#METABOLOMICS WORKBENCH cnoecker_20230322_170413 DATATRACK_ID:3810 STUDY_ID:ST002518 ANALYSIS_ID:AN004148
VERSION                          	1
CREATED_ON                       	02-08-2024
#PROJECT
PR:PROJECT_TITLE                 	Systems biology illuminates the alternative metabolic niche of the human gut
PR:PROJECT_TITLE                 	bacterium Eggerthella lenta
PR:PROJECT_TYPE                  	Untargeted LC-MS
PR:PROJECT_SUMMARY               	Human gut bacteria perform diverse metabolic functions with consequences for
PR:PROJECT_SUMMARY               	host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta
PR:PROJECT_SUMMARY               	performs several unusual chemical transformations, but it does not metabolize
PR:PROJECT_SUMMARY               	sugars and its core growth strategy remains unclear. To obtain a comprehensive
PR:PROJECT_SUMMARY               	view of the metabolic network of E. lenta, we generated several complementary
PR:PROJECT_SUMMARY               	resources: defined culture media, metabolomics profiles of strain isolates, and
PR:PROJECT_SUMMARY               	a curated genome-scale metabolic reconstruction. Stable isotope-resolved
PR:PROJECT_SUMMARY               	metabolomics revealed that E. lenta uses acetate as a key carbon source while
PR:PROJECT_SUMMARY               	catabolizing arginine to generate ATP, traits which could be recapitulated in
PR:PROJECT_SUMMARY               	silico by our updated metabolic model. We compared these in vitro findings with
PR:PROJECT_SUMMARY               	metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying
PR:PROJECT_SUMMARY               	shared signatures across environments and highlighting catabolism of the host
PR:PROJECT_SUMMARY               	signaling metabolite agmatine as an alternative energy pathway. Together, our
PR:PROJECT_SUMMARY               	results elucidate a distinctive metabolic niche filled by E. lenta in the gut
PR:PROJECT_SUMMARY               	ecosystem.
PR:INSTITUTE                     	University of California, San Francisco
PR:DEPARTMENT                    	Microbiology and Immunology
PR:LABORATORY                    	Peter Turnbaugh
PR:LAST_NAME                     	Noecker
PR:FIRST_NAME                    	Cecilia
PR:ADDRESS                       	513 Parnassus Ave HSW1501, San Francisco, CA 94143
PR:EMAIL                         	cecilia.noecker@ucsf.edu
PR:PHONE                         	415-502-3264
PR:FUNDING_SOURCE                	This work was supported by the National Institutes of Health (2R01HL122593;
PR:FUNDING_SOURCE                	1R01AT011117; 1R01DK114034 to P.J.T., F32GM140808 to C.N.). P.J.T. is a Chan
PR:FUNDING_SOURCE                	Zuckerberg Biohub Investigator and held an Investigators in the Pathogenesis of
PR:FUNDING_SOURCE                	Infectious Disease Award from the Burroughs Wellcome Fund.
PR:PUBLICATIONS                  	https://doi.org/10.1101/2022.09.19.508335
PR:DOI                           	http://dx.doi.org/10.21228/M89B04
#STUDY
ST:STUDY_TITLE                   	Time course 3: Growth of Eggerthella lenta in defined media with some samples
ST:STUDY_TITLE                   	receiving 13C6 stable isotope labeled arginine
ST:STUDY_TYPE                    	Untargeted LC-MS
ST:STUDY_SUMMARY                 	This dataset contains untargeted metabolomics analysis of supernatants from
ST:STUDY_SUMMARY                 	Eggerthella lenta DSM 2243 grown in defined EDM1 media. One set of samples grew
ST:STUDY_SUMMARY                 	in EDM1 containing 13C6 stable isotope labeled arginine.
