was as follows: LC solvent A (water/0.1% formic acid [FA]), solvent B (acetonitrile/0.1% FA), and solvent C (isopropanol/0.1% FA). Operating conditions for ESI were, capillary voltage 3 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 600 L/Hr. The gradient for serum was: 4 min 98% A 2% B, 4 min 40% A 60% B, 1.5 min 2% A 98% B, 2 min 11.8% B 88.2% C, 0.5 min 50% A 50% B, and 1 min 98% A 2% B at a flow rate of 0.5 ml/min, column temp 60 °C (S3 Fig).","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity","COLUMN_NAME":"Waters ACQUITY UPLC BEH C18 (50 x 2.1mm,1.7um)","SOLVENT_A":"100% water; 0.1% formic acid","SOLVENT_B":"100% acetonitrile; 0.1% formic acid","SOLVENT_C":"100% isopropanol; 0.1% formic acid","FLOW_GRADIENT":"4 min 98% A 2% B, 4 min 40% A 60% B, 1.5 min 2% A 98% B, 2 min 11.8% B 88.2% C, 0.5 min 50% A 50% B, and 1 min 98% A 2% B","FLOW_RATE":"0.5 ml/min","COLUMN_TEMPERATURE":"60"},

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

"MS":{"INSTRUMENT_NAME":"Waters Xevo-G2-S","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Operating conditions for ESI were, capillary voltage 3 kV, cone voltage 30 V, desolvation temperature 500°C, desolvation gas flow 600 L/Hr.","MS_RESULTS_FILE":"ST003000_AN004927_Results.txt UNITS:peak area Has m/z:Yes Has RT:Yes RT units:Minutes"}

}