Summary of study ST001520

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 PR001024. The data can be accessed directly via it's Project DOI: 10.21228/M8B984 This work is supported by NIH grant, U2C- DK119886.

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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 IDST001520
Study TitleStool unknowns profiled using hybrid nontargeted methods (part-II)
Study SummaryWe determined the effect of diet on the composition and metabolic function of human gut microbiome using a controlled feeding experiment with three divergent diets (vegan, omnivore, and an exclusive enteral nutrition diet (EEN) devoid of dietary fiber) in the Food And Resulting Microbial Metabolites (FARMM) study. The study included an antibiotic and polyethylene glycol (Abx/PEG) intervention to dynamically assess the effect of diet on the reconstitution of the gut microbiota and its associated fecal and plasma metabolome. Samples from thirty healthy volunteers between the ages of 18 and 60, 10 mper diet group were analyzed. Self-reported vegans were required to have followed a vegan diet for a minimum of 6 months prior to enrollment. Key exclusion criteria included inflammatory bowel disease, celiac disease, or other chronic intestinal disorders; prior bowel resection surgery other than appendectomy; baseline bowel frequency less than every 2 days or greater than 3 times daily; creatinine concentration greater than the upper limit of normal; diabetes mellitus; currently smoking; body mass index (BMI) <18.5 or >35; and use of antibiotics and probiotics in the prior 6 months. The 10 vegans continued to follow their usual diet as outpatients. All participants completed the Diet History Questionnaire II (DHQ II), a food frequency questionnaire developed by the Risk Factor Monitoring and Methods Branch of the National Cancer Institute. The vegan participants also completed three 24 hour diet recalls with a dietitian in the week prior to starting antibiotics. We randomly assigned the 20 omnivores to receive an omnivore diet or EEN (Modulen® IBD) while residing in an inpatient research unit. The macronutrient composition of Modulen® is protein 36g, fat 47g, and carbohydrate 110g per 1000 Kcal. The two omnivore diets were engineered to have a similar composition to EEN. All the subjects consumed the menu A on day 11 and menu B on days 4 and 14. Diets for omnivores were constructed to provide the expected total calories required per day for the participant to maintain their current weight and were adjusted if there was weight gain or loss of more than 2.5 pounds. On days 6, 7, and 8, inpatients participants received vancomycin 500mg orally every 6 hours and neomycin 1000mg orally every 6 hours. On day 7, participants consumed 4L of polyethylene glycol (PEG) based bowel purgative (GoLytely®). Participants in the omnivore and EEN arms left the inpatient research unit only under the direct supervision of a research staff member. The vegan outpatients reported to the hospital twice on days 6,7 and 8 to receive antibiotics and to consume PEG on day 7. The first stool sample of each day of the inpatient groups was collected, aliquoted and frozen immediately at -80oC. Blood was collected on days 1, 5, 9, 12 and 15 from which plasma aliquots were immediately isolated and frozen at -80oC. The outpatient participants following the vegan diet also had blood collected on days 1, 5, 9, 12, and 15 from which plasma aliquots were immediately isolated and frozen at -80oC. Among these participants, the first stool of the day was collected at home daily and kept on ice packs until it was brought to the research unit where it could be aliquoted and frozen. Samples from vegans were received for aliquoting within 24 hours and on average within 4 hours (Wu et al., 2010). Day 0 stool was not collected from vegans since their diet did not change. The aliquoted amounts for all samples ranged from 500 mg to 1 g. The aliquots were taken from different areas of the sample. Remaining sample was then collected into one residual 50 ml conical tube with a tongue depressor. Any remaining stool was discarded. The University of Pennsylvania Institutional Review Board (IRB) approved the research protocol.
Institute
Broad Institute of MIT and Harvard
Last NameClish
First NameClary
Address415 Main Street, Cambridge, MA, 02142, USA
Emailclary@broadinstitute.org
Phone617-714-7654
Submit Date2020-11-05
Num Groups3
Total Subjects30
Num Males20
Num Females10
Study Commentsstool samples collected at baseline and 3-4 timepoints
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2021-04-01
Release Version1
Clary Clish Clary Clish
https://dx.doi.org/10.21228/M8B984
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001024
Project DOI:doi: 10.21228/M8B984
Project Title:Role of Diet in the Reconstitution of the Human Gut Microbiome and its Metabolome
Project Type:Observational study
Project Summary:We studied the impact of three divergent diets, vegan, omnivore, and a synthetic enteral nutrition (EEN) diet lacking fiber, on the human gut microbiome and its metabolome in a longitudinal analysis that included a microbiota depletion intervention. Hybrid nontargeted LC-MS methods were used to profile stool and plasma metabolites.
Institute:Broad Institute of MIT and Harvard
Last Name:Clish
First Name:Clary
Address:415 Main Street, Cambridge, MA, 02142, USA
Email:clary@broadinstitute.org
Phone:617-714-7654
Funding Source:Crohn’s & Colitis Foundation, P30 DK 050306, PennCHOP Microbiome Program, and the Penn Center for Nutritional Science and Medicine
Contributors:Ceylan Tanes, Kyle Bittinger, Yuan Gao, Elliot S. Friedman, Lisa Nessel, Unmesha Roy Paladhi, Lillian Chau, Erika Panfen, Michael A. Fischbach, Jonathan Braun, Ramnik J. Xavier, Clary B. Clish, Hongzhe Li, Frederic D. Bushman, James D. Lewis, Gary D. Wu