ST:INSTITUTE                     	University of California, San Francisco
ST:LAST_NAME                     	Noecker
ST:FIRST_NAME                    	Cecilia
ST:ADDRESS                       	513 Parnassus Ave HSW1501, San Francisco, CA 94143
ST:EMAIL                         	cecilia.noecker@ucsf.edu
ST:PHONE                         	415-502-3264
ST:SUBMIT_DATE                   	2023-03-22
#SUBJECT
SU:SUBJECT_TYPE                  	Bacteria
SU:SUBJECT_SPECIES               	Eggerthella lenta
SU:TAXONOMY_ID                   	84112
SU:GENOTYPE_STRAIN               	DSM 2243
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	MSA0029	Strain:2243 | ArgGroup:HR | TimePoint:TP0 | Time:0	Sample=HR_2243_TP0_2; F_ID=F29; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0029.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0029.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0029.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0029.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0043	Strain:2243 | ArgGroup:HR | TimePoint:TP0 | Time:0	Sample=HR_2243_TP0_1; F_ID=F43; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0043.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0043.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0043.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0043.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0050	Strain:2243 | ArgGroup:HR | TimePoint:TP0 | Time:0	Sample=HR_2243_TP0_3; F_ID=F50; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0050.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0050.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0050.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0050.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0004	Strain:2243 | ArgGroup:HR | TimePoint:TP1 | Time:20	Sample=HR_2243_TP1_3; F_ID=F4; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0004.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0004.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0004.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0049	Strain:2243 | ArgGroup:HR | TimePoint:TP1 | Time:20	Sample=HR_2243_TP1_1; F_ID=F49; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0049.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0049.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0049.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0049.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0056	Strain:2243 | ArgGroup:HR | TimePoint:TP1 | Time:20	Sample=HR_2243_TP1_2; F_ID=F56; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0056.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0056.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0056.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0056.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0031	Strain:2243 | ArgGroup:HR | TimePoint:TP2 | Time:32	Sample=HR_2243_TP2_1; F_ID=F31; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0031.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0031.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0031.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0031.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0032	Strain:2243 | ArgGroup:HR | TimePoint:TP2 | Time:32	Sample=HR_2243_TP2_3; F_ID=F32; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0032.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0032.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0032.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0032.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0064	Strain:2243 | ArgGroup:HR | TimePoint:TP2 | Time:32	Sample=HR_2243_TP2_2; F_ID=F64; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0064.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0064.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0064.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0064.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0007	Strain:2243 | ArgGroup:HR | TimePoint:TP3 | Time:44	Sample=HR_2243_TP3_1; F_ID=F7; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0007.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0007.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0007.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0014	Strain:2243 | ArgGroup:HR | TimePoint:TP3 | Time:44	Sample=HR_2243_TP3_2; F_ID=F14; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0014.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0014.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0014.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0014.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0025	Strain:2243 | ArgGroup:HR | TimePoint:TP3 | Time:44	Sample=HR_2243_TP3_3; F_ID=F25; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0025.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0025.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0025.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0025.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0044	Strain:2243 | ArgGroup:HR | TimePoint:TP4 | Time:56	Sample=HR_2243_TP4_3; F_ID=F44; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0044.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0044.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0044.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0044.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0053	Strain:2243 | ArgGroup:HR | TimePoint:TP4 | Time:56	Sample=HR_2243_TP4_2; F_ID=F53; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0053.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0053.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0053.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0053.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0060	Strain:2243 | ArgGroup:HR | TimePoint:TP4 | Time:56	Sample=HR_2243_TP4_1; F_ID=F60; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0060.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0060.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0060.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0060.