Summary of Study ST004028

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002520. The data can be accessed directly via it's Project DOI: 10.21228/M8WZ6W This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST004028
Study Title	Bacterial consumption of nutrients in blood environment
Study Summary	Staphylococcus aureus adapts to diverse host environments during infection. Here, the authors study how S. aureus adapts in the blood environment by studying which nutrients are consumed by methicillin-resistant S. aureus upon inoculation into human whole blood or tryptic soy broth (TSB) media as a control. For this, USA300 is inoculated into human whole blood or TSB for up to 36 h, during which the supernatant is collected and measured by LC-MS for the amounts of glucose and lactate remaining after consumption by the bacteria. Additionally, USA300 is cultured in human whole blood up to 24 h, during which the supernatant is collected for the measurement of amino acid consumption by the bacteria in blood. Lastly, USA300 is cultured in whole blood or TSB for up to 24 h, during which the bacterial cells are collected for the measurement of the intracellular bacillithiol produced by the bacterial cells during growth in blood or TSB. Our results show that glucose and lactate are simultaneously consumed in human whole blood, while in TSB, glucose is consumed before the consumption of lactate. S. aureus exhibited the ability to adapt its mode of catabolic repression and shifted to a simultaneous mode only in the blood environment, which conferred a fitness advantage. Additionally, we observed that S. aureus actively consumed all amino acids except cystine. Such accumulation of cystine was associated with the increased intracellular bacillithiol when USA300 was cultured in the blood environment. These results indicate that to survive in blood, S. aureus depends on genes related to response to oxidative stress, including those associated with bacterial thiol synthesis. In sum, our results indicate that S. aureus adjusts its metabolism to better adapt to the extracellular host environment, allowing for more efficient utilization of available carbon sources and response to oxidative stress.
Institute	Sungkyunkwan University
Last Name	Lee
First Name	Wonsik
Address	2066, Seobu-ro, Jangan-gu, Suwon-si, South Korea
Email	manager2.leelab@gmail.com
Phone	010-4686-0544
Submit Date	2025-06-30
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2025-07-09
Release Version	1

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Project:

Project ID:	PR002520
Project DOI:	doi: 10.21228/M8WZ6W
Project Title:	Environmental cues in different host niches shape the survival fitness of Staphylococcus aureus
Project Summary:	The ability of Staphylococcus aureus to adapt and thrive in diverse host niches adds to the challenge in combating this ubiquitous pathogen. While extensive research has been pursued on the adaptive mechanisms of methicillin-resistant S. aureus (MRSA) in various infection models, a comprehensive analysis of its fitness across different host niches is lacking. In this study, we employ transposon sequencing to analyze the adaptive strategies of MRSA in various infection niches. Our analysis encompasses a cell model that mimics an intracellular niche, human blood, which represents a major extracellular environment as well as a major intermediary route encountered by bacteria during systemic infection, and a murine sepsis model that recapitulates intra-organ environments. Our findings reveal substantial differences in the genetic determinants essential for bacterial survival in intracellular and blood environments. Moreover, we show that each organ imposes unique growth constraints, thus fostering heterogeneity within the mutant population that can enter and survive in each organ of the male mouse. By comparing genes important for survival across all examined host environments, we identify 27 core genes that represent potential therapeutic targets for treating S. aureus infections. Additionally, our findings aid in understanding how bacteria adapt to diverse host environments.
Institute:	Sungkyunkwan University
Last Name:	Lee
First Name:	Wonsik
Address:	2066, Seobu-ro, Jangan-gu, Suwon-si, South Korea
Email:	manager2.leelab@gmail.com
Phone:	010-4686-0544

Subject:

Subject ID:	SU004174
Subject Type:	Bacteria
Subject Species:	Staphylococcus aureus
Taxonomy ID:	1280

Factors:

Subject type: Bacteria; Subject species: Staphylococcus aureus (Factor headings shown in green)