Subject:

Subject ID:SU001594
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:20-60
Weight Or Weight Range:BMI range: 20-35
Gender:Male and female
Human Race:White; American Indian/Alaskan Native; Black/African American
Human Ethnicity:Hispanic or Latino; Non-Hispanic or Latino
Human Trial Type:Intervention trial
Human Exclusion Criteria:Key exclusion criteria included inflammatory bowel disease, celiac disease, or other chronic intestinal disorders; prior bowel resection surgery other than appendectomy; baseline bowel frequency less than every 2 days or greater than 3 times daily; creatinine concentration greater than the upper limit of normal; diabetes mellitus; currently smoking; body mass index (BMI) <18.5 or >35; and use of antibiotics and probiotics in the prior 6 months

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Study_Diet Sex Time
SA1279529024-2-SEModulen Female Baseline
SA1279769016-2-SEModulen Female Baseline
SA1279869034-2-SEModulen Female Baseline
SA1280069038-2-SEModulen Female Baseline
SA1279539024-2-SBModulen Female Day 12
SA1279779016-2-SBModulen Female Day 12
SA1279879034-2-SBModulen Female Day 12
SA1280079038-2-SBModulen Female Day 12
SA1279549024-2-SAModulen Female Day 15
SA1279789016-2-SAModulen Female Day 15
SA1279889034-2-SAModulen Female Day 15
SA1280089038-2-SAModulen Female Day 15
SA1279559024-2-SDModulen Female Day 5
SA1279799016-2-SDModulen Female Day 5
SA1279899034-2-SDModulen Female Day 5
SA1280099038-2-SDModulen Female Day 5
SA1279809016-2-SCModulen Female Day 9
SA1279909034-2-SCModulen Female Day 9
SA1280109038-2-SCModulen Female Day 9
SA1278699003-2-SEModulen Male Baseline
SA1278979009-2-SEModulen Male Baseline
SA1279479029-2-SEModulen Male Baseline
SA1279569025-2-SEModulen Male Baseline
SA1279819013-2-SEModulen Male Baseline
SA1279969032-2-SEModulen Male Baseline
SA1278709003-2-SBModulen Male Day 12
SA1278989009-2-SBModulen Male Day 12
SA1279489029-2-SBModulen Male Day 12
SA1279579025-2-SBModulen Male Day 12
SA1279829013-2-SBModulen Male Day 12
SA1279979032-2-SBModulen Male Day 12
SA1278719003-2-SAModulen Male Day 15
SA1278999009-2-SAModulen Male Day 15
SA1279499029-2-SAModulen Male Day 15
SA1279589025-2-SAModulen Male Day 15
SA1279839013-2-SAModulen Male Day 15
SA1279989032-2-SAModulen Male Day 15
SA1279009009-2-SDModulen Male Day 5
SA1279509029-2-SDModulen Male Day 5
SA1279599025-2-SDModulen Male Day 5
SA1279849013-2-SDModulen Male Day 5
SA1279999032-2-SDModulen Male Day 5
SA1278729003-2-SCModulen Male Day 9
SA1279019009-2-SCModulen Male Day 9
SA1279519029-2-SCModulen Male Day 9
SA1279609025-2-SCModulen Male Day 9
SA1279859013-2-SCModulen Male Day 9
SA1280009032-2-SCModulen Male Day 9
SA128016QCPS15NA NA NA
SA128017QCPS13NA NA NA
SA128018QCPS16NA NA NA
SA128019QCPS14NA NA NA
SA128020QCPS19NA NA NA
SA128021QCPS20NA NA NA
SA128022QCPS12NA NA NA
SA128023QCPS18NA NA NA
SA128024QCPS17NA NA NA
SA128025QCPS09NA NA NA
SA128026QCPS04NA NA NA
SA128027QCPS03NA NA NA
SA128028QCPS02NA NA NA
SA128029QCPS05NA NA NA
SA128030QCPS06NA NA NA
SA128031QCPS10NA NA NA
SA128032QCPS08NA NA NA
SA128033QCPS07NA NA NA
SA128034QCPS11NA NA NA
SA1278789027-3-SEVegan Female Baseline
SA1278879014-3-SEVegan Female Baseline
SA1279129026-3-SEVegan Female Baseline
SA1279669031-3-SEVegan Female Baseline
SA1278799027-3-SBVegan Female Day 12
SA1278889014-3-SBVegan Female Day 12
SA1279139026-3-SBVegan Female Day 12
SA1279679031-3-SBVegan Female Day 12
SA1278899014-3-SAVegan Female Day 15
SA1279149026-3-SAVegan Female Day 15
SA1279689031-3-SAVegan Female Day 15
SA1278809027-3-SDVegan Female Day 5
SA1278909014-3-SDVegan Female Day 5
