Summary of study ST000880

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 IDST000880
Study TitleDiet, genetics and gut microbiome drive dynamic changes in plasma metabolites [cecal]
Study TypeCecal 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 Date2017-10-03
Num Groups12
Total Subjects47
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:SU000914
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
SA05108933_Chow_129JaxChow none 129Jax
SA05109036_Chow_129JaxChow none 129Jax
SA05109135_Chow_129JaxChow none 129Jax
SA05109234_Chow_129JaxChow none 129Jax
SA05109317_Chow_129TacChow none 129Tac
SA05109419_Chow_129TacChow none 129Tac
SA05109518_Chow_129TacChow none 129Tac
SA05109620_Chow_129TacChow none 129Tac
SA0510971_Chow_B6JaxChow none B6Jax
SA0510983_Chow_B6JaxChow none B6Jax
SA0510992_Chow_B6JaxChow none B6Jax
SA05110047_HFD Metronidazole_129JaxHFD metronidazole 129Jax
SA05110148_HFD Metronidazole_129JaxHFD metronidazole 129Jax
SA05110245_HFD Metronidazole_129JaxHFD metronidazole 129Jax
SA05110346_HFD Metronidazole_129JaxHFD metronidazole 129Jax
SA05110429_HFD Metronidazole_129TacHFD metronidazole 129Tac
SA05110531_HFD Metronidazole_129TacHFD metronidazole 129Tac
SA05110632_HFD Metronidazole_129TacHFD metronidazole 129Tac
SA05110730_HFD Metronidazole_129TacHFD metronidazole 129Tac
SA05110815_HFD Metronidazole_B6JaxHFD metronidazole B6Jax
SA05110916_HFD Metronidazole_B6JaxHFD metronidazole B6Jax
SA05111013_HFD Metronidazole_B6JaxHFD metronidazole B6Jax
SA05111114_HFD Metronidazole_B6JaxHFD metronidazole B6Jax
SA05111240_HFD Placebo_129JaxHFD placebo 129Jax
SA05111339_HFD Placebo_129JaxHFD placebo 129Jax
SA05111437_HFD Placebo_129JaxHFD placebo 129Jax
SA05111538_HFD Placebo_129JaxHFD placebo 129Jax
SA05111621_HFD Placebo_129TacHFD placebo 129Tac
SA05111722_HFD Placebo_129TacHFD placebo 129Tac
SA05111824_HFD Placebo_129TacHFD placebo 129Tac
SA05111923_HFD Placebo_129TacHFD placebo 129Tac
SA0511207_HFD Placebo_B6JaxHFD placebo B6Jax
SA0511218_HFD Placebo_B6JaxHFD placebo B6Jax
SA0511225_HFD Placebo_B6JaxHFD placebo B6Jax
SA0511236_HFD Placebo_B6JaxHFD placebo B6Jax
SA05112441_HFD Vancomycin_129JaxHFD vancomycin 129Jax
SA05112542_HFD Vancomycin_129JaxHFD vancomycin 129Jax
SA05112644_HFD Vancomycin_129JaxHFD vancomycin 129Jax
SA05112743_HFD Vancomycin_129JaxHFD vancomycin 129Jax
SA05112825_HFD Vancomycin_129TacHFD vancomycin 129Tac
SA05112928_HFD Vancomycin_129TacHFD vancomycin 129Tac
SA05113026_HFD Vancomycin_129TacHFD vancomycin 129Tac
SA05113127_HFD Vancomycin_129TacHFD vancomycin 129Tac
SA0511329_HFD Vancomycin_B6JaxHFD vancomycin B6Jax
SA05113310_HFD Vancomycin_B6JaxHFD vancomycin B6Jax
SA05113412_HFD Vancomycin_B6JaxHFD vancomycin B6Jax
SA05113511_HFD Vancomycin_B6JaxHFD vancomycin B6Jax
Showing results 1 to 47 of 47

Collection:

Collection ID:CO000908
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:TR000928
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:SP000921
Sampleprep Summary:Cecal contents were homogenized in 10 volumes (weight:volume) of H2O using a bead beater HILIC-posLC-MS samples were prepared from cecal homogenates (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 onto column. HILIC-neg:Cecal homogenates (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 onto column.. C18-neg: Cecal homogenates (30 μL) were extracted using 90 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). The supernatants (10 μL) were injected onto column.. C8-pos: Lipids were extracted from cecal homogenates (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 onto column.

Combined analysis:

Analysis ID AN001433 AN001434 AN001435 AN001436
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:CH001004
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:CH001005
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:CH001006
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:CH001007
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:MS001323
Analysis ID:AN001433
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS001324
Analysis ID:AN001434
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001325
Analysis ID:AN001435
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001326
Analysis ID:AN001436
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
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