Summary of Study ST000351

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 PR000280. The data can be accessed directly via it's Project DOI: 10.21228/M8QK55 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000351
Study TitleDetermining the metabolic profile of wildtype, lrgAB, and atlA mutant Steptococcus mutans grown aerobically and anaerobically
Study TypeSingle time point, aerobic vs. anaerobic cultures
Study SummaryWhole cells from both aerobic and anaerobic cultures of wild-type,lrgAB and atlA strain will be isolated for analysis of the whole cytosolic metabolome. Supernatants will be also analyzed for their metabolite profile in wild type and lrgAB cultures.
Institute
University of Florida
DepartmentSECIM
Last NameAhn
First NameSang-Joon
Address1395 Center Drive, Room D5-29 Gainesville FL 32610
Emailsahn@dental.ufl.edu
Phone352-273-8834
Submit Date2015-11-16
Num Groups3
Total Subjects36
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2019-01-22
Release Version1
Sang-Joon Ahn Sang-Joon Ahn
https://dx.doi.org/10.21228/M8QK55
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000280
Project DOI:doi: 10.21228/M8QK55
Project Title:Application of a targeted metabolomic profiling for the delineation of mechanisms of autolytic systems in Streptococcus mutans cells under oxidative stresses
Project Summary:Streptococcus mutans is capable of withstanding a variety of stressors encountered in the oral cavity. The ability to efficiently and rapidly adjust to the changing environment is essential for its pathogenic lifestyle. Oxidative stress is one of the most important environmental variables affecting the pathogenic potential of S. mutans, as high oxygen concentrations disfavor growth of S. mutans and other oral bacteria. In order to fulfill its role as a major constituent of cariogenic oral biofilms and sustain virulence, S. mutans must overcome oxidative stress. Oxidation sensing and response is a complex yet highly-regulated process, particularly because it is cross-regulated with other metabolic pathways, stress responses and virulence physiology. In addition, we previously showed that exposure of S. mutans to oxygen strongly inhibits biofilm formation and alters cell surface biogenesis, possibly through AtlA, a major autolysin of the organism. More recently, we have also shown that S. mutans Cid/Lrg system, potentially mediating cell lysis/death in a programmed fashion, uniquely leads a global readjustment in central metabolism and virulence processes, particularly in coping with oxidative stress. To this end, a targeted metabolomics approach will be employed to understand how these autolytic systems influence the metabolism of S. mutans, ultimately leading to a more complete appreciation of how S. mutans survives and persists in hostile host microenvironment.
Institute:University of Florida
Department:College of Dentistry
Last Name:Ahn
First Name:Sang-Joon
Address:1395 Center Drive, Room D5-29 Gainesville FL 32610
Email:sahn@dental.ufl.edu
Phone:352-273-8834
Funding Source:NIH R03

Subject:

Subject ID:SU000371
Subject Type:Bacterial cells
Subject Species:Streptococcus mutans
Taxonomy ID:1309
Species Group:Microorganism

Factors:

Subject type: Bacterial cells; Subject species: Streptococcus mutans (Factor headings shown in green)

mb_sample_id local_sample_id Strain Sample type Growth condition
SA01540116atlA mutant Whole cells aerobically
SA01540226atlA mutant Whole cells aerobically
SA0154036atlA mutant Whole cells aerobically
SA01540423atlA mutant Whole cells anaerobically
SA01540513atlA mutant Whole cells anaerobically
SA0154063atlA mutant Whole cells anaerobically
SA01540710lrgAB mutant Supernatant aerobically
SA01540830lrgAB mutant Supernatant aerobically
SA01540920lrgAB mutant Supernatant aerobically
SA01541028lrgAB mutant Supernatant anaerobically
SA01541118lrgAB mutant Supernatant anaerobically
SA0154128lrgAB mutant Supernatant anaerobically
SA0154135lrgAB mutant Whole cells aerobically
SA01541425lrgAB mutant Whole cells aerobically
SA01541515lrgAB mutant Whole cells aerobically
SA0154162lrgAB mutant Whole cells anaerobically
SA01541722lrgAB mutant Whole cells anaerobically
SA01541812lrgAB mutant Whole cells anaerobically
SA015386C1-1N/A Media only N/A
SA015387C1-2N/A Media only N/A
SA015388C1-3N/A Media only N/A
SA01538919UA159 wild type Supernatant aerobically
SA01539029UA159 wild type Supernatant aerobically
SA0153919UA159 wild type Supernatant aerobically
SA01539227UA159 wild type Supernatant anaerobically
SA01539317UA159 wild type Supernatant anaerobically
SA0153947UA159 wild type Supernatant anaerobically
SA01539524UA159 wild type Whole cells aerobically
SA0153964UA159 wild type Whole cells aerobically
SA01539714UA159 wild type Whole cells aerobically
SA0153981UA159 wild type Whole cells anaerobically
SA01539921UA159 wild type Whole cells anaerobically
SA01540011UA159 wild type Whole cells anaerobically
Showing results 1 to 33 of 33

