Summary of study ST001521

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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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Study IDST001521
Study TitlePlasma metabolites of known identity profiled using hybrid nontargeted methods (part-III)
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.
Broad Institute of MIT and Harvard
Last NameClish
First NameClary
Address415 Main Street, Cambridge, MA, 02142, USA
Submit Date2020-11-05
Num Groups3
Total Subjects30
Num Males20
Num Females10
Study Commentsplasma 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 application/zip

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

mb_sample_id local_sample_id Study_Diet Sex Time
SA1280509024-2-PEModulen Female Baseline
SA1280609016-2-PEModulen Female Baseline
SA1280709034-2-PEModulen Female Baseline
SA1280809038-2-PEModulen Female Baseline
SA1280519024-2-PBModulen Female Day 12
SA1280619016-2-PBModulen Female Day 12
SA1280719034-2-PBModulen Female Day 12
SA1280819038-2-PBModulen Female Day 12
SA1280529024-2-PAModulen Female Day 15
SA1280629016-2-PAModulen Female Day 15
SA1280729034-2-PAModulen Female Day 15
SA1280829038-2-PAModulen Female Day 15
SA1280539024-2-PDModulen Female Day 5
SA1280639016-2-PDModulen Female Day 5
SA1280739034-2-PDModulen Female Day 5
SA1280839038-2-PDModulen Female Day 5
SA1280549024-2-PCModulen Female Day 9
SA1280649016-2-PCModulen Female Day 9
SA1280749034-2-PCModulen Female Day 9
SA1280849038-2-PCModulen Female Day 9
SA1280359003-2-PEModulen Male Baseline
SA1280409009-2-PEModulen Male Baseline
SA1280459029-2-PEModulen Male Baseline
SA1280559025-2-PEModulen Male Baseline
SA1280659013-2-PEModulen Male Baseline
SA1280759032-2-PEModulen Male Baseline
SA1280369003-2-PBModulen Male Day 12
SA1280419009-2-PBModulen Male Day 12
SA1280469029-2-PBModulen Male Day 12
SA1280569025-2-PBModulen Male Day 12
SA1280669013-2-PBModulen Male Day 12
SA1280769032-2-PBModulen Male Day 12
SA1280379003-2-PAModulen Male Day 15
SA1280429009-2-PAModulen Male Day 15
SA1280479029-2-PAModulen Male Day 15
SA1280579025-2-PAModulen Male Day 15
SA1280679013-2-PAModulen Male Day 15
SA1280779032-2-PAModulen Male Day 15
SA1280389003-2-PDModulen Male Day 5
SA1280439009-2-PDModulen Male Day 5
SA1280489029-2-PDModulen Male Day 5
SA1280589025-2-PDModulen Male Day 5
SA1280689013-2-PDModulen Male Day 5
SA1280789032-2-PDModulen Male Day 5
SA1280399003-2-PCModulen Male Day 9
SA1280449009-2-PCModulen Male Day 9
SA1280499029-2-PCModulen Male Day 9
SA1280599025-2-PCModulen Male Day 9
SA1280699013-2-PCModulen Male Day 9
SA1280799032-2-PCModulen Male Day 9
SA1281009027-3-PEVegan Female Baseline
SA1281059014-3-PEVegan Female Baseline
SA1281159026-3-PEVegan Female Baseline
SA1281409031-3-PEVegan Female Baseline
SA1281019027-3-PBVegan Female Day 12
SA1281069014-3-PBVegan Female Day 12
SA1281169026-3-PBVegan Female Day 12
SA1281419031-3-PBVegan Female Day 12
SA1281029027-3-PAVegan Female Day 15
SA1281079014-3-PAVegan Female Day 15
SA1281179026-3-PAVegan Female Day 15
SA1281429031-3-PAVegan Female Day 15
SA1281039027-3-PDVegan Female Day 5
SA1281089014-3-PDVegan Female Day 5
SA1281189026-3-PDVegan Female Day 5
SA1281439031-3-PDVegan Female Day 5
SA1281049027-3-PCVegan Female Day 9
SA1281099014-3-PCVegan Female Day 9
SA1281199026-3-PCVegan Female Day 9
SA1281449031-3-PCVegan Female Day 9
SA1280959002-3-PEVegan Male Baseline
SA1281109008-3-PEVegan Male Baseline
SA1281209004-3-PEVegan Male Baseline
SA1281259017-3-PEVegan Male Baseline
SA1281269035-3-PEVegan Male Baseline
SA1281279022-3-PEVegan Male Baseline
SA1280969002-3-PBVegan Male Day 12
SA1281119008-3-PBVegan Male Day 12
SA1281219004-3-PBVegan Male Day 12
SA1281289022-3-PBVegan Male Day 12
SA1281299017-3-PBVegan Male Day 12
SA1281309035-3-PBVegan Male Day 12
SA1280979002-3-PAVegan Male Day 15
SA1281129008-3-PAVegan Male Day 15
SA1281229004-3-PAVegan Male Day 15
SA1281319017-3-PAVegan Male Day 15
SA1281329035-3-PAVegan Male Day 15
SA1281339022-3-PAVegan Male Day 15
SA1280989002-3-PDVegan Male Day 5
SA1281139008-3-PDVegan Male Day 5
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