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.
| Study ID | ST001519 |
| Study Title | Stool metabolites of known identity profiled using hybrid nontargeted methods (part-I) |
| Study Summary | We 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 Name | Clish |
| First Name | Clary |
| Address | 415 Main Street, Cambridge, MA, 02142, USA |
| clary@broadinstitute.org | |
| Phone | 617-714-7654 |
| Submit Date | 2020-11-05 |
| Num Groups | 3 |
| Total Subjects | 30 |
| Num Males | 20 |
| Num Females | 10 |
| Study Comments | stool samples collected at baseline and 3-4 timepoints |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-04-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Study_Diet |
|---|---|---|
| SA127786 | 9024-2-SE | Modulen | Sex:Female | Time:Baseline |
| SA127813 | 9016-2-SE | Modulen | Sex:Female | Time:Baseline |
| SA127820 | 9034-2-SE | Modulen | Sex:Female | Time:Baseline |
| SA127840 | 9038-2-SE | Modulen | Sex:Female | Time:Baseline |
| SA127788 | 9024-2-SB | Modulen | Sex:Female | Time:Day 12 |
| SA127811 | 9016-2-SB | Modulen | Sex:Female | Time:Day 12 |
| SA127824 | 9034-2-SB | Modulen | Sex:Female | Time:Day 12 |
| SA127844 | 9038-2-SB | Modulen | Sex:Female | Time:Day 12 |
| SA127789 | 9024-2-SA | Modulen | Sex:Female | Time:Day 15 |
| SA127814 | 9016-2-SA | Modulen | Sex:Female | Time:Day 15 |
| SA127822 | 9034-2-SA | Modulen | Sex:Female | Time:Day 15 |
| SA127842 | 9038-2-SA | Modulen | Sex:Female | Time:Day 15 |
| SA127787 | 9024-2-SD | Modulen | Sex:Female | Time:Day 5 |
| SA127812 | 9016-2-SD | Modulen | Sex:Female | Time:Day 5 |
| SA127821 | 9034-2-SD | Modulen | Sex:Female | Time:Day 5 |
| SA127841 | 9038-2-SD | Modulen | Sex:Female | Time:Day 5 |
| SA127810 | 9016-2-SC | Modulen | Sex:Female | Time:Day 9 |
| SA127823 | 9034-2-SC | Modulen | Sex:Female | Time:Day 9 |
| SA127843 | 9038-2-SC | Modulen | Sex:Female | Time:Day 9 |
| SA127704 | 9003-2-SE | Modulen | Sex:Male | Time:Baseline |
| SA127731 | 9009-2-SE | Modulen | Sex:Male | Time:Baseline |
| SA127782 | 9029-2-SE | Modulen | Sex:Male | Time:Baseline |
| SA127790 | 9025-2-SE | Modulen | Sex:Male | Time:Baseline |
| SA127815 | 9013-2-SE | Modulen | Sex:Male | Time:Baseline |
| SA127831 | 9032-2-SE | Modulen | Sex:Male | Time:Baseline |
| SA127706 | 9003-2-SB | Modulen | Sex:Male | Time:Day 12 |
| SA127733 | 9009-2-SB | Modulen | Sex:Male | Time:Day 12 |
| SA127781 | 9029-2-SB | Modulen | Sex:Male | Time:Day 12 |
| SA127792 | 9025-2-SB | Modulen | Sex:Male | Time:Day 12 |
| SA127818 | 9013-2-SB | Modulen | Sex:Male | Time:Day 12 |
| SA127834 | 9032-2-SB | Modulen | Sex:Male | Time:Day 12 |
| SA127705 | 9003-2-SA | Modulen | Sex:Male | Time:Day 15 |
| SA127734 | 9009-2-SA | Modulen | Sex:Male | Time:Day 15 |
| SA127784 | 9029-2-SA | Modulen | Sex:Male | Time:Day 15 |
| SA127791 | 9025-2-SA | Modulen | Sex:Male | Time:Day 15 |
| SA127817 | 9013-2-SA | Modulen | Sex:Male | Time:Day 15 |
| SA127830 | 9032-2-SA | Modulen | Sex:Male | Time:Day 15 |
| SA127732 | 9009-2-SD | Modulen | Sex:Male | Time:Day 5 |
| SA127785 | 9029-2-SD | Modulen | Sex:Male | Time:Day 5 |
| SA127793 | 9025-2-SD | Modulen | Sex:Male | Time:Day 5 |
| SA127816 | 9013-2-SD | Modulen | Sex:Male | Time:Day 5 |
