#METABOLOMICS WORKBENCH joc123_20250630_023553 DATATRACK_ID:6116 STUDY_ID:ST004028 ANALYSIS_ID:AN006655 PROJECT_ID:PR002520
VERSION             	1
CREATED_ON             	July 7, 2025, 6:48 pm
#PROJECT
PR:PROJECT_TITLE                 	Environmental cues in different host niches shape the survival fitness of
PR:PROJECT_TITLE                 	Staphylococcus aureus
PR:PROJECT_SUMMARY               	The ability of Staphylococcus aureus to adapt and thrive in diverse host niches
PR:PROJECT_SUMMARY               	adds to the challenge in combating this ubiquitous pathogen. While extensive
PR:PROJECT_SUMMARY               	research has been pursued on the adaptive mechanisms of methicillin-resistant S.
PR:PROJECT_SUMMARY               	aureus (MRSA) in various infection models, a comprehensive analysis of its
PR:PROJECT_SUMMARY               	fitness across different host niches is lacking. In this study, we employ
PR:PROJECT_SUMMARY               	transposon sequencing to analyze the adaptive strategies of MRSA in various
PR:PROJECT_SUMMARY               	infection niches. Our analysis encompasses a cell model that mimics an
PR:PROJECT_SUMMARY               	intracellular niche, human blood, which represents a major extracellular
PR:PROJECT_SUMMARY               	environment as well as a major intermediary route encountered by bacteria during
PR:PROJECT_SUMMARY               	systemic infection, and a murine sepsis model that recapitulates intra-organ
PR:PROJECT_SUMMARY               	environments. Our findings reveal substantial differences in the genetic
PR:PROJECT_SUMMARY               	determinants essential for bacterial survival in intracellular and blood
PR:PROJECT_SUMMARY               	environments. Moreover, we show that each organ imposes unique growth
PR:PROJECT_SUMMARY               	constraints, thus fostering heterogeneity within the mutant population that can
PR:PROJECT_SUMMARY               	enter and survive in each organ of the male mouse. By comparing genes important
PR:PROJECT_SUMMARY               	for survival across all examined host environments, we identify 27 core genes
PR:PROJECT_SUMMARY               	that represent potential therapeutic targets for treating S. aureus infections.
PR:PROJECT_SUMMARY               	Additionally, our findings aid in understanding how bacteria adapt to diverse
PR:PROJECT_SUMMARY               	host environments.
PR:INSTITUTE                     	Sungkyunkwan University
PR:LAST_NAME                     	Lee
PR:FIRST_NAME                    	Wonsik
PR:ADDRESS                       	2066, Seobu-ro, Jangan-gu, Suwon-si, South Korea
PR:EMAIL                         	manager2.leelab@gmail.com
PR:PHONE                         	010-4686-0544
#STUDY
ST:STUDY_TITLE                   	Bacterial consumption of nutrients in blood environment
ST:STUDY_SUMMARY                 	Staphylococcus aureus adapts to diverse host environments during infection.
ST:STUDY_SUMMARY                 	Here, the authors study how S. aureus adapts in the blood environment by
ST:STUDY_SUMMARY                 	studying which nutrients are consumed by methicillin-resistant S. aureus upon
ST:STUDY_SUMMARY                 	inoculation into human whole blood or tryptic soy broth (TSB) media as a
ST:STUDY_SUMMARY                 	control. For this, USA300 is inoculated into human whole blood or TSB for up to
ST:STUDY_SUMMARY                 	36 h, during which the supernatant is collected and measured by LC-MS for the
ST:STUDY_SUMMARY                 	amounts of glucose and lactate remaining after consumption by the bacteria.
