Summary of Study ST002978

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 PR001854. The data can be accessed directly via it's Project DOI: 10.21228/M82M8R This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST002978
Study TitleMetabolite Profiling Of Vaginal Microbes In Suspension And Biofilm Cultures: Potential Target Against Bacterial Vaginosis
Study SummaryThis study facilitates better understanding of the differential metabolism and growth requirements of vaginal microbes in suspension and biofilm growth conditions. Comparison of metabolite profiles between Bacterial Vaginosis (BV) associated, protective and intermediate microbes for identifying target metabolite to manipulate growth and biofilm formation of Lactobacillus crispatus and Gardnerella vaginalis as a therapeutic approach against BV.
Institute
Purdue University
DepartmentBME
LaboratoryBrubaker Lab
Last NameJena
First NameSmrutiti
AddressS. martin Jischke drive
Emailsjena@purdue.edu
Phone5715659650
Submit Date2023-11-16
Num Groups10
Total Subjects3
Num MalesNA
Num FemalesNA
Analysis Type DetailOther
Release Date2025-11-15
Release Version1
Smrutiti Jena Smrutiti Jena
https://dx.doi.org/10.21228/M82M8R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001854
Project DOI:doi: 10.21228/M82M8R
Project Title:Metabolite Profiling Of Vaginal Microbes In Suspension And Biofilm Cultures: Potential Target Against Bacterial Vaginosis
Project Summary:This study facilitates better understanding of the differential metabolism and growth requirements of vaginal microbes in suspension and biofilm growth conditions. Comparison of metabolite profiles between Bacterial Vaginosis (BV) associated, protective and intermediate microbes for identifying target metabolite to manipulate growth and biofilm formation of Lactobacillus crispatus and Gardnerella vaginalis as a therapeutic approach against BV.
Institute:Purdue University
Department:BME
Laboratory:Brubaker Lab
Last Name:Jena
First Name:Smrutiti
Address:S. martin Jischke drive
Email:sjena@purdue.edu
Phone:5715659650

Subject:

Subject ID:SU003091
Subject Type:Bacteria
Subject Species:Lactobacillus crispatus; Gardnerella vaginalis; Lactobacillus iners
Taxonomy ID:47770; 2702; 147802
Genotype Strain:DSM 20584; ATCC55195; ATCC14018
Cell Biosource Or Supplier:ATCC
Cell Strain Details:Lactobacillus crispatus, Lactobacillus iners, Gardnerella vaginalis
Species Group:Bacteria

Factors:

Subject type: Bacteria; Subject species: Lactobacillus crispatus; Gardnerella vaginalis; Lactobacillus iners (Factor headings shown in green)

mb_sample_id local_sample_id Sample type
SA323339BL_BHI.1Blank media, BHI
SA323340BL_BHIBlank media, BHI
SA323341BL_BHI.2Blank media, BHI
SA323342BL_MRS.2Blank media, MRS
SA323343BL_MRSBlank media, MRS
SA323344BL_MRS.1Blank media, MRS
SA323345BL_NYCBlank media, NYC
SA323346BL_NYC.1Blank media, NYC
SA323347BL_NYC.2Blank media, NYC
SA323348Bl_sBHI.1Blank media, sBHI
SA323349Bl_sBHI.2Blank media, sBHI
SA323350Bl_sBHIBlank media, sBHI
SA323351G_vag_B1.2G. vaginalis biofilm #1
SA323352G_vag_B1.1G. vaginalis biofilm #1
SA323353G_vag_B1G. vaginalis biofilm #1
SA323354G_vag_B2.2G. vaginalis biofilm #2
SA323355G_vag_B2G. vaginalis biofilm #2
SA323356G_vag_B2.1G. vaginalis biofilm #2
SA323357G_vag_S.1G. vaginalis suspension
SA323358G_vag_SG. vaginalis suspension
SA323359G_vag_S.2G. vaginalis suspension
SA323360L_cris_B.1L. crispatus biofilm
SA323361L_cris_BL. crispatus biofilm
SA323362L_cris_B.2L. crispatus biofilm
SA323363L_cris_SL. crispatus suspension
SA323364L_cris_S.1L. crispatus suspension
SA323365L_cris_S.2L. crispatus suspension
SA323366L_iners_S.1L. iners suspension
SA323367L_iners_S.2L. iners suspension
SA323368L_iners_SL. iners suspension
Showing results 1 to 30 of 30

Collection:

Collection ID:CO003084
Collection Summary:L. crispatus cultures were grown in MRS media at 37oC, 5% CO2 for 24 and 48 hours to grow suspension and biofilm respectively. L. iners suspension cultures were grown in BHI at 37oC, 5% CO2 for 24hrs. G. vaginalis suspension and biofilm type I was grown in NYCIII at 37oC, 5% CO2 for 24 and 48 hours respectively. The type II biofilm of G. vaginalis was grown in supplemented BHI in the same incubation conditions as biofilm type I. All suspension cultures were grown on shakers and biofilms were grown as static cultures. The cultures were then centrifuged at 4000g for 8mins and filtered using 0.2micron syringe filter. The sample were then shipped with dry ice in triplicates to the metabolomics facility.
Collection Protocol Filename:Smrutiti_Vag Sample collection Protocol
Sample Type:Bacterial cells
Collection Method:Centrifugation
Collection Location:Purdue University
Volumeoramount Collected:5ml
Storage Conditions:-80?
Collection Vials:tubes
Storage Vials:Cryovials
Collection Tube Temp:4

Treatment:

Treatment ID:TR003100
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP003097
Sampleprep Summary:Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis.
Sampleprep Protocol Filename:Smrutiti_Vag Sample collection protocol, Smrutiti_Vag Metabolomics Protocol
Processing Storage Conditions:-80?

Chromatography:

Chromatography ID:CH003690
Chromatography Summary:Low pH polar (LC/MS Pos early)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 5% B to 80% B over 3.35 minutes
Flow Rate:0.35 mL/min
Solvent A:100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:100% methanol; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:Reversed phase
  
Chromatography ID:CH003691
Chromatography Summary:Low pH Lipophilic (LC/MS Pos late)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes.
Flow Rate:0.60 mL/min
Solvent A:100% water; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Solvent B:50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% PFPA, pH ~2.5
Chromatography Type:Reversed phase
  
Chromatography ID:CH003692
Chromatography Summary:High pH (LC/MS Neg)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99% B in 0.5 minutes.
Flow Rate:0.35 mL/min
Solvent A:100% water; 6.5 mM ammonium bicarbonate, pH 8
Solvent B:95% methanol/5% water; 6.5 mM ammonium bicarbonate
Chromatography Type:Reversed phase
  
Chromatography ID:CH003693
Chromatography Summary:HILIC (LC/MS Polar Neg)
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:40-50
Flow Gradient:Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes.
Flow Rate:0.50 mL/min
Solvent A:15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with NH4OH)
Solvent B:50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with NH4OH)
Chromatography Type:HILIC

Analysis:

Analysis ID:AN004891
Analysis Type:MS
Chromatography ID:CH003690
Num Factors:10
Num Metabolites:224
Units:pmol/l
  
Analysis ID:AN004892
Analysis Type:MS
Chromatography ID:CH003691
Num Factors:10
Num Metabolites:29
Units:pmol/l
  
Analysis ID:AN004893
Analysis Type:MS
Chromatography ID:CH003692
Num Factors:10
Num Metabolites:210
Units:pmol/l
  
Analysis ID:AN004894
Analysis Type:MS
Chromatography ID:CH003693
Num Factors:10
Num Metabolites:94
Units:pmol/l
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