| SA127832 | 9032-2-SD | Modulen | Sex:Male | Time:Day 5 |
| SA127703 | 9003-2-SC | Modulen | Sex:Male | Time:Day 9 |
| SA127735 | 9009-2-SC | Modulen | Sex:Male | Time:Day 9 |
| SA127783 | 9029-2-SC | Modulen | Sex:Male | Time:Day 9 |
| SA127794 | 9025-2-SC | Modulen | Sex:Male | Time:Day 9 |
| SA127819 | 9013-2-SC | Modulen | Sex:Male | Time:Day 9 |
| SA127833 | 9032-2-SC | Modulen | Sex:Male | Time:Day 9 |
| SA127850 | QCPS15 | NA | Sex:NA | Time:NA |
| SA127851 | QCPS13 | NA | Sex:NA | Time:NA |
| SA127852 | QCPS16 | NA | Sex:NA | Time:NA |
| SA127853 | QCPS14 | NA | Sex:NA | Time:NA |
| SA127854 | QCPS18 | NA | Sex:NA | Time:NA |
| SA127855 | QCPS12 | NA | Sex:NA | Time:NA |
| SA127856 | QCPS20 | NA | Sex:NA | Time:NA |
| SA127857 | QCPS19 | NA | Sex:NA | Time:NA |
| SA127858 | QCPS17 | NA | Sex:NA | Time:NA |
| SA127859 | QCPS02 | NA | Sex:NA | Time:NA |
| SA127860 | QCPS05 | NA | Sex:NA | Time:NA |
| SA127861 | QCPS04 | NA | Sex:NA | Time:NA |
| SA127862 | QCPS03 | NA | Sex:NA | Time:NA |
| SA127863 | QCPS06 | NA | Sex:NA | Time:NA |
| SA127864 | QCPS07 | NA | Sex:NA | Time:NA |
| SA127865 | QCPS10 | NA | Sex:NA | Time:NA |
| SA127866 | QCPS09 | NA | Sex:NA | Time:NA |
| SA127867 | QCPS08 | NA | Sex:NA | Time:NA |
| SA127868 | QCPS11 | NA | Sex:NA | Time:NA |
| SA127713 | 9027-3-SE | Vegan | Sex:Female | Time:Baseline |
| SA127722 | 9014-3-SE | Vegan | Sex:Female | Time:Baseline |
| SA127748 | 9026-3-SE | Vegan | Sex:Female | Time:Baseline |
| SA127802 | 9031-3-SE | Vegan | Sex:Female | Time:Baseline |
| SA127715 | 9027-3-SB | Vegan | Sex:Female | Time:Day 12 |
| SA127724 | 9014-3-SB | Vegan | Sex:Female | Time:Day 12 |
| SA127749 | 9026-3-SB | Vegan | Sex:Female | Time:Day 12 |
| SA127800 | 9031-3-SB | Vegan | Sex:Female | Time:Day 12 |
| SA127721 | 9014-3-SA | Vegan | Sex:Female | Time:Day 15 |
| SA127750 | 9026-3-SA | Vegan | Sex:Female | Time:Day 15 |
| SA127803 | 9031-3-SA | Vegan | Sex:Female | Time:Day 15 |
| SA127712 | 9027-3-SD | Vegan | Sex:Female | Time:Day 5 |
| SA127723 | 9014-3-SD | Vegan | Sex:Female | Time:Day 5 |
| SA127747 | 9026-3-SD | Vegan | Sex:Female | Time:Day 5 |
| SA127804 | 9031-3-SD | Vegan | Sex:Female | Time:Day 5 |
| SA127714 | 9027-3-SC | Vegan | Sex:Female | Time:Day 9 |
| SA127725 | 9014-3-SC | Vegan | Sex:Female | Time:Day 9 |
| SA127746 | 9026-3-SC | Vegan | Sex:Female | Time:Day 9 |
| SA127801 | 9031-3-SC | Vegan | Sex:Female | Time:Day 9 |
| SA127709 | 9002-3-SE | Vegan | Sex:Male | Time:Baseline |
| SA127740 | 9008-3-SE | Vegan | Sex:Male | Time:Baseline |
| SA127759 | 9004-3-SE | Vegan | Sex:Male | Time:Baseline |
| SA127767 | 9017-3-SE | Vegan | Sex:Male | Time:Baseline |
| SA127773 | 9022-3-SE | Vegan | Sex:Male | Time:Baseline |
| SA127777 | 9035-3-SE | Vegan | Sex:Male | Time:Baseline |
| SA127707 | 9002-3-SB | Vegan | Sex:Male | Time:Day 12 |
| SA127737 | 9008-3-SB | Vegan | Sex:Male | Time:Day 12 |
| SA127758 | 9004-3-SB | Vegan | Sex:Male | Time:Day 12 |
| SA127769 | 9017-3-SB | Vegan | Sex:Male | Time:Day 12 |
| SA127778 | 9022-3-SB | Vegan | Sex:Male | Time:Day 12 |
| SA127780 | 9035-3-SB | Vegan | Sex:Male | Time:Day 12 |
| SA127708 | 9002-3-SA | Vegan | Sex:Male | Time:Day 15 |
| SA127738 | 9008-3-SA | Vegan | Sex:Male | Time:Day 15 |
