Summary of Study ST001263

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 PR000848. The data can be accessed directly via it's Project DOI: 10.21228/M82T2J 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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001263
Study TitleMetabolomic Profiling of Oxalate-Degrading Probiotic Lactobacillus acidophilus and Lactobacillus gasseri
Study TypeMetabolomic/Lipidomic Profiling
Study SummaryMetabolomic and lipidomic profiling of Lactobacillus acidophilus and Lactobacillus gasseri to identify unique differences in their biochemistry that could potentially influence their ability to serve as probiotic agents for oxalate diseases.
Institute
University of Florida
DepartmentPathology, Immunology and Laboratory Medicine
LaboratoryTimothy J. Garrett, PhD
Last NameChamberlain
First NameCasey
AddressUF Dept of Pathology PO Box 100275 Gainesville, FL 32610
Emailchamberlainc@ufl.edu
Phone3522735720
Submit Date2019-08-30
Num Groups2
Total Subjects16
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2019-10-11
Release Version1
Casey Chamberlain Casey Chamberlain
https://dx.doi.org/10.21228/M82T2J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000848
Project DOI:doi: 10.21228/M82T2J
Project Title:Metabolomic Profiling of Oxalate-Degrading Probiotic Lactobacillus acidophilus and Lactobacillus gasseri
Project Type:Metabolomic/Lipidomic Profiling
Project Summary:Metabolomic and lipidomic profiling of Lactobacillus acidophilus and Lactobacillus gasseri
Institute:University of Florida
Department:Pathology, Immunology and Laboratory Medicine
Laboratory:Timothy J. Garrett, PhD
Last Name:Chamberlain
First Name:Casey
Address:UF Dept of Pathology PO Box 100275 Gainesville, FL 32610
Email:chamberlainc@ufl.edu
Phone:3522735720
Funding Source:NIH

Subject:

Subject ID:SU001331
Subject Type:Bacteria
Subject Species:Lactobacillus
Taxonomy ID:1578
Gender:Not applicable
Cell Biosource Or Supplier:American Type Culture Collection (ATCC)
Cell Strain Details:L. acidophilus (ATCC 4357), L. gasseri (ATCC 33323)

Factors:

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

mb_sample_id local_sample_id Factor
SA091956L. gasseri_4data1
SA091957L. gasseri_3data1
SA091958L. gasseri_5data1
SA091959L. gasseri_7data1
SA091960L. gasseri_8data1
SA091961L. gasseri_2data1
SA091962L. gasseri_6data1
SA091963L. gasseri_1data1
SA091964L. acidophilus_4data1
SA091965L. acidophilus_3data1
SA091966L. acidophilus_2data1
SA091967L. acidophilus_5data1
SA091968L. acidophilus_6data1
SA091969L. acidophilus_8data1
SA091970L. acidophilus_7data1
SA091971L. acidophilus_1data1
Showing results 1 to 16 of 16

Collection:

Collection ID:CO001325
Collection Summary:Cultured in MRS media from frozen glycerol stocks for 24 hours. Harvested, washed, and resuspended in PBS-based buffer solution. Individual cultures treated as biological replicates.
Sample Type:Bacterial cells
Storage Conditions:-80℃
Collection Tube Temp:-80C

Treatment:

Treatment ID:TR001346
Treatment Summary:No treatment. Simply a metabolomic comparison between species.

Sample Preparation:

Sampleprep ID:SP001339
Sampleprep Summary:Normalized to 75 mg/mL in PBS-based buffer solution. Metabolites extracted by protein precipitation using 8:1:1 acetonitrile:methanol:acetone. Lipids extracted using the Folch method with 4:2:1 chloroform:methanol:water.

Combined analysis:

Analysis ID AN002096 AN002097 AN002098 AN002099
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Intensity Intensity Intensity Intensity

Chromatography:

Chromatography ID:CH001531
Chromatography Summary:Gradient elution was performed with 0.1% formic acid in water as solvent A and acetonitrile as solvent B, at a flow rate of 0.35 mL/min, as such: 0 - 3 min: 100% A, 3 - 13 min: 100% → 20% A, 13 - 16.5 min: 20% A, 16.5 - 20 min: 100% A at 0.6 mL/min (column flush & equilibration).
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Column Temperature:25
Flow Rate:0.35 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase
  
Chromatography ID:CH001532
Chromatography Summary:Gradient elution was performed with 60:40 acetonitrile:water with 0.1% formic acid and 10mM ammonium formate as solvent A and 90:8:2 isopropanol:acetonitrile:water with 0.1% formic acid and 10mM ammonium formate as solvent B, at a flow rate of 0.5 mL/min, as such: 0 - 1 min: 80% A, 1 - 3 min: 80% → 70% A, 3 - 4 min: 70% → 55% A, 4 - 6 min: 55% → 40% A, 6 - 8 min: 40% → 35% A, 8 - 10 min: 35% A, 10 -15 min: 35% → 10% A, 15 - 17 min: 10% → 2% A, 17 - 18 min: 2% A, 18 - 19 min: 2% → 80% A, 19 - 23 min: 80% A (column flush & equilibration)
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:50
Flow Rate:0.5 mL/min
Solvent A:40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Solvent B:90% isopropanol/8% acetonitrile/2% water; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:HILIC

MS:

MS ID:MS001947
Analysis ID:AN002096
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See manuscript
Ion Mode:POSITIVE
  
MS ID:MS001948
Analysis ID:AN002097
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See manuscript
Ion Mode:NEGATIVE
  
MS ID:MS001949
Analysis ID:AN002098
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See manuscript
Ion Mode:POSITIVE
  
MS ID:MS001950
Analysis ID:AN002099
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See manuscript
Ion Mode:NEGATIVE
  logo