SA1279159026-3-SDVegan Female Day 5
SA1279699031-3-SDVegan Female Day 5
SA1278819027-3-SCVegan Female Day 9
SA1278919014-3-SCVegan Female Day 9
SA1279169026-3-SCVegan Female Day 9
SA1279709031-3-SCVegan Female Day 9
SA1278739002-3-SEVegan Male Baseline
SA1279029008-3-SEVegan Male Baseline
SA1279229004-3-SEVegan Male Baseline
SA1279329017-3-SEVegan Male Baseline
SA1279339035-3-SEVegan Male Baseline
SA1279349022-3-SEVegan Male Baseline
SA1278749002-3-SBVegan Male Day 12
SA1279039008-3-SBVegan Male Day 12
SA1279239004-3-SBVegan Male Day 12
SA1279359022-3-SBVegan Male Day 12
SA1279369035-3-SBVegan Male Day 12
SA1279379017-3-SBVegan Male Day 12
SA1278759002-3-SAVegan Male Day 15
SA1279049008-3-SAVegan Male Day 15
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 166

Collection:

Collection ID:CO001589
Collection Summary:The first stool sample of each day of the inpatient groups was collected, aliquoted and frozen immediately at -80oC. Blood was collected on days 1, 5, 9, 12 and 15 from which plasma aliquots were immediately isolated and frozen at -80oC. The outpatient participants following the vegan diet also had blood collected on days 1, 5, 9, 12, and 15 from which plasma aliquots were immediately isolated and frozen at -80oC. Among these participants, the first stool of the day was collected at home daily and kept on ice packs until it was brought to the research unit where it could be aliquoted and frozen. Samples from vegans were received for aliquoting within 24 hours and on average within 4 hours (Wu et al., 2010). Day 0 stool was not collected from vegans since their diet did not change. The aliquoted amounts for all samples ranged from 500 mg to 1 g. The aliquots were taken from different areas of the sample. Remaining sample was then collected into one residual 50 ml conical tube with a tongue depressor. Any remaining stool was discarded. The University of Pennsylvania Institutional Review Board (IRB) approved the research protocol.
Sample Type:Feces
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001609
Treatment Summary:The 10 vegan participants continued to follow their usual diet as outpatients. All participants completed the Diet History Questionnaire II (DHQ II), a food frequency questionnaire developed by the Risk Factor Monitoring and Methods Branch of the National Cancer Institute. The vegan participants also completed three 24 hour diet recalls with a dietitian in the week prior to starting antibiotics. 20 omnivores were randomly assigned to receive an omnivore diet or EEN (Modulen® IBD) while residing in an inpatient research unit. The macronutrient composition of Modulen® is protein 36g, fat 47g, and carbohydrate 110g per 1000 Kcal. The two omnivore diets were engineered to have a similar composition to EEN. All the subjects consumed the menu A on day 11 and menu B on days 4 and 14. Diets for omnivores were constructed to provide the expected total calories required per day for the participant to maintain their current weight and were adjusted if there was weight gain or loss of more than 2.5 pounds. On days 6, 7, and 8, inpatients participants received vancomycin 500mg orally every 6 hours and neomycin 1000mg orally every 6 hours. On day 7, participants consumed 4L of polyethylene glycol (PEG) based bowel purgative (GoLytely®). Participants in the omnivore and EEN arms left the inpatient research unit only under the direct supervision of a research staff member. The vegan outpatients reported to the hospital twice on days 6,7 and 8 to receive antibiotics and to consume PEG on day 7.