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0013	Strain:2243 | ArgGroup:R | TimePoint:TP0 | Time:0	Sample=R_2243_TP0_1; F_ID=F13; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0013.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0013.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0013.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0054	Strain:2243 | ArgGroup:R | TimePoint:TP0 | Time:0	Sample=R_2243_TP0_3; F_ID=F54; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0054.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0054.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0054.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0054.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0055	Strain:2243 | ArgGroup:R | TimePoint:TP0 | Time:0	Sample=R_2243_TP0_2; F_ID=F55; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0055.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0055.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0055.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0055.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0018	Strain:2243 | ArgGroup:R | TimePoint:TP1 | Time:20	Sample=R_2243_TP1_3; F_ID=F18; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0018.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0018.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0018.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0018.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0033	Strain:2243 | ArgGroup:R | TimePoint:TP1 | Time:20	Sample=R_2243_TP1_2; F_ID=F33; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0033.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0033.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0033.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0033.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0048	Strain:2243 | ArgGroup:R | TimePoint:TP1 | Time:20	Sample=R_2243_TP1_1; F_ID=F48; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0048.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0048.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0048.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0048.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0017	Strain:2243 | ArgGroup:R | TimePoint:TP2 | Time:32	Sample=R_2243_TP2_2; F_ID=F17; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0017.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0017.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0017.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0017.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0026	Strain:2243 | ArgGroup:R | TimePoint:TP2 | Time:32	Sample=R_2243_TP2_3; F_ID=F26; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0026.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0026.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0026.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0026.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0042	Strain:2243 | ArgGroup:R | TimePoint:TP2 | Time:32	Sample=R_2243_TP2_1; F_ID=F42; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0042.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0042.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0042.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0042.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0008	Strain:2243 | ArgGroup:R | TimePoint:TP3 | Time:44	Sample=R_2243_TP3_1; F_ID=F8; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0008.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0008.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0008.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0009	Strain:2243 | ArgGroup:R | TimePoint:TP3 | Time:44	Sample=R_2243_TP3_3; F_ID=F9; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0009.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0009.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0009.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0039	Strain:2243 | ArgGroup:R | TimePoint:TP3 | Time:44	Sample=R_2243_TP3_2; F_ID=F39; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0039.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0039.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0039.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0039.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0001	Strain:2243 | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_2243_TP4_2; F_ID=F1; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0001.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0001.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0001.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0002	Strain:2243 | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_2243_TP4_1; F_ID=F2; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0002.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0002.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0002.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0034	Strain:2243 | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_2243_TP4_3; F_ID=F34; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0034.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0034.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0034.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0034.mzML
SUBJECT_SAMPLE_FACTORS           	-	BK1	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_BK1.raw; RAW_FILE_NAME=M00182_20220405Pos_BK1.raw; RAW_FILE_NAME=M00182_20220405Neg_BK1.mzML; RAW_FILE_NAME=M00182_20220405Pos_BK1.mzML
SUBJECT_SAMPLE_FACTORS           	-	BK2	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_BK2.raw; RAW_FILE_NAME=M00182_20220405Pos_BK2.raw; RAW_FILE_NAME=M00182_20220405Neg_BK2.mzML; RAW_FILE_NAME=-
SUBJECT_SAMPLE_FACTORS           	-	BK3	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_BK3.raw; RAW_FILE_NAME=M00182_20220405Pos_BK3.raw; RAW_FILE_NAME=M00182_20220405Neg_BK3.mzML; RAW_FILE_NAME=M00182_20220405Pos_BK3.mzML
SUBJECT_SAMPLE_FACTORS           	-	BK4	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_BK4.raw; RAW_FILE_NAME=M00182_20220405Pos_BK4.raw; RAW_FILE_NAME=M00182_20220405Neg_BK4.mzML; RAW_FILE_NAME=M00182_20220405Pos_BK4.mzML