ST:STUDY_SUMMARY                 	Additionally, USA300 is cultured in human whole blood up to 24 h, during which
ST:STUDY_SUMMARY                 	the supernatant is collected for the measurement of amino acid consumption by
ST:STUDY_SUMMARY                 	the bacteria in blood. Lastly, USA300 is cultured in whole blood or TSB for up
ST:STUDY_SUMMARY                 	to 24 h, during which the bacterial cells are collected for the measurement of
ST:STUDY_SUMMARY                 	the intracellular bacillithiol produced by the bacterial cells during growth in
ST:STUDY_SUMMARY                 	blood or TSB. Our results show that glucose and lactate are simultaneously
ST:STUDY_SUMMARY                 	consumed in human whole blood, while in TSB, glucose is consumed before the
ST:STUDY_SUMMARY                 	consumption of lactate. S. aureus exhibited the ability to adapt its mode of
ST:STUDY_SUMMARY                 	catabolic repression and shifted to a simultaneous mode only in the blood
ST:STUDY_SUMMARY                 	environment, which conferred a fitness advantage. Additionally, we observed that
ST:STUDY_SUMMARY                 	S. aureus actively consumed all amino acids except cystine. Such accumulation of
ST:STUDY_SUMMARY                 	cystine was associated with the increased intracellular bacillithiol when USA300
ST:STUDY_SUMMARY                 	was cultured in the blood environment. These results indicate that to survive in
ST:STUDY_SUMMARY                 	blood, S. aureus depends on genes related to response to oxidative stress,
ST:STUDY_SUMMARY                 	including those associated with bacterial thiol synthesis. In sum, our results
ST:STUDY_SUMMARY                 	indicate that S. aureus adjusts its metabolism to better adapt to the
ST:STUDY_SUMMARY                 	extracellular host environment, allowing for more efficient utilization of
ST:STUDY_SUMMARY                 	available carbon sources and response to oxidative stress.
ST:INSTITUTE                     	Sungkyunkwan University
ST:LAST_NAME                     	Lee
ST:FIRST_NAME                    	Wonsik
ST:ADDRESS                       	2066, Seobu-ro, Jangan-gu, Suwon-si, South Korea
ST:EMAIL                         	manager2.leelab@gmail.com
ST:PHONE                         	010-4686-0544
#SUBJECT
SU:SUBJECT_TYPE                  	Bacteria
SU:SUBJECT_SPECIES               	Staphylococcus aureus
SU:TAXONOMY_ID                   	1280
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_0_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_0_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_0_4	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_0_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_0_5	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_0_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_3_2	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):3	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_3_2.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_3_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):3	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_3_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_3_5	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):3	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_3_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_6_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):6	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_6_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_6_4	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):6	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_6_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_6_5	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):6	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_6_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_9_1	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_9_1.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_9_2	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_9_2.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_9_5	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_9_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_12_1	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_12_1.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_12_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_12_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_12_5	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_12_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_24_2	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_24_2.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_24_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_24_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_24_4	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_24_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_36_1	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):36	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_36_1.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_36_2	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):36	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_36_2.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_GL_36_4	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):36	RAW_FILE_NAME(Raw_File_Name)=Blood_GL_36_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_0_2	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_0_2.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_0_3	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_0_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_0_5	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_0_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_3_3	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):3	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_3_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_3_4	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):3	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_3_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_3_5	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):3	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_3_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_6_2	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):6	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_6_2.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_6_3	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):6	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_6_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_6_4	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):6	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_6_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_9_2	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_9_2.