Sample Preparation:

Sampleprep ID:SP001602
Sampleprep Summary:Stool samples (weight range 42.99-90.35 mg) were homogenized in 4 μL of water per milligram stool sample weight using a bead mill (TissueLyser II; Qiagen) and the aqueous homogenates were aliquoted for metabolite profiling analyses. Plasma samples were thawed and aliquoted for each LC-MS method. LC-MS samples were prepared for four profiling methods as follows: HILIC-pos: Metabolites were extracted by adding 90 μL 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) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C8-pos: Lipids were extracted by adding 190 μL of isopropanol containing 1-dodecanoyl-2-tridecanoyl-sn-glycero-3-phosphocholine as an internal standard (Avanti Polar Lipids; Alabaster, AL) to a 10 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, ambient temperature) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. HILIC-neg: Metabolites were extracted by adding 120 μL of 80% methanol containing inosine-15N4, thymine-d4 and glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover, MA) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis. C18-neg: Metabolites were extracted by adding 90 μL of methanol containing PGE2-d4 as an internal standard (Cayman Chemical Co.; Ann Arbor, MI) to a 30 μL aliquot of stool homogenate or plasma. Samples were vortexed and then centrifuged (10 min, 9,000 x g, 4°C) to pellet protein precipitates. Supernatants were transferred to glass autosampler vials containing inserts for LC-MS analysis.

Combined analysis:

Analysis ID AN002529 AN002530 AN002531 AN002532
Analysis type MS MS MS MS
Chromatography type HILIC Reversed phase HILIC Reversed phase
Chromatography system Shimadzu Nexera X2 Shimadzu Nexera X2 Shimadzu Nexera X2 Shimadzu Nexera X2
Column Waters Atlantis HILIC (150 x 2 mm, 3 μm) Waters Acquity BEH C8 (100 x 2.1mm, 1.7um) Phenomenex Luna NH2 (150 x 2.1mm, 3um) Waters Acquity T3 (150 x 2.1 mm, 1.7 um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Exactive Plus Orbitrap Thermo Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units peak area peak area peak area peak area

Chromatography:

Chromatography ID:CH001849
Chromatography Summary:HILIC-pos: high resolution and accurate mass profiling of polar metabolites using HILIC and positive ion mode full scan MS
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Atlantis HILIC (150 x 2 mm, 3 μm)
Column Temperature:30 ℃
Flow Gradient:linear
Flow Rate:250 uL/min
Injection Temperature:4
Solvent A:10 mM Ammonium formate/0.1% Formic acid in water
Solvent B:0.1% Formic acid in Acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH001850
Chromatography Summary:C8-pos: high resolution and accurate mass profiling of polar and nonpolar lipids using reversed phase C8 chromatography and positive ion mode full scan MS
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity BEH C8 (100 x 2.1mm, 1.7um)
Column Temperature:40 ℃
Flow Gradient:linear
Flow Rate:450 uL/min
Solvent A:10 mM Ammonium Acetate in 95:5:0.1, v:v:v Water: Methanol: Formic Acid
Solvent B:0.1% Formic Acid in Methanol
Chromatography Type:Reversed phase
  
