Summary of Study ST001522

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 IDST001522
Study TitlePlasma unknowns profiled using hybrid nontargeted methods (part-IV)
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 Commentsplasma samples collected at baseline and 3-4 timepoints
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-08-10
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
SA1281989024-2-PEModulen Female Baseline
SA1282139016-2-PEModulen Female Baseline
SA1282159034-2-PEModulen Female Baseline
SA1282209038-2-PEModulen Female Baseline
SA1281979024-2-PBModulen Female Day 12
SA1282129016-2-PBModulen Female Day 12
SA1282199038-2-PBModulen Female Day 12
SA1282239034-2-PBModulen Female Day 12
SA1282029024-2-PAModulen Female Day 15
SA1282099016-2-PAModulen Female Day 15
SA1282189038-2-PAModulen Female Day 15
SA1282249034-2-PAModulen Female Day 15
SA1281959024-2-PDModulen Female Day 5
SA1282049016-2-PDModulen Female Day 5
SA1282169034-2-PDModulen Female Day 5
SA1282219038-2-PDModulen Female Day 5
SA1281969024-2-PCModulen Female Day 9
SA1282119016-2-PCModulen Female Day 9
SA1282179034-2-PCModulen Female Day 9
SA1282229038-2-PCModulen Female Day 9
SA1282009025-2-PEModulen Male Baseline
SA1282089013-2-PEModulen Male Baseline
SA1282259029-2-PEModulen Male Baseline
SA1282309032-2-PEModulen Male Baseline
SA1282439009-2-PEModulen Male Baseline
SA1282449003-2-PEModulen Male Baseline
SA1282039025-2-PBModulen Male Day 12
SA1282079013-2-PBModulen Male Day 12
SA1282299032-2-PBModulen Male Day 12
SA1282339029-2-PBModulen Male Day 12
SA1282369009-2-PBModulen Male Day 12
SA1282419003-2-PBModulen Male Day 12
SA1282109029-2-PAModulen Male Day 15
SA1282279013-2-PAModulen Male Day 15
SA1282289032-2-PAModulen Male Day 15
SA1282349025-2-PAModulen Male Day 15
SA1282359009-2-PAModulen Male Day 15
SA1282409003-2-PAModulen Male Day 15
SA1282019025-2-PDModulen Male Day 5
SA1282059013-2-PDModulen Male Day 5
SA1282269029-2-PDModulen Male Day 5
SA1282319032-2-PDModulen Male Day 5
SA1282399003-2-PDModulen Male Day 5
SA1282429009-2-PDModulen Male Day 5
SA1281999025-2-PCModulen Male Day 9
SA1282069013-2-PCModulen Male Day 9
SA1282149029-2-PCModulen Male Day 9
SA1282329032-2-PCModulen Male Day 9
SA1282379009-2-PCModulen Male Day 9
SA1282389003-2-PCModulen Male Day 9
SA128245QPP10NA NANA
SA128246QPP09NA NANA
SA128247QPP02NA NANA
SA128248QPP08NA NANA
SA128249QPP03NA NANA
SA128250QPP07NA NANA
SA128251QPP06NA NANA
SA128252QPP05NA NANA
SA128253QPP04NA NANA
SA128254QPP01NA NANA
SA1282619026-3-PEVegan Female Baseline
SA1282659027-3-PEVegan Female Baseline
SA1282699031-3-PEVegan Female Baseline
SA1282859014-3-PEVegan Female Baseline
SA1282559026-3-PBVegan Female Day 12
SA1282589027-3-PBVegan Female Day 12
SA1282729031-3-PBVegan Female Day 12
SA1282899014-3-PBVegan Female Day 12
SA1282599027-3-PAVegan Female Day 15
SA1282739031-3-PAVegan Female Day 15
SA1282769026-3-PAVegan Female Day 15
SA1282889014-3-PAVegan Female Day 15
SA1282629026-3-PDVegan Female Day 5
SA1282639027-3-PDVegan Female Day 5
SA1282679031-3-PDVegan Female Day 5
SA1282869014-3-PDVegan Female Day 5
SA1282569026-3-PCVegan Female Day 9
SA1282649027-3-PCVegan Female Day 9
SA1282689031-3-PCVegan Female Day 9
SA1282909014-3-PCVegan Female Day 9
SA1282609002-3-PEVegan Male Baseline
SA1282719004-3-PEVegan Male Baseline
SA1282779035-3-PEVegan Male Baseline
SA1282799008-3-PEVegan Male Baseline
SA1282849017-3-PEVegan Male Baseline
SA1283049022-3-PEVegan Male Baseline
SA1282749004-3-PBVegan Male Day 12
SA1282809017-3-PBVegan Male Day 12
SA1282879002-3-PBVegan Male Day 12
SA1282939008-3-PBVegan Male Day 12
SA1282979035-3-PBVegan Male Day 12
SA1283019022-3-PBVegan Male Day 12
SA1282789004-3-PAVegan Male Day 15
SA1282819017-3-PAVegan Male Day 15
SA1282929035-3-PAVegan Male Day 15
SA1282959002-3-PAVegan Male Day 15
SA1282969008-3-PAVegan Male Day 15
SA1283029022-3-PAVegan Male Day 15
SA1282579002-3-PDVegan Male Day 5
SA1282669035-3-PDVegan Male Day 5
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