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_9_3	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_9_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_9_4	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_9_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_12_3	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_12_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_12_4	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_12_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_12_5	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_12_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_24_3	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_24_3.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_24_4	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_24_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_24_5	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_24_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_36_1	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):36	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_36_1.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_36_4	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):36	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_36_4.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	TSB_GL_36_5	Growth_Medium:TSB | Sample source:Supernatant | Incubation_Time_(h):36	RAW_FILE_NAME(Raw_File_Name)=TSB_GL_36_5.mzML; MS_mode=Negative; Metabolites_extracted=Glucose and lactate
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_0_1	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_0_1.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_0_2	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_0_3.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_0_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_0_5.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_9_2	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_9_2.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_9_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_9_3.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_9_5	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_9_5.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_12_2	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_12_2.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_12_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_12_3.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_12_5	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_12_5.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_24_1	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_24_1.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_24_3	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_24_3.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	Blood_AA_24_5	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_AA_24_5.mzML; MS_mode=Positive; Metabolites_extracted=Amino acids
SUBJECT_SAMPLE_FACTORS           	-	TSB_Con_0_1	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=TSB_Con_0_1.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	TSB_Con_0_2	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=TSB_Con_0_2.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	TSB_Con_0_3	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):0	RAW_FILE_NAME(Raw_File_Name)=TSB_Con_0_3.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	TSB_bac_12_1	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=TSB_bac_12_1.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	TSB_bac_12_2	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=TSB_bac_12_2.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	TSB_bac_12_3	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=TSB_bac_12_3.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	TSB_bac_24_1	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=TSB_bac_24_1.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	TSB_bac_24_2	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=TSB_bac_24_2.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	TSB_bac_24_3	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=TSB_bac_24_3.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	Blood_bac_12_1	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_bac_12_1.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	Blood_bac_12_2	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_bac_12_2.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	Blood_bac_12_4	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):12	RAW_FILE_NAME(Raw_File_Name)=Blood_bac_12_4.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	Blood_bac_24_2	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_bac_24_2.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	Blood_bac_24_3	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_bac_24_3.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
SUBJECT_SAMPLE_FACTORS           	-	Blood_bac_24_4	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):24	RAW_FILE_NAME(Raw_File_Name)=Blood_bac_24_4.mzML; MS_mode=Positive; Metabolites_extracted=Bacillithiol
#COLLECTION
CO:COLLECTION_SUMMARY            	Staphylococcus aureus has been cultured in tryptic soy broth (TSB) media or
CO:COLLECTION_SUMMARY            	blood for various time points up to 36 hours. At designated time points,
CO:COLLECTION_SUMMARY            	supernatant was collected for the measurement of glucose/lactate or amino acid
CO:COLLECTION_SUMMARY            	consumption. For the measurement of bacillithiol production, bacterial cells
CO:COLLECTION_SUMMARY            	were collected by centrifugation and prepared for mass spectrometric analysis.
CO:SAMPLE_TYPE                   	Bacterial cells
#TREATMENT
TR:TREATMENT_SUMMARY             	Staphylococcus aureus has been grown in TSB and human whole blood. The samples
TR:TREATMENT_SUMMARY             	were incubated at 37 ºC, with shaking at 150 rpm for various time points from 3
TR:TREATMENT_SUMMARY             	to 36 h. For determination of bacterial bacillithiol levels, USA300 was
TR:TREATMENT_SUMMARY             	inoculated into whole blood or TSB at an OD600=0.02 with shaking at 150 rpm at
TR:TREATMENT_SUMMARY             	37 ºC. At 9, 12, and 24 h post-inoculation, samples were centrifuged at 4 ºC,
TR:TREATMENT_SUMMARY             	6,010 x g for 6 min for the collection of bacterial cells. Bacterial cells
TR:TREATMENT_SUMMARY             	collected at a log phase (OD600=0.5) were defined as a 0 h sample. The resulting
TR:TREATMENT_SUMMARY             	pellet was quenched by the addition of quenching buffer (40:40:20;
TR:TREATMENT_SUMMARY             	Acetonitrile:Methanol:Water).
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	At the designated time points, whole blood or TSB samples were centrifuged for 2
SP:SAMPLEPREP_SUMMARY            	min at 13,523 x g, 4 ºC. The supernatant was vortexed and mixed with cold
SP:SAMPLEPREP_SUMMARY            	methanol (v/v ratio 1:2). All samples mixed with methanol were centrifuged for 2
SP:SAMPLEPREP_SUMMARY            	minutes at 4 ºC, 15,871 x g. Supernatant was added to Spin-X centrifuge tubes
SP:SAMPLEPREP_SUMMARY            	(Corning Inc., Corning, NY) and centrifuged at 4 ºC, 15,871 x g one more time.