mb_sample_id	local_sample_id	Growth_Medium	Sample source	Incubation_Time_(h)
SA464592	Blood_bac_12_4	Blood	Bacterial cells	12
SA464593	Blood_bac_12_2	Blood	Bacterial cells	12
SA464594	Blood_bac_12_1	Blood	Bacterial cells	12
SA464595	Blood_bac_24_4	Blood	Bacterial cells	24
SA464596	Blood_bac_24_3	Blood	Bacterial cells	24
SA464597	Blood_bac_24_2	Blood	Bacterial cells	24
SA464598	Blood_GL_0_4	Blood	Plasma	0
SA464599	Blood_AA_0_3	Blood	Plasma	0
SA464600	Blood_AA_0_2	Blood	Plasma	0
SA464601	Blood_AA_0_1	Blood	Plasma	0
SA464602	Blood_GL_0_3	Blood	Plasma	0
SA464603	Blood_GL_0_5	Blood	Plasma	0
SA464604	Blood_GL_12_1	Blood	Plasma	12
SA464605	Blood_GL_12_5	Blood	Plasma	12
SA464606	Blood_AA_12_5	Blood	Plasma	12
SA464607	Blood_AA_12_3	Blood	Plasma	12
SA464608	Blood_AA_12_2	Blood	Plasma	12
SA464609	Blood_GL_12_3	Blood	Plasma	12
SA464610	Blood_AA_24_5	Blood	Plasma	24
SA464611	Blood_AA_24_3	Blood	Plasma	24
SA464612	Blood_AA_24_1	Blood	Plasma	24
SA464613	Blood_GL_24_4	Blood	Plasma	24
SA464614	Blood_GL_24_3	Blood	Plasma	24
SA464615	Blood_GL_24_2	Blood	Plasma	24
SA464616	Blood_GL_3_2	Blood	Plasma	3
SA464617	Blood_GL_3_3	Blood	Plasma	3
SA464618	Blood_GL_3_5	Blood	Plasma	3
SA464619	Blood_GL_36_4	Blood	Plasma	36
SA464620	Blood_GL_36_2	Blood	Plasma	36
SA464621	Blood_GL_36_1	Blood	Plasma	36
SA464622	Blood_GL_6_4	Blood	Plasma	6
SA464623	Blood_GL_6_3	Blood	Plasma	6
SA464624	Blood_GL_6_5	Blood	Plasma	6
SA464625	Blood_AA_9_3	Blood	Plasma	9
SA464626	Blood_GL_9_5	Blood	Plasma	9
SA464627	Blood_GL_9_1	Blood	Plasma	9
SA464628	Blood_AA_9_5	Blood	Plasma	9
SA464629	Blood_GL_9_2	Blood	Plasma	9
SA464630	Blood_AA_9_2	Blood	Plasma	9
SA464631	TSB_Con_0_3	TSB	Bacterial cells	0
SA464632	TSB_Con_0_1	TSB	Bacterial cells	0
SA464633	TSB_Con_0_2	TSB	Bacterial cells	0
SA464634	TSB_bac_12_1	TSB	Bacterial cells	12
SA464635	TSB_bac_12_3	TSB	Bacterial cells	12
SA464636	TSB_bac_12_2	TSB	Bacterial cells	12
SA464637	TSB_bac_24_1	TSB	Bacterial cells	24
SA464638	TSB_bac_24_3	TSB	Bacterial cells	24
SA464639	TSB_bac_24_2	TSB	Bacterial cells	24
SA464640	TSB_GL_0_5	TSB	Supernatant	0
SA464641	TSB_GL_0_2	TSB	Supernatant	0
SA464642	TSB_GL_0_3	TSB	Supernatant	0
SA464643	TSB_GL_12_5	TSB	Supernatant	12
SA464644	TSB_GL_12_3	TSB	Supernatant	12
SA464645	TSB_GL_12_4	TSB	Supernatant	12
SA464646	TSB_GL_24_5	TSB	Supernatant	24
SA464647	TSB_GL_24_4	TSB	Supernatant	24
SA464648	TSB_GL_24_3	TSB	Supernatant	24
SA464649	TSB_GL_3_5	TSB	Supernatant	3
SA464650	TSB_GL_3_3	TSB	Supernatant	3
SA464651	TSB_GL_3_4	TSB	Supernatant	3
SA464652	TSB_GL_36_4	TSB	Supernatant	36
SA464653	TSB_GL_36_5	TSB	Supernatant	36
SA464654	TSB_GL_36_1	TSB	Supernatant	36
SA464655	TSB_GL_6_4	TSB	Supernatant	6
SA464656	TSB_GL_6_3	TSB	Supernatant	6
SA464657	TSB_GL_6_2	TSB	Supernatant	6
SA464658	TSB_GL_9_2	TSB	Supernatant	9
SA464659	TSB_GL_9_4	TSB	Supernatant	9
SA464660	TSB_GL_9_3	TSB	Supernatant	9

Showing results 1 to 69 of 69

Showing results 1 to 69 of 69

Collection:

Collection ID:	CO004167
Collection Summary:	Staphylococcus aureus has been cultured in tryptic soy broth (TSB) media or blood for various time points up to 36 hours. At designated time points, supernatant was collected for the measurement of glucose/lactate or amino acid consumption. For the measurement of bacillithiol production, bacterial cells were collected by centrifugation and prepared for mass spectrometric analysis.
Sample Type:	Plasma, Supernatant, Bacterial cells