Collection:

Collection ID:CO000365
Collection Summary:Bacterial cells were harvested at mid-exponential phase of growth by centrifugation. The cell pellets were washed with PBS buffer and then flash frozen in liquid nitrogen. The culture supernatants were filtered and then flash frozen in liquid nitrogen
Sample Type:Bacterial cells

Treatment:

Treatment ID:TR000385
Treatment Summary:Bacterial cells were grown under aerobic and anaerobic conditions.

Sample Preparation:

Sampleprep ID:SP000378
Sampleprep Summary:see attached protocols

Combined analysis:

Analysis ID AN000567 AN000568 AN000569 AN000570 AN000571
Analysis type MS MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity Thermo Dionex Ultimate 3000 Agilent 1290 Infinity Agilent 1290 Infinity
Column Waters AccQ Tag (100 x 2mm,1.7um) Waters Acquity BEH C18 (100 x 2.1mm,1.7um) Waters Acquity BEH C18 (100 x 2mm,1.7um) Thermo Hypercarb (50 x 2.1mm,3um) Waters Acquity BEH C18 (50 x 2mm,1.7um)
MS Type ESI ESI ESI ESI ESI
MS instrument type Triple quadrupole Triple quadrupole Triple quadrupole Triple quadrupole Triple quadrupole
MS instrument name Agilent 6490 QQQ Agilent 6490 QQQ Thermo Quantiva QQQ Agilent 6490 QQQ Agilent 6490 QQQ
Ion Mode POSITIVE POSITIVE POSITIVE POSITIVE POSITIVE
Units nmol/mg nmol/mg nmol/mg nmol/mg nmol/mg

Chromatography:

Chromatography ID:CH000404
Chromatography Summary:Amino Acid method
Methods Filename:SB_AA_Assay.pdf
Instrument Name:Agilent 1290 Infinity
Column Name:Waters AccQ Tag (100 x 2mm,1.7um)
Column Temperature:55
Flow Rate:0.7 mL/min
Solvent A:AccQ·Tag Eluent A
Solvent B:accQ·Tag Eluent B
Chromatography Type:Reversed phase
  
Chromatography ID:CH000405
Chromatography Summary:Acylcarnitine method
Methods Filename:SB_Acylcarnitine_Assay.pdf
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH C18 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH000406
Chromatography Summary:Organic acid method
Methods Filename:SB_OA_Assay.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:45
Flow Rate:0.3 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH000407
Chromatography Summary:NAD-ATP method
Methods Filename:SB_NAD-ATP_Assay_Agilent.pdf
Instrument Name:Agilent 1290 Infinity
Column Name:Thermo Hypercarb (50 x 2.1mm,3um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH000408
Chromatography Summary:CoA method
Methods Filename:SB_CoA_Assay.pdf
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH C18 (50 x 2mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS000503
Analysis ID:AN000567
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000504
Analysis ID:AN000568
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000505
Analysis ID:AN000569
Instrument Name:Thermo Quantiva QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000506
Analysis ID:AN000570
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000507
Analysis ID:AN000571
Instrument Name:Agilent 6490 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:POSITIVE
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