SUBJECT_SAMPLE_FACTORS           	-	BK5	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_BK5.raw; RAW_FILE_NAME=M00182_20220405Pos_BK5.raw; RAW_FILE_NAME=M00182_20220405Neg_BK5.mzML; RAW_FILE_NAME=M00182_20220405Pos_BK5.mzML
SUBJECT_SAMPLE_FACTORS           	-	BK6	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_BK6.raw; RAW_FILE_NAME=M00182_20220405Pos_BK6.raw; RAW_FILE_NAME=M00182_20220405Neg_BK6.mzML; RAW_FILE_NAME=M00182_20220405Pos_BK6.mzML
SUBJECT_SAMPLE_FACTORS           	-	BK7	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_BK7.raw; RAW_FILE_NAME=M00182_20220405Pos_BK7.raw; RAW_FILE_NAME=M00182_20220405Neg_BK7.mzML; RAW_FILE_NAME=M00182_20220405Pos_BK7.mzML
SUBJECT_SAMPLE_FACTORS           	-	QC1	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_QC1.raw; RAW_FILE_NAME=M00182_20220405Pos_QC1.raw; RAW_FILE_NAME=M00182_20220405Neg_QC1.mzML; RAW_FILE_NAME=M00182_20220405Pos_QC1.mzML
SUBJECT_SAMPLE_FACTORS           	-	QC2	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_QC2.raw; RAW_FILE_NAME=M00182_20220405Pos_QC2.raw; RAW_FILE_NAME=M00182_20220405Neg_QC2.mzML; RAW_FILE_NAME=M00182_20220405Pos_QC2.mzML
SUBJECT_SAMPLE_FACTORS           	-	QC3	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_QC3.raw; RAW_FILE_NAME=M00182_20220405Pos_QC3.raw; RAW_FILE_NAME=M00182_20220405Neg_QC3.mzML; RAW_FILE_NAME=M00182_20220405Pos_QC3.mzML
SUBJECT_SAMPLE_FACTORS           	-	QC4	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_QC4.raw; RAW_FILE_NAME=M00182_20220405Pos_QC4.raw; RAW_FILE_NAME=M00182_20220405Neg_QC4.mzML; RAW_FILE_NAME=M00182_20220405Pos_QC4.mzML
SUBJECT_SAMPLE_FACTORS           	-	QC5	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_QC5.raw; RAW_FILE_NAME=M00182_20220405Pos_QC5.raw; RAW_FILE_NAME=M00182_20220405Neg_QC5.mzML; RAW_FILE_NAME=M00182_20220405Pos_QC5.mzML
SUBJECT_SAMPLE_FACTORS           	-	QC6	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_QC6.raw; RAW_FILE_NAME=M00182_20220405Pos_QC6.raw; RAW_FILE_NAME=M00182_20220405Neg_QC6.mzML; RAW_FILE_NAME=M00182_20220405Pos_QC6.mzML
SUBJECT_SAMPLE_FACTORS           	-	QC7	Strain:- | ArgGroup:- | TimePoint:- | Time:-	Sample=-; F_ID=-; RAW_FILE_NAME=M00182_20220405Neg_QC7.raw; RAW_FILE_NAME=M00182_20220405Pos_QC7.raw; RAW_FILE_NAME=M00182_20220405Neg_QC7.mzML; RAW_FILE_NAME=-
SUBJECT_SAMPLE_FACTORS           	-	MSA0028	Strain:c | ArgGroup:HR | TimePoint:TP0 | Time:0	Sample=HR_c_TP0_2; F_ID=F28; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0028.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0028.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0028.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0028.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0059	Strain:c | ArgGroup:HR | TimePoint:TP0 | Time:0	Sample=HR_c_TP0_3; F_ID=F59; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0059.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0059.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0059.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0059.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0062	Strain:c | ArgGroup:HR | TimePoint:TP0 | Time:0	Sample=HR_c_TP0_1; F_ID=F62; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0062.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0062.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0062.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0062.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0012	Strain:c | ArgGroup:HR | TimePoint:TP1 | Time:20	Sample=HR_c_TP1_3; F_ID=F12; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0012.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0012.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0012.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0012.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0024	Strain:c | ArgGroup:HR | TimePoint:TP1 | Time:20	Sample=HR_c_TP1_1; F_ID=F24; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0024.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0024.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0024.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0024.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0046	Strain:c | ArgGroup:HR | TimePoint:TP1 | Time:20	Sample=HR_c_TP1_2; F_ID=F46; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0046.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0046.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0046.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0046.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0030	Strain:c | ArgGroup:HR | TimePoint:TP2 | Time:32	Sample=HR_c_TP2_2; F_ID=F30; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0030.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0030.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0030.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0030.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0038	Strain:c | ArgGroup:HR | TimePoint:TP2 | Time:32	Sample=HR_c_TP2_3; F_ID=F38; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0038.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0038.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0038.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0038.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0057	Strain:c | ArgGroup:HR | TimePoint:TP2 | Time:32	Sample=HR_c_TP2_1; F_ID=F57; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0057.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0057.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0057.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0057.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0016	Strain:c | ArgGroup:HR | TimePoint:TP3 | Time:44	Sample=HR_c_TP3_1; F_ID=F16; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0016.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0016.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0016.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0016.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0027	Strain:c | ArgGroup:HR | TimePoint:TP3 | Time:44	Sample=HR_c_TP3_3; F_ID=F27; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0027.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0027.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0027.mzML; RAW_FILE_NAME=-
