Summary of Study ST001436
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 PR000987. The data can be accessed directly via it's Project DOI: 10.21228/M8410G 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 | ST001436 |
| Study Title | Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet induced diabetes |
| Study Type | Supplementation of mice with probiotic bacteria |
| Study Summary | For WD + Microbes 1 and WD + Microbes 3 experiments, C57BL/6 mice were fed western diet or western diet supplemented with Lactobacillus gasseri or Lactobacillus johnsonii for 8 weeks and serum was collected from each mice. For Pooled_1 (control group, western diet only), and Pooled_2 (western diet + Lactobacillus gasseri) groups, serum from 5 mice each was pooled. For Pooled_3 (western diet + Lactobacillus johnsonii) group, serum from 4 mice was pooled. For Pooled_7 (control group, western diet only), Pooled_8 (western diet + Lactobacillus gasseri) and Pooled_9 (western diet + Lactobacillus johnsonii) groups, serum from 6 mice each was pooled. For WD + Microbes 6 experiment, C57BL/6 mice were fed western diet for 8 weeks. Then, one group (n = 5) of mice was supplemented with Lactobacillus gasseri for 12 weeks along with continuation of western diet and serum was collected. For Pooled_10 (control group, western diet only) and Pooled_11 (western diet + Lactobacillus gasseri) groups, serum from 5 mice each was pooled. For GF + WD + LG experiment, C57BL/6 germ free mice were fed western diet or western diet supplemented with Lactobacillus gasseri for 2 weeks. For Pooled_12 (control, western diet only) and Pooled_13 (western diet + Lactobacillus gasseri) groups, serum from 2 mice each was pooled. |
| Institute | Oregon State University |
| Department | Pharmaceutical Sciences |
| Laboratory | Morgun and Shulzhenko |
| Last Name | Morgun |
| First Name | Andriy |
| Address | 203 Pharmacy Bldg |
| andriy.morgun@oregonstate.edu | |
| Phone | 1 541 737 8047 |
| Submit Date | 2020-07-28 |
| Num Groups | 7 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-09-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000987 |
| Project DOI: | doi: 10.21228/M8410G |
| Project Title: | Gut microbiota mediates the interplay between immunity and glucose metabolism |
| Project Type: | preclinical studies |
| Project Summary: | Diabetes, obesity and metabolic disease have reached epidemic proportions. Much research on these diseases has focused on tissues such as adipose, liver, muscle and pancreas. The role of the gut in glucose metabolism is relatively unstudied; however, it can also have a significant effect on systemic glucose control. Residing in the gut is a complex community of microbes, termed microbiota, which are important contributors to immunity and metabolism, frequently mediating cross-talks between these two functions. Changes in the gut microbiota of type 2 diabetes (T2D) patients are directly linked to metabolic dysregulation in the disease. Therefore, the goal of the project is to identify and test microbes and microbial factors involved in regulation of glucose metabolism. For this, microbiota perturbation by western diet followed by global analyses of gut microbiome and host transcriptome combined with causal inference analysis is employed. Newly inferred probiotics are tested in mice fed with western diet followed by metabolomics analysis. This research provides a mechanistic explanation of how probiotics helps disclose mechanisms of T2D as well as will identify protective microbial factors for development of therapy of diabetes. |
| Institute: | Oregon State University |
| Department: | Pharmaceutical Sciences |
| Laboratory: | Morgun and Shulzhenko |
| Last Name: | Andriy |
| First Name: | Morgun |
| Address: | 203 Pharmacy Bldg, Corvallis, OR 97331 |
| Email: | andriy.morgun@oregonstate.edu |
| Phone: | 1 541 737 8047 |
| Funding Source: | NIH R01 DK103761 |
Subject:
| Subject ID: | SU001510 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57Bl/6 |
| Age Or Age Range: | 10-20 weeks |
| Gender: | Male |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA122008 | Sample_01 | Western diet |
| SA122009 | Sample_12 | Western diet |
| SA122010 | Sample_07 | Western diet |
| SA122011 | Sample_10 | Western diet |
| SA122012 | Sample_11 | Western diet + Lactobacillus gasseri |
| SA122013 | Sample_08 | Western diet + Lactobacillus gasseri |
| SA122014 | Sample_02 | Western diet + Lactobacillus gasseri |
| SA122015 | Sample_13 | Western diet + Lactobacillus gasseri |
| SA122016 | Sample_09 | Western diet + Lactobacillus johnsonii |
| SA122017 | Sample_03 | Western diet + Lactobacillus johnsonii |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO001505 |
| Collection Summary: | After the end of the experiment, whole blood was collected in BD Microtainer Serum Separator Tube and allowed to clot by leaving undistubred at room temperature for 30 minutes. Then the tubes were centrifuged at 2000 x g for 10 minutes in 4°C and the supernatant was immediately transferred into a polypropylene tube and stored at -80°C until further analysis. |
| Sample Type: | Blood (serum) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001525 |
| Treatment Summary: | Western diet fed mice were supplemented with Lactobacillus gasseri or Lactobacillus johnsonii. For control groups, equal volume of vehicle (PBS) was gavaged. Supplementation was done for 2 to 8 weeks. |
Sample Preparation:
| Sampleprep ID: | SP001518 |
| Sampleprep Summary: | Metabolites were extracted with 4 volumes of cold methanol/acetonitrile (1:1, v/v). To precipitate proteins, the samples were incubated for 1h at -20°C. After the samples were centrifuged at 4°C for 15 min at 13,000 rpm, the supernatant was collected and evaporated to dryness in a vacuum concentrator. The dry extracts were then reconstituted in 90 μL of acetonitrile/H2O (1:1, v/v) containing 10 ng/mL CUDA (12-[[(cyclohexylamino)carbonyl] amino]-dodecanoic acid). |
Combined analysis:
| Analysis ID | AN002399 | AN002400 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 1290 Infinity | Agilent 1290 Infinity |
| Column | Poroshell EC-C18 (100 x 3.0 mm,2.7um) | Poroshell EC-C18 (100 x 3.0 mm,2.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6545 QToF | Agilent 6545 QToF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | AUC | AUC |
Chromatography:
| Chromatography ID: | CH001763 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Poroshell EC-C18 (100 x 3.0 mm,2.7um) |
| Column Temperature: | 40 |
| Flow Rate: | 0.4 ml/min |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002240 |
| Analysis ID: | AN002399 |
| Instrument Name: | Agilent 6545 QToF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | None |
| Ion Mode: | POSITIVE |
| MS ID: | MS002241 |
| Analysis ID: | AN002400 |
| Instrument Name: | Agilent 6545 QToF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | None |
| Ion Mode: | NEGATIVE |