SP:SAMPLEPREP_SUMMARY            	Bacterial cells were lysed by mechanical disruption using 0.1 mm glass beads and
SP:SAMPLEPREP_SUMMARY            	a precellys homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France)
SP:SAMPLEPREP_SUMMARY            	with 12 cycles of 10,000 rpm, 30 sec cycle. Samples were placed on ice
SP:SAMPLEPREP_SUMMARY            	in-between each cycle for the prevention of protein degradation. Lysates were
SP:SAMPLEPREP_SUMMARY            	centrifuged at 4 ºC, 15,871 x g for 5 min, after which supernatant was added to
SP:SAMPLEPREP_SUMMARY            	Spin-X centrifuge tubes (Corning Inc.) and centrifuged at 4 ºC, 15,871 x g one
SP:SAMPLEPREP_SUMMARY            	more time.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	HILIC
CH:INSTRUMENT_NAME               	Agilent 1290 Infinity II
CH:COLUMN_NAME                   	Cogent Diamond Hydride (150 x 2.1mm, 4um, 100A)
CH:SOLVENT_A                     	100% water; 0.2% formic acid
CH:SOLVENT_B                     	100% acetonitrile; 0.2% formic acid
CH:FLOW_GRADIENT                 	0–2 min, 85% B; 3–5 min, 80% B; 6–7 min, 75% B; 8–9 min, 70% B;
CH:FLOW_GRADIENT                 	10–11.1 min, 50% B; 11.1–14 min 20% B; 14.1–24 min 5% B followed by a 10
CH:FLOW_GRADIENT                 	min re-equilibration period at 85% B
CH:FLOW_RATE                     	0.4 mL/min
CH:COLUMN_TEMPERATURE            	25
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent 6230 TOF
MS:INSTRUMENT_TYPE               	TOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	Profinder 6.0
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	abundance
MS_METABOLITE_DATA_START
Samples	Blood_AA_0_1	Blood_AA_0_2	Blood_AA_0_3	Blood_AA_9_2	Blood_AA_9_3	Blood_AA_9_5	Blood_AA_12_2	Blood_AA_12_3	Blood_AA_12_5	Blood_AA_24_1	Blood_AA_24_3	Blood_AA_24_5	TSB_Con_0_1	TSB_Con_0_2	TSB_Con_0_3	TSB_bac_12_1	TSB_bac_12_2	TSB_bac_12_3	TSB_bac_24_1	TSB_bac_24_2	TSB_bac_24_3	Blood_bac_12_1	Blood_bac_12_2	Blood_bac_12_4	Blood_bac_24_2	Blood_bac_24_3	Blood_bac_24_4
Factors	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):0	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):9	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):12	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	Growth_Medium:Blood | Sample source:Plasma | Incubation_Time_(h):24	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):0	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):0	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):0	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):12	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):12	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):12	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):24	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):24	Growth_Medium:TSB | Sample source:Bacterial cells | Incubation_Time_(h):24	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):12	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):12	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):12	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):24	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):24	Growth_Medium:Blood | Sample source:Bacterial cells | Incubation_Time_(h):24