Chromatography ID:CH001851
Chromatography Summary:HILIC-neg: high resolution and accurate mass profiling of polar metabolites using HILIC and negative ion mode full scan MS
Instrument Name:Shimadzu Nexera X2
Column Name:Phenomenex Luna NH2 (150 x 2.1mm, 3um)
Column Temperature:30 ℃
Flow Gradient:linear
Flow Rate:400 uL/min
Injection Temperature:4
Solvent A:20 mM Ammonium Acetate, 20 mM Ammonium Hydroxide in water
Solvent B:10 mM Ammonium Hydroxide in 25% Methanol/75% Acetonitrile
Chromatography Type:HILIC
  
Chromatography ID:CH001852
Chromatography Summary:C18-neg: high resolution and accurate mass profiling of metabolites of intermediate polarity using reversed phase C18 chromatography and negative ion mode full scan MS
Instrument Name:Shimadzu Nexera X2
Column Name:Waters Acquity T3 (150 x 2.1 mm, 1.7 um)
Column Temperature:45 ℃
Flow Gradient:linear
Flow Rate:450 uL/min
Injection Temperature:4
Solvent A:0.01% Formic acid in water
Solvent B:0.01% Acetic acid in Acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS002347
Analysis ID:AN002529
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over m/z 70-800 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, 3.5 kV; capillary temperature, 350°C; probe heater temperature, 300°C; sheath gas, 40; auxiliary gas, 15; and S-lens RF level 40. All raw data were processed using Progenesis QI software (NonLinear Dynamics) for feature alignment, nontargeted signal detection, and signal integration. Targeted processing of a subset of known metabolites was conducted using TraceFinder software (Thermo Fisher Scientific; Waltham, MA). Compound identities were confirmed using reference standards
Ion Mode:POSITIVE
  
MS ID:MS002348
Analysis ID:AN002530
Instrument Name:Thermo Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS analyses were carried out using electrospray ionization in the positive ion mode using full scan analysis over m/z 200-1100 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, 3.0 kV; capillary temperature, 300°C; probe heater temperature, 300°C; sheath gas, 50; auxiliary gas, 15; and S-lens RF level 60. All raw data were processed using Progenesis QI software (NonLinear Dynamics) for feature alignment, nontargeted signal detection, and signal integration. Targeted processing of a subset of known lipids was conducted using TraceFinder software (Thermo Fisher Scientific; Waltham, MA). Lipid identities were confirmed using reference standards representative of different lipid classes and previously characterized reference samples. Lipids were denoted by headgroup and total acyl carbon number and double bond content.
Ion Mode:POSITIVE
  
MS ID:MS002349
Analysis ID:AN002531
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS analyses were carried out using electrospray ionization in the negative ion mode using full scan analysis over m/z 60-750 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, -3.0 kV; capillary temperature, 350°C; probe heater temperature, 325°C; sheath gas, 55; auxiliary gas, 10; and S-lens RF level 40. All raw data were processed using Progenesis QI software (NonLinear Dynamics) for feature alignment, nontargeted signal detection, and signal integration. Targeted processing of a subset of known metabolites was conducted using TraceFinder software (Thermo Fisher Scientific; Waltham, MA). Compound identities were confirmed using reference standards.
Ion Mode:NEGATIVE
  
MS ID:MS002350
Analysis ID:AN002532
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS analyses were carried out using electrospray ionization in the negative ion mode using full scan analysis over m/z 70-850 at 70,000 resolution and 3 Hz data acquisition rate. Additional MS settings were: ion spray voltage, -3.5 kV; capillary temperature, 320°C; probe heater temperature, 300°C; sheath gas, 45; auxiliary gas, 10; and S-lens RF level 60All raw data were processed using Progenesis QI software (NonLinear Dynamics) for feature alignment, nontargeted signal detection, and signal integration. Targeted processing of a subset of known metabolites was conducted using TraceFinder software (Thermo Fisher Scientific; Waltham, MA). Compound identities were confirmed using reference standards.
Ion Mode:NEGATIVE
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