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.
| Study ID | ST001263 |
| Study Title | Metabolomic Profiling of Oxalate-Degrading Probiotic Lactobacillus acidophilus and Lactobacillus gasseri |
| Study Type | Metabolomic/Lipidomic Profiling |
| Study Summary | Metabolomic 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 |
| 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 |
| chamberlainc@ufl.edu | |
| Phone | 3522735720 |
| Submit Date | 2019-08-30 |
| Num Groups | 2 |
| Total Subjects | 16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-10-11 |
| Release Version | 1 |
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) |
| Species Group: | Bacteria |
Factors:
Subject type: Bacteria; Subject species: Lactobacillus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA091956 | L. gasseri_4 | data1 |
| SA091957 | L. gasseri_3 | data1 |
| SA091958 | L. gasseri_5 | data1 |
| SA091959 | L. gasseri_7 | data1 |
| SA091960 | L. gasseri_8 | data1 |
| SA091961 | L. gasseri_2 | data1 |
| SA091962 | L. gasseri_6 | data1 |
| SA091963 | L. gasseri_1 | data1 |
| SA091964 | L. acidophilus_4 | data1 |
| SA091965 | L. acidophilus_3 | data1 |
| SA091966 | L. acidophilus_2 | data1 |
| SA091967 | L. acidophilus_5 | data1 |
| SA091968 | L. acidophilus_6 | data1 |
| SA091969 | L. acidophilus_8 | data1 |
| SA091970 | L. acidophilus_7 | data1 |
| SA091971 | L. acidophilus_1 | data1 |
| 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 |
