Summary of study ST000879

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 PR000610. The data can be accessed directly via it's Project DOI: 10.21228/M8TH6S 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.

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Study IDST000879
Study TitleDiet, genetics and gut microbiome drive dynamic changes in plasma metabolites [plasma]
Study TypePlasma data
Study SummaryC57BL/6J mice (B6) and 129S1 mice (129J) were purchased from Jackson Laboratory (Bar Harbor, ME) and 129S6 mice (129T) were purchased from Taconic Farms (Germantown, NY). Mice were maintained on normal chow containing 22% calories from fat, 23% from protein and 55% from carbohydrates (Mouse Diet 9F 5020, PharmaServ, Framingham, MA) or a high fat diet (Open Source Diet, D12492, Research Diets, New Brunswick, NJ) containing 60% calories from fat, 20% from protein and 20% from carbohydrates. For antibiotic treatment, 6-week old mice were treated with either placebo, vancomycin (1g/L) or metronidazole (1g/L) (Sigma-Aldrich, St. Louis, MO) in drinking water then started on HFD from age 7 to 11 weeks. The mice were fasted for 2 hours and anesthetized with isoflurane before collecting cecum and plasma.
Institute
Broad Institute of MIT and Harvard
Last NameAvila-Pacheco
First NameJulian
Address415 Main Street
Emailjravilap@broadinstitute.org
Phone617-714-8264
Submit Date2017-10-02
Num Groups12
Total Subjects47
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2018-01-29
Release Version1
Julian Avila-Pacheco Julian Avila-Pacheco
https://dx.doi.org/10.21228/M8TH6S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000610
Project DOI:doi: 10.21228/M8TH6S
Project Title:Diet, genetics and gut microbiome drive dynamic changes in plasma metabolites
Project Type:Metabolite profiling of stool and cecal contents in mice of different genotypes, vendors, diets, and antibiotic treatments.
Project Summary:Diet, genetics and the gut microbiome are determinants of metabolic status, in part through production of metabolites by gut microbiota. To understand mechanisms linking these factors, we performed LC-MS-based metabolomic analysis of cecal contents and plasma from C57BL/6J, 129S1/SvImJ and 129S6/SvEvTac mice on chow, high-fat diet (HFD), and HFD-treated with vancomycin or metronidazole. Prediction of the functional metagenome of gut bacteria by PICRUSt analysis of 16S sequences revealed dramatic differences in microbial metabolism. Cecal and plasma metabolites showed multifold differences reflecting the combined and integrated effects of diet, antibiotics, host background, and the gut microbiome. Eighteen plasma metabolites correlated positively or negatively with host insulin resistance across strains and diets. Over 1,000 as-of-yet-unidentified metabolite peaks were also highly regulated by diet, antibiotics and genetic background. Thus diet, host genetics and gut microbiota interact to create unique responses in plasma metabolites, which can contribute to regulation of metabolism and insulin resistance. 
Institute:Broad Institute of MIT and Harvard
Department:Metabolomics Platform
Last Name:Avila-Pacheco
First Name:Julian
Address:415 Main Street, Rm 7175, Cambridge, MA, 02142, USA
Email:jravilap@broadinstitute.org
Phone:6177148264
Contributors:Shiho Fujisaka, Julian Avila-Pacheco, Marion Soto, Aleksandar Kostic, Jonathan M. Dreyfuss, Hui Pan, Siegfried Ussar, Emrah Altindis, Ning Li, Lynn Bry, Clary B. Clish, and C. Ronald Kahn

Subject:

Subject ID:SU000913
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammal

Factors:

Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Diet Treatment Strain
SA05104233_Chow_129JaxChow none 129Jax
SA05104336_Chow_129JaxChow none 129Jax
SA05104435_Chow_129JaxChow none 129Jax
SA05104534_Chow_129JaxChow none 129Jax
SA05104617_Chow_129TacChow none 129Tac
SA05104719_Chow_129TacChow none 129Tac
SA05104818_Chow_129TacChow none 129Tac
SA05104920_Chow_129TacChow none 129Tac
SA0510501_Chow_B6JaxChow none B6Jax
SA0510513_Chow_B6JaxChow none B6Jax
SA0510522_Chow_B6JaxChow none B6Jax
SA05105347_HFD Metronidazole_129JaxHFD metronidazole 129Jax
SA05105448_HFD Metronidazole_129JaxHFD metronidazole 129Jax
SA05105545_HFD Metronidazole_129JaxHFD metronidazole 129Jax
SA05105646_HFD Metronidazole_129JaxHFD metronidazole 129Jax
SA05105729_HFD Metronidazole_129TacHFD metronidazole 129Tac
SA05105831_HFD Metronidazole_129TacHFD metronidazole 129Tac
SA05105932_HFD Metronidazole_129TacHFD metronidazole 129Tac
SA05106030_HFD Metronidazole_129TacHFD metronidazole 129Tac
SA05106115_HFD Metronidazole_B6JaxHFD metronidazole B6Jax
SA05106216_HFD Metronidazole_B6JaxHFD metronidazole B6Jax
SA05106313_HFD Metronidazole_B6JaxHFD metronidazole B6Jax
SA05106414_HFD Metronidazole_B6JaxHFD metronidazole B6Jax
SA05106540_HFD Placebo_129JaxHFD placebo 129Jax
SA05106639_HFD Placebo_129JaxHFD placebo 129Jax
SA05106737_HFD Placebo_129JaxHFD placebo 129Jax
SA05106838_HFD Placebo_129JaxHFD placebo 129Jax
SA05106921_HFD Placebo_129TacHFD placebo 129Tac
SA05107022_HFD Placebo_129TacHFD placebo 129Tac
SA05107124_HFD Placebo_129TacHFD placebo 129Tac
SA05107223_HFD Placebo_129TacHFD placebo 129Tac
SA0510737_HFD Placebo_B6JaxHFD placebo B6Jax
SA0510748_HFD Placebo_B6JaxHFD placebo B6Jax
SA0510755_HFD Placebo_B6JaxHFD placebo B6Jax
SA0510766_HFD Placebo_B6JaxHFD placebo B6Jax
SA05107741_HFD Vancomycin_129JaxHFD vancomycin 129Jax
SA05107842_HFD Vancomycin_129JaxHFD vancomycin 129Jax
SA05107944_HFD Vancomycin_129JaxHFD vancomycin 129Jax
SA05108043_HFD Vancomycin_129JaxHFD vancomycin 129Jax
SA05108125_HFD Vancomycin_129TacHFD vancomycin 129Tac
SA05108228_HFD Vancomycin_129TacHFD vancomycin 129Tac
SA05108326_HFD Vancomycin_129TacHFD vancomycin 129Tac
SA05108427_HFD Vancomycin_129TacHFD vancomycin 129Tac
SA0510859_HFD Vancomycin_B6JaxHFD vancomycin B6Jax
SA05108610_HFD Vancomycin_B6JaxHFD vancomycin B6Jax
SA05108712_HFD Vancomycin_B6JaxHFD vancomycin B6Jax
SA05108811_HFD Vancomycin_B6JaxHFD vancomycin B6Jax
Showing results 1 to 47 of 47