SUBJECT_SAMPLE_FACTORS           	-	MSA0035	Strain:c | ArgGroup:HR | TimePoint:TP3 | Time:44	Sample=HR_c_TP3_2; F_ID=F35; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0035.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0035.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0035.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0035.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0015	Strain:c | ArgGroup:HR | TimePoint:TP4 | Time:56	Sample=HR_c_TP4_3; F_ID=F15; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0015.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0015.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0015.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0015.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0036	Strain:c | ArgGroup:HR | TimePoint:TP4 | Time:56	Sample=HR_c_TP4_1; F_ID=F36; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0036.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0036.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0036.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0036.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0047	Strain:c | ArgGroup:HR | TimePoint:TP4 | Time:56	Sample=HR_c_TP4_2; F_ID=F47; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0047.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0047.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0047.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0047.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0045	Strain:c | ArgGroup:R | TimePoint:TP0 | Time:0	Sample=R_c_TP0_3; F_ID=F45; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0045.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0045.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0045.mzML; RAW_FILE_NAME=-
SUBJECT_SAMPLE_FACTORS           	-	MSA0052	Strain:c | ArgGroup:R | TimePoint:TP0 | Time:0	Sample=R_c_TP0_2; F_ID=F52; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0052.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0052.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0052.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0052.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0061	Strain:c | ArgGroup:R | TimePoint:TP0 | Time:0	Sample=R_c_TP0_1; F_ID=F61; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0061.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0061.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0061.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0061.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0010	Strain:c | ArgGroup:R | TimePoint:TP1 | Time:20	Sample=R_c_TP1_1; F_ID=F10; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0010.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0010.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0010.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0010.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0021	Strain:c | ArgGroup:R | TimePoint:TP1 | Time:20	Sample=R_c_TP1_3; F_ID=F21; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0021.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0021.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0021.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0021.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0041	Strain:c | ArgGroup:R | TimePoint:TP1 | Time:20	Sample=R_c_TP1_2; F_ID=F41; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0041.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0041.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0041.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0041.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0019	Strain:c | ArgGroup:R | TimePoint:TP2 | Time:32	Sample=R_c_TP2_3; F_ID=F19; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0019.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0019.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0019.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0019.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0022	Strain:c | ArgGroup:R | TimePoint:TP2 | Time:32	Sample=R_c_TP2_2; F_ID=F22; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0022.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0022.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0022.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0022.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0023	Strain:c | ArgGroup:R | TimePoint:TP2 | Time:32	Sample=R_c_TP2_1; F_ID=F23; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0023.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0023.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0023.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0023.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0006	Strain:c | ArgGroup:R | TimePoint:TP3 | Time:44	Sample=R_c_TP3_1; F_ID=F6; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0006.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0006.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0006.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0020	Strain:c | ArgGroup:R | TimePoint:TP3 | Time:44	Sample=R_c_TP3_3; F_ID=F20; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0020.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0020.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0020.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0020.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0058	Strain:c | ArgGroup:R | TimePoint:TP3 | Time:44	Sample=R_c_TP3_2; F_ID=F58; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0058.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0058.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0058.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0058.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0003	Strain:c | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_c_TP4_2_extra4; F_ID=F3; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0003.