Treatment:

Treatment ID:	TR004183
Treatment Summary:	Staphylococcus aureus has been grown in TSB and human whole blood. The samples were incubated at 37 ºC, with shaking at 150 rpm for various time points from 3 to 36 h. For determination of bacterial bacillithiol levels, USA300 was inoculated into whole blood or TSB at an OD600=0.02 with shaking at 150 rpm at 37 ºC. At 9, 12, and 24 h post-inoculation, samples were centrifuged at 4 ºC, 6,010 x g for 6 min for the collection of bacterial cells. Bacterial cells collected at a log phase (OD600=0.5) were defined as a 0 h sample. The resulting pellet was quenched by the addition of quenching buffer (40:40:20; Acetonitrile:Methanol:Water).

Treatment ID:

TR004183

Treatment Summary:

Staphylococcus aureus has been grown in TSB and human whole blood. The samples were incubated at 37 ºC, with shaking at 150 rpm for various time points from 3 to 36 h. For determination of bacterial bacillithiol levels, USA300 was inoculated into whole blood or TSB at an OD600=0.02 with shaking at 150 rpm at 37 ºC. At 9, 12, and 24 h post-inoculation, samples were centrifuged at 4 ºC, 6,010 x g for 6 min for the collection of bacterial cells. Bacterial cells collected at a log phase (OD600=0.5) were defined as a 0 h sample. The resulting pellet was quenched by the addition of quenching buffer (40:40:20; Acetonitrile:Methanol:Water).

Sample Preparation:

Sampleprep ID:	SP004180
Sampleprep Summary:	At the designated time points, whole blood or TSB samples were centrifuged for 2 min at 13,523 x g, 4 ºC. The supernatant was vortexed and mixed with cold methanol (v/v ratio 1:2). All samples mixed with methanol were centrifuged for 2 minutes at 4 ºC, 15,871 x g. Supernatant was added to Spin-X centrifuge tubes (Corning Inc., Corning, NY) and centrifuged at 4 ºC, 15,871 x g one more time. Bacterial cells were lysed by mechanical disruption using 0.1 mm glass beads and a precellys homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) with 12 cycles of 10,000 rpm, 30 sec cycle. Samples were placed on ice in-between each cycle for the prevention of protein degradation. Lysates were centrifuged at 4 ºC, 15,871 x g for 5 min, after which supernatant was added to Spin-X centrifuge tubes (Corning Inc.) and centrifuged at 4 ºC, 15,871 x g one more time.

Sampleprep ID:

SP004180

Sampleprep Summary:

At the designated time points, whole blood or TSB samples were centrifuged for 2 min at 13,523 x g, 4 ºC. The supernatant was vortexed and mixed with cold methanol (v/v ratio 1:2). All samples mixed with methanol were centrifuged for 2 minutes at 4 ºC, 15,871 x g. Supernatant was added to Spin-X centrifuge tubes (Corning Inc., Corning, NY) and centrifuged at 4 ºC, 15,871 x g one more time. Bacterial cells were lysed by mechanical disruption using 0.1 mm glass beads and a precellys homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) with 12 cycles of 10,000 rpm, 30 sec cycle. Samples were placed on ice in-between each cycle for the prevention of protein degradation. Lysates were centrifuged at 4 ºC, 15,871 x g for 5 min, after which supernatant was added to Spin-X centrifuge tubes (Corning Inc.) and centrifuged at 4 ºC, 15,871 x g one more time.

Chromatography:

Chromatography ID:	CH005057
Instrument Name:	Agilent 1290 Infinity II
Column Name:	Cogent Diamond Hydride (150 x 2.1mm, 4um, 100A)
Column Temperature:	25
Flow Gradient:	0–2 min, 85% B; 3–5 min, 80% B; 6–7 min, 75% B; 8–9 min, 70% B; 10–11.1 min, 50% B; 11.1–14 min 20% B; 14.1–24 min 5% B followed by a 10 min re-equilibration period at 85% B
Flow Rate:	0.4 mL/min
Solvent A:	100% water; 0.2% formic acid
Solvent B:	100% acetonitrile; 0.2% formic acid
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN006655
Analysis Type:	MS
Chromatography ID:	CH005057
Num Factors:	19
Num Metabolites:	18
Units:	abundance

Analysis ID:	AN006656
Analysis Type:	MS
Chromatography ID:	CH005057
Num Factors:	19
Num Metabolites:	2
Units:	abundance