Bacillithiol													ND	ND	ND	1.2.E+04	2.1.E+04	2.9.E+04	2.4.E+03	2.4.E+03	2.4.E+03	3.0.E+05	3.6.E+05	3.9.E+05	4.0.E+05	4.2.E+05	4.3.E+05
L-alanine	1.9.E+06	2.9.E+06	2.2.E+06	5.1.E+05	5.0.E+05	6.0.E+05	3.9.E+05	5.4.E+05	3.9.E+05	2.1.E+05	3.4.E+05	2.7.E+05															
L-Proline	1.8.E+06	1.6.E+06	1.9.E+06	4.1.E+05	3.9.E+05	3.8.E+05	2.9.E+05	3.2.E+05	2.6.E+05	9.0.E+04	1.7.E+05	1.5.E+05															
L-Valine	2.1.E+07	3.2.E+07	2.5.E+07	2.6.E+07	2.6.E+07	3.1.E+07	1.7.E+07	2.2.E+07	1.2.E+07	5.8.E+06	7.1.E+06	5.2.E+06															
L-Threonine	2.2.E+05	2.1.E+05	2.1.E+05	5.5.E+03	8.3.E+03	2.1.E+03	2.9.E+03	3.1.E+03	8.6.E+03	ND	5.5.E+02	9.4.E+02															
L-Leucine	3.1.E+08	3.0.E+08	3.0.E+08	8.0.E+07	7.1.E+07	7.3.E+07	4.4.E+07	4.9.E+07	3.1.E+07	1.5.E+07	2.1.E+07	1.7.E+07															
L-Asparagine	1.1.E+05	1.1.E+05	1.0.E+05	ND	ND	ND	ND	ND	ND	ND	ND	ND															
L-Aspartate	5.5.E+06	5.8.E+06	5.6.E+06	1.4.E+06	1.4.E+06	1.7.E+06	1.8.E+06	1.7.E+06	1.2.E+06	2.7.E+06	2.5.E+06	2.1.E+06															
L-Glutamine	1.3.E+06	1.2.E+06	1.3.E+06	4.6.E+05	9.8.E+04	5.1.E+05	4.3.E+05	1.6.E+05	4.8.E+05	3.7.E+05	3.4.E+05	3.4.E+05															
L-Glutamate	1.8.E+07	2.2.E+07	2.0.E+07	1.4.E+06	1.3.E+06	1.5.E+06	9.9.E+05	1.2.E+06	1.0.E+06	6.8.E+05	1.0.E+06	6.7.E+05															
L-Arginine	1.2.E+08	1.2.E+08	1.2.E+08	5.7.E+06	3.7.E+06	3.4.E+06	2.8.E+06	2.3.E+06	1.8.E+06	1.0.E+06	4.6.E+05	5.4.E+05															
L-Tryptophan	2.6.E+07	2.4.E+07	2.4.E+07	1.7.E+07	1.6.E+07	1.5.E+07	1.6.E+07	1.5.E+07	1.5.E+07	1.3.E+07	1.3.E+07	1.1.E+07															
L-Cystine	3.1.E+06	2.7.E+06	2.6.E+06	4.5.E+06	4.7.E+06	4.9.E+06	6.5.E+06	5.5.E+06	5.1.E+06	6.4.E+06	6.1.E+06	5.8.E+06															
L-Lysine	1.4.E+08	1.3.E+08	1.3.E+08	8.4.E+07	8.2.E+07	7.1.E+07	8.2.E+07	7.1.E+07	6.3.E+07	3.0.E+07	2.7.E+07	2.0.E+07															
L-Methionine	2.0.E+07	2.1.E+07	2.1.E+07	1.2.E+07	1.2.E+07	1.3.E+07	1.0.E+07	1.1.E+07	7.7.E+06	4.6.E+06	4.1.E+06	2.6.E+06															
L-Histidine	2.1.E+07	2.0.E+07	2.0.E+07	8.5.E+06	5.6.E+06	6.2.E+06	4.0.E+06	3.5.E+06	3.0.E+06	1.5.E+06	2.0.E+06	1.7.E+06															
L-Phenylalanine	1.1.E+08	1.0.E+08	1.0.E+08	7.3.E+07	7.2.E+07	6.5.E+07	7.2.E+07	6.5.E+07	6.4.E+07	4.8.E+07	4.6.E+07	4.5.E+07															
L-Tyrosine	1.6.E+07	1.5.E+07	1.5.E+07	1.0.E+07	1.0.E+07	8.8.E+06	1.1.E+07	8.7.E+06	7.8.E+06	7.1.E+06	5.6.E+06	4.8.E+06															
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Mass	KEGG ID
Bacillithiol	398.0995	NA
L-alanine	89.047678	C00041
L-Proline	115.063328	C00148
L-Valine	117.078978	C00183
L-Threonine	119.058243	C00188
L-Leucine	131.094628	C00123
L-Asparagine	132.053492	C00152
L-Aspartate	133.037507	C00049
L-Glutamine	146.069142	C00064
L-Glutamate	147.053157	C00025
L-Arginine	174.111675	C00062
L-Tryptophan	204.089877	C00078
L-Cystine	240.023849	C00491
L-Lysine	146.105527	C00047
L-Methionine	149.051049	C00073
L-Histidine	155.069476	C00135
L-Phenylalanine	165.078978	C00079
L-Tyrosine	181.073893	C00082
METABOLITES_END
#END