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0003.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0003.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0005	Strain:c | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_c_TP4_1; F_ID=F5; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0005.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0005.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0005.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0011	Strain:c | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_c_TP4_2_extra1; F_ID=F11; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0011.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0011.raw; RAW_FILE_NAME=-; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0011.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0037	Strain:c | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_c_TP4_2_extra2; F_ID=F37; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0037.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0037.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0037.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0037.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0040	Strain:c | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_c_TP4_2_extra3; F_ID=F40; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0040.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0040.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0040.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0040.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0051	Strain:c | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_c_TP4_2; F_ID=F51; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0051.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0051.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0051.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0051.mzML
SUBJECT_SAMPLE_FACTORS           	-	MSA0063	Strain:c | ArgGroup:R | TimePoint:TP4 | Time:56	Sample=R_c_TP4_3; F_ID=F63; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0063.raw; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0063.raw; RAW_FILE_NAME=M00182_20220405_Neg_1_MSA0063.mzML; RAW_FILE_NAME=M00182_20220405_Pos_1_MSA0063.mzML
#COLLECTION
CO:COLLECTION_SUMMARY            	Time course experiments were conducted in tubes in the anaerobic chamber in a
CO:COLLECTION_SUMMARY            	37°C incubator. For all metabolomics experiments, three independent culture
CO:COLLECTION_SUMMARY            	replicates were included for each condition, with an equal number of
CO:COLLECTION_SUMMARY            	uninoculated control tubes. Starter cultures and inocula were prepared as
CO:COLLECTION_SUMMARY            	described above for growth assays. 5mLs of defined media was added to VWR glass
CO:COLLECTION_SUMMARY            	culture tubes (53283-800) with screw caps. The PBS-washed inoculum was added to
CO:COLLECTION_SUMMARY            	culture tubes to obtain an approximate starting OD600 of 0.001. A preliminary
CO:COLLECTION_SUMMARY            	growth assay was conducted to define time points spanning the exponential growth
CO:COLLECTION_SUMMARY            	phase in the tested conditions. At each time point, OD600 measurements of all
CO:COLLECTION_SUMMARY            	inoculated tubes were first measured using a Hach DR1900 spectrophotometer, with
CO:COLLECTION_SUMMARY            	a paired control tube to normalize for the background. 100 μL from each tube
CO:COLLECTION_SUMMARY            	were then transferred into a 96-well microplate, which was sealed and removed
CO:COLLECTION_SUMMARY            	from the anaerobic chamber. Plates were centrifuged at 1,928 rcf at 4°C for 8
CO:COLLECTION_SUMMARY            	minutes, after which supernatants were collected into fresh polypropylene tubes
CO:COLLECTION_SUMMARY            	or plates, sealed, and flash-frozen in liquid nitrogen. Two time course
CO:COLLECTION_SUMMARY            	experiments were carried out with stable isotope-labeled substrates.
CO:COLLECTION_SUMMARY            	Experimental groups included conditions in which sodium arginine in the defined
CO:COLLECTION_SUMMARY            	media was replaced with 13C6 labeled arginine HCl, along with a matched
CO:COLLECTION_SUMMARY            	experimental group with the same concentration of unlabeled substrate.
CO:SAMPLE_TYPE                   	Bacterial culture supernatant
CO:COLLECTION_FREQUENCY          	at time points specified in study design table over 56 hours (full growth phase)
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	For growth and metabolomics experiments, glycerol stocks of the 3 E. lenta
TR:TREATMENT_SUMMARY             	strains were first streaked on BHI+ agar plates and incubated at 37°C for 2-3
TR:TREATMENT_SUMMARY             	days. Individual colonies were inoculated into 3-4 mL liquid BHI+ and incubated
TR:TREATMENT_SUMMARY             	at 37°C for 40-48 hours, or until approximately early stationary phase. Culture
TR:TREATMENT_SUMMARY             	optical density (600 nm wavelength absorbance, OD600) was measured using a Hach
TR:TREATMENT_SUMMARY             	DR1900 spectrophotometer. 1 mL samples of BHI starter cultures were then
TR:TREATMENT_SUMMARY             	centrifuged at 1,568 rcf for 4 minutes in a microcentrifuge (ThermoScientific
TR:TREATMENT_SUMMARY             	mySpin 12) in the anaerobic chamber and resuspended in 1 mL sterile
TR:TREATMENT_SUMMARY             	phosphate-buffered saline (PBS). The resulting suspension was vortexed and
TR:TREATMENT_SUMMARY             	diluted to an approximate OD600 of 0.1, and used as inoculum into defined
TR:TREATMENT_SUMMARY             	experimental conditions. Varying media conditions were prepared separately and
TR:TREATMENT_SUMMARY             	all allowed to fully reduce in the anaerobic chamber prior to inoculation.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Bacterial culture supernatant and sterile media, used in culture, were thawed on
SP:SAMPLEPREP_SUMMARY            	wet ice. Once thawed, samples were homogenized by inversion five times.
