Summary of study ST001519

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.

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 IDST001519
Study TitleStool metabolites of known identity profiled using hybrid nontargeted methods (part-I)
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

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Factors:

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

mb_sample_id local_sample_id Study_Diet Sex Time
SA1277869024-2-SEModulen Female Baseline
SA1278139016-2-SEModulen Female Baseline
SA1278209034-2-SEModulen Female Baseline
SA1278409038-2-SEModulen Female Baseline
SA1277889024-2-SBModulen Female Day 12
SA1278119016-2-SBModulen Female Day 12
SA1278249034-2-SBModulen Female Day 12
SA1278449038-2-SBModulen Female Day 12
SA1277899024-2-SAModulen Female Day 15
SA1278149016-2-SAModulen Female Day 15
SA1278229034-2-SAModulen Female Day 15
SA1278429038-2-SAModulen Female Day 15
SA1277879024-2-SDModulen Female Day 5
SA1278129016-2-SDModulen Female Day 5
SA1278219034-2-SDModulen Female Day 5
SA1278419038-2-SDModulen Female Day 5
SA1278109016-2-SCModulen Female Day 9
SA1278239034-2-SCModulen Female Day 9
SA1278439038-2-SCModulen Female Day 9
SA1277049003-2-SEModulen Male Baseline
SA1277319009-2-SEModulen Male Baseline
SA1277829029-2-SEModulen Male Baseline
SA1277909025-2-SEModulen Male Baseline
SA1278159013-2-SEModulen Male Baseline
SA1278319032-2-SEModulen Male Baseline
SA1277069003-2-SBModulen Male Day 12
SA1277339009-2-SBModulen Male Day 12
SA1277819029-2-SBModulen Male Day 12
SA1277929025-2-SBModulen Male Day 12
SA1278189013-2-SBModulen Male Day 12
SA1278349032-2-SBModulen Male Day 12
SA1277059003-2-SAModulen Male Day 15
SA1277349009-2-SAModulen Male Day 15
SA1277849029-2-SAModulen Male Day 15
SA1277919025-2-SAModulen Male Day 15
SA1278179013-2-SAModulen Male Day 15
SA1278309032-2-SAModulen Male Day 15
SA1277329009-2-SDModulen Male Day 5
SA1277859029-2-SDModulen Male Day 5
SA1277939025-2-SDModulen Male Day 5
SA1278169013-2-SDModulen Male Day 5
SA1278329032-2-SDModulen Male Day 5
SA1277039003-2-SCModulen Male Day 9
SA1277359009-2-SCModulen Male Day 9
SA1277839029-2-SCModulen Male Day 9
SA1277949025-2-SCModulen Male Day 9
SA1278199013-2-SCModulen Male Day 9
SA1278339032-2-SCModulen Male Day 9
SA127850QCPS15NA NA NA
SA127851QCPS13NA NA NA
SA127852QCPS16NA NA NA
SA127853QCPS14NA NA NA
SA127854QCPS18NA NA NA
SA127855QCPS12NA NA NA
SA127856QCPS20NA NA NA
SA127857QCPS19NA NA NA
SA127858QCPS17NA NA NA
SA127859QCPS02NA NA NA
SA127860QCPS05NA NA NA
SA127861QCPS04NA NA NA
SA127862QCPS03NA NA NA
SA127863QCPS06NA NA NA
SA127864QCPS07NA NA NA
SA127865QCPS10NA NA NA
SA127866QCPS09NA NA NA
SA127867QCPS08NA NA NA
SA127868QCPS11NA NA NA
SA1277139027-3-SEVegan Female Baseline
SA1277229014-3-SEVegan Female Baseline
SA1277489026-3-SEVegan Female Baseline
SA1278029031-3-SEVegan Female Baseline
SA1277159027-3-SBVegan Female Day 12
SA1277249014-3-SBVegan Female Day 12
SA1277499026-3-SBVegan Female Day 12
SA1278009031-3-SBVegan Female Day 12
SA1277219014-3-SAVegan Female Day 15
SA1277509026-3-SAVegan Female Day 15
SA1278039031-3-SAVegan Female Day 15
SA1277129027-3-SDVegan Female Day 5
SA1277239014-3-SDVegan Female Day 5
SA1277479026-3-SDVegan Female Day 5
SA1278049031-3-SDVegan Female Day 5
SA1277149027-3-SCVegan Female Day 9
SA1277259014-3-SCVegan Female Day 9
SA1277469026-3-SCVegan Female Day 9
SA1278019031-3-SCVegan Female Day 9
SA1277099002-3-SEVegan Male Baseline
SA1277409008-3-SEVegan Male Baseline
SA1277599004-3-SEVegan Male Baseline
SA1277679017-3-SEVegan Male Baseline
SA1277739022-3-SEVegan Male Baseline
SA1277779035-3-SEVegan Male Baseline
SA1277079002-3-SBVegan Male Day 12
SA1277379008-3-SBVegan Male Day 12
SA1277589004-3-SBVegan Male Day 12
SA1277699017-3-SBVegan Male Day 12
SA1277789022-3-SBVegan Male Day 12
SA1277809035-3-SBVegan Male Day 12
SA1277089002-3-SAVegan Male Day 15
SA1277389008-3-SAVegan Male Day 15
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