Collection:

Collection ID:CO000907
Collection Summary:The mice were fasted for 2 hours and anesthetized with isoflurane before collecting cecum and plasma.
Blood Serum Or Plasma:Plasma

Treatment:

Treatment ID:TR000927
Treatment Summary:Mice were maintained on normal chow containing 22% calories from fat, 23% from protein and 55% from carbohydrates (Mouse Diet 9F 5020, PharmaServ, Framingham, MA) or a high fat diet (Open Source Diet, D12492, Research Diets, New Brunswick, NJ) containing 60% calories from fat, 20% from protein and 20% from carbohydrates. For antibiotic treatment, 6-week old mice were treated with either placebo, vancomycin (1g/L) or metronidazole (1g/L) (Sigma-Aldrich, St. Louis, MO) in drinking water then started on HFD from age 7 to 11 weeks.

Sample Preparation:

Sampleprep ID:SP000920
Sampleprep Summary:HILIC-pos: LC-MS samples were prepared from plasma (10 μL) via protein precipitation with the addition of nine volumes of 74.9:24.9:0.2 v/v/v acetonitrile/methanol/formic acid containing stable isotope-labeled internal standards (valine-d8, Isotec; and phenylalanine-d8, Cambridge Isotope Laboratories; Andover, MA). The samples are centrifuged (10 min, 9,000 x g, 4°C), and the supernatants were injected directly. HILIC-neg:Plasma samples (30μL) were extracted using 120 μL of 80% methanol (VWR) containing 0.05 ng/μL inosine-15N4, 0.05 ng/μL thymine-d4, and 0.1 ng/μL glycocholate-d4 as internal standards (Cambridge Isotope Laboratories). The samples were centrifuged (10 min, 9,000 x g, 4ºC) and the supernatants (10 μL) were injected directly. C18-neg: Plasma samples (20 μL) were extracted using 60 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) and centrifuged (10 min, 9,000 x g, 4°C). C8-pos: Lipids were extracted from plasma (10 μL) using 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL). After centrifugation (10 min, 9,000 x g, ambient temperature), supernatants (10 μL) were injected directly

Combined analysis:

Analysis ID AN001429 AN001430 AN001431 AN001432
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Shimadzu Nexera X2 Waters Acquity Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters Atlantis HILIC (150 x 2 mm) Phenomenex Luna NH2 (150 x 2.0mm) Waters Acquity BEH C18 (150 x 2.1mm, 1.7um) Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Triple quadrupole Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap ABI Sciex 5500 QTrap Thermo Q Exactive Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE NEGATIVE POSITIVE
Units Peak area Peak area Peak area peak area

Chromatography:

Chromatography ID:CH001000
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Atlantis HILIC (150 x 2 mm)
Solvent A:10 mM ammonium formate and 0.1% formic acid in water
Solvent B:acetonitrile with 0.1% formic acid
Chromatography Type:HILIC
  
Chromatography ID:CH001001
Instrument Name:Waters Acquity
Column Name:Phenomenex Luna NH2 (150 x 2.0mm)
Solvent A:20 mM ammonium acetate and 20 mM ammonium hydroxide (Sigma-Aldrich) in water (VWR)
Solvent B:10 mM ammonium hydroxide in 75:25 v/v acetonitrile/methanol (VWR)
Chromatography Type:HILIC
  
Chromatography ID:CH001002
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C18 (150 x 2.1mm, 1.7um)
Solvent A:0.1% formic acid in water
Solvent B:acetonitrile with 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001003
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Solvent A:95:5:0.1 vol/vol/vol 10 mM ammonium acetate/methanol/acetic acid
Solvent B:99.9:0.1 vol/vol methanol/acetic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS001319
Analysis ID:AN001429
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001320
Analysis ID:AN001430
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001321
Analysis ID:AN001431
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001322
Analysis ID:AN001432
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
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