SP:SAMPLEPREP_SUMMARY            	Extracellular culture supernatant samples were prepared as follows: 20 μL of
SP:SAMPLEPREP_SUMMARY            	culture supernatant were extracted using 80 μL of a chilled extraction solvent
SP:SAMPLEPREP_SUMMARY            	at −20°C (1:1 acetonitrile:methanol, 5% water containing stable
SP:SAMPLEPREP_SUMMARY            	isotope-labeled internal standards). Samples were homogenized via pipette
SP:SAMPLEPREP_SUMMARY            	action, incubated for 1 hour at −20°C, centrifuged at 4°C at 6000 rcf for 5
SP:SAMPLEPREP_SUMMARY            	min. The supernatant was transferred to a new plate and immediately sealed and
SP:SAMPLEPREP_SUMMARY            	kept at 4°C prior to prompt analysis via LC-MS/MS.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Samples, sterile media, pools, and blanks were promptly added to a Thermo
CH:CHROMATOGRAPHY_SUMMARY        	Vanquish Autosampler at 4°C in a Vanquish UHPLC (Thermo Fisher Scientific,
CH:CHROMATOGRAPHY_SUMMARY        	Waltham, MA). Chromatographic separation was performed using an ACQUITY Bridged
CH:CHROMATOGRAPHY_SUMMARY        	Ethylene Hybrid (BEH) Amide column 2.1 x 150 mm, 1.7-micron particle size,
CH:CHROMATOGRAPHY_SUMMARY        	(Waters Corp. Milford, MA), using chromatographic conditions published elsewhere
CH:CHROMATOGRAPHY_SUMMARY        	(HILIC method described in the Supplementary Methods of
CH:CHROMATOGRAPHY_SUMMARY        	doi.org/10.1038/s41586-021-03707-9).
CH:INSTRUMENT_NAME               	Thermo Vanquish
CH:COLUMN_NAME                   	Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
CH:COLUMN_TEMPERATURE            	40
CH:FLOW_GRADIENT                 	The gradient profile was held at 100% B for 2 minutes, from 100% B to 70% B in 5
CH:FLOW_GRADIENT                 	minutes, holding at 70% B for 0.7 minute, from 70% B to 40% B for 1.3 minutes,
CH:FLOW_GRADIENT                 	holding at 40% B for 0.5 minutes, from 40% B to 30% B for 0.75 minutes, before
CH:FLOW_GRADIENT                 	returning to 100% B for 2.5 minutes and holding at 100% B for 4 minutes.
CH:FLOW_RATE                     	400 μL per minute
CH:SOLVENT_A                     	100% water; 0.125% formic acid; 10 mM ammonium formate, pH 3
CH:SOLVENT_B                     	95% acetonitrile/5% water; 0.125% formic acid; 10 mM ammonium formate
CH:CHROMATOGRAPHY_TYPE           	HILIC
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive HF hybrid Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:MS_COMMENTS                   	Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2
MS:MS_COMMENTS                   	selection of metabolites from our in-house ‘local’ library, when additional
MS:MS_COMMENTS                   	scan bandwidth was available MS2 was collected in a data-dependent manner. Mass
MS:MS_COMMENTS                   	range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was
MS:MS_COMMENTS                   	collected, loop count was 4, isolation window was 1.5 Da. In SIRM samples,
MS:MS_COMMENTS                   	deuterated internal standards were replaced with CUDA and Val-Tyr-Val to enable
MS:MS_COMMENTS                   	untargeted enrichment analysis. LC-MS/MS analysis conditions for SIRM
MS:MS_COMMENTS                   	metabolomics were identical to those used for standard untargeted metabolomics.
MS:MS_COMMENTS                   	Intra- and extracellular untargeted data generated from SIRM experiments was
MS:MS_COMMENTS                   	analyzed separately using Compound Discoverer version 3.3 (Thermo Scientific,
MS:MS_COMMENTS                   	Bremen, Germany). Samples treated with labeled compounds were always paired with
MS:MS_COMMENTS                   	matched samples treated with unlabeled compounds in order to correct for
MS:MS_COMMENTS                   	naturally occurring isotope abundances. Unlabeled samples were used for compound
MS:MS_COMMENTS                   	detection and formula assignment via isotope pattern-based prediction, spectral
MS:MS_COMMENTS                   	library matches, or mass lists matches. The isotope patterns and formulas from
MS:MS_COMMENTS                   	the sample files then served as a reference for the detection of potential
MS:MS_COMMENTS                   	isotopologues per compound in the labeled sample type. A specification of the
MS:MS_COMMENTS                   	full Compound Discoverer workflow is available at
MS:MS_COMMENTS                   	https://github.com/turnbaughlab/2022_Noecker_ElentaMetabolism.
MS:ION_MODE                      	NEGATIVE
#END