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.
Study ID | ST000879 |
Study Title | Diet, genetics and gut microbiome drive dynamic changes in plasma metabolites [plasma] |
Study Type | Plasma data |
Study Summary | C57BL/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 Name | Avila-Pacheco |
First Name | Julian |
Address | 415 Main Street |
jravilap@broadinstitute.org | |
Phone | 617-714-8264 |
Submit Date | 2017-10-02 |
Num Groups | 12 |
Total Subjects | 47 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2018-01-29 |
Release Version | 1 |
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 |
---|---|---|---|---|
SA051042 | 33_Chow_129Jax | Chow | none | 129Jax |
SA051043 | 36_Chow_129Jax | Chow | none | 129Jax |
SA051044 | 35_Chow_129Jax | Chow | none | 129Jax |
SA051045 | 34_Chow_129Jax | Chow | none | 129Jax |
SA051046 | 17_Chow_129Tac | Chow | none | 129Tac |
SA051047 | 19_Chow_129Tac | Chow | none | 129Tac |
SA051048 | 18_Chow_129Tac | Chow | none | 129Tac |
SA051049 | 20_Chow_129Tac | Chow | none | 129Tac |
SA051050 | 1_Chow_B6Jax | Chow | none | B6Jax |
SA051051 | 3_Chow_B6Jax | Chow | none | B6Jax |
SA051052 | 2_Chow_B6Jax | Chow | none | B6Jax |
SA051053 | 47_HFD Metronidazole_129Jax | HFD | metronidazole | 129Jax |
SA051054 | 48_HFD Metronidazole_129Jax | HFD | metronidazole | 129Jax |
SA051055 | 45_HFD Metronidazole_129Jax | HFD | metronidazole | 129Jax |
SA051056 | 46_HFD Metronidazole_129Jax | HFD | metronidazole | 129Jax |
SA051057 | 29_HFD Metronidazole_129Tac | HFD | metronidazole | 129Tac |
SA051058 | 31_HFD Metronidazole_129Tac | HFD | metronidazole | 129Tac |
SA051059 | 32_HFD Metronidazole_129Tac | HFD | metronidazole | 129Tac |
SA051060 | 30_HFD Metronidazole_129Tac | HFD | metronidazole | 129Tac |
SA051061 | 15_HFD Metronidazole_B6Jax | HFD | metronidazole | B6Jax |
SA051062 | 16_HFD Metronidazole_B6Jax | HFD | metronidazole | B6Jax |
SA051063 | 13_HFD Metronidazole_B6Jax | HFD | metronidazole | B6Jax |
SA051064 | 14_HFD Metronidazole_B6Jax | HFD | metronidazole | B6Jax |
SA051065 | 40_HFD Placebo_129Jax | HFD | placebo | 129Jax |
SA051066 | 39_HFD Placebo_129Jax | HFD | placebo | 129Jax |
SA051067 | 37_HFD Placebo_129Jax | HFD | placebo | 129Jax |
SA051068 | 38_HFD Placebo_129Jax | HFD | placebo | 129Jax |
SA051069 | 21_HFD Placebo_129Tac | HFD | placebo | 129Tac |
SA051070 | 22_HFD Placebo_129Tac | HFD | placebo | 129Tac |
SA051071 | 24_HFD Placebo_129Tac | HFD | placebo | 129Tac |
SA051072 | 23_HFD Placebo_129Tac | HFD | placebo | 129Tac |
SA051073 | 7_HFD Placebo_B6Jax | HFD | placebo | B6Jax |
SA051074 | 8_HFD Placebo_B6Jax | HFD | placebo | B6Jax |
SA051075 | 5_HFD Placebo_B6Jax | HFD | placebo | B6Jax |
SA051076 | 6_HFD Placebo_B6Jax | HFD | placebo | B6Jax |
SA051077 | 41_HFD Vancomycin_129Jax | HFD | vancomycin | 129Jax |
SA051078 | 42_HFD Vancomycin_129Jax | HFD | vancomycin | 129Jax |
SA051079 | 44_HFD Vancomycin_129Jax | HFD | vancomycin | 129Jax |
SA051080 | 43_HFD Vancomycin_129Jax | HFD | vancomycin | 129Jax |
SA051081 | 25_HFD Vancomycin_129Tac | HFD | vancomycin | 129Tac |
SA051082 | 28_HFD Vancomycin_129Tac | HFD | vancomycin | 129Tac |
SA051083 | 26_HFD Vancomycin_129Tac | HFD | vancomycin | 129Tac |
SA051084 | 27_HFD Vancomycin_129Tac | HFD | vancomycin | 129Tac |
SA051085 | 9_HFD Vancomycin_B6Jax | HFD | vancomycin | B6Jax |
SA051086 | 10_HFD Vancomycin_B6Jax | HFD | vancomycin | B6Jax |
SA051087 | 12_HFD Vancomycin_B6Jax | HFD | vancomycin | B6Jax |
SA051088 | 11_HFD Vancomycin_B6Jax | HFD | 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 2mm) | 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 2mm) |
Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate |
Solvent B: | 100% acetonitrile; 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: | 100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide (Sigma-Aldrich) (VWR) |
Solvent B: | 75% acetonitrile/25% methanol; 10 mM ammonium hydroxide |
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: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile; 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% water/5% methanol; 0.1% acetic acid; 10 mM ammonium acetate |
Solvent B: | 100% methanol; 0.1% 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 |