Summary of Study ST002112

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 PR001338. The data can be accessed directly via it's Project DOI: 10.21228/M8RX2S 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 IDST002112
Study TitleGlobal, distinctive and personal changes in molecular and microbial profiles induced by specific fibers in humans (Untargeted)
Study SummaryDietary fibers act through the microbiome and improve cardiovascular health, metabolic disorders and cancer prevention. To understand health benefits of dietary fiber supplementation we investigated two popular purified fibers, arabinoxylan (AX) and long-chain inulin (LCI), and a mixture of five fibers. We present multi-omic signatures of metabolomics, lipidomics, proteomics, metagenomics, a cytokine panel and clinical measurements on healthy and insulin resistant participants. Each fiber is associated with fiber-dependent biochemical and microbial responses. AX consumption associates with a significant reduction in LDL and an increase in bile acids, contributing to its observed cholesterol reduction. LCI is associated with an increase in Bifidobacterium. However, at the highest LCI dose there is increased inflammation and elevation in the liver enzyme alanine aminotransferase. This study yields insights into the effects of fiber supplementation, it provides insights into mechanisms behind fiber induced cholesterol reduction, and it shows effects of individual, purified fibers on the microbiome.
Institute
Stanford University
Last NameLancaster
First NameSamuel
Address240 Pasteur Dr, BMI bldg 4400, Stanford California, 94305
Emailslancast@stanford.edu
Phone6126004033
Submit Date2022-05-06
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-03-13
Release Version1
Samuel Lancaster Samuel Lancaster
https://dx.doi.org/10.21228/M8RX2S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001338
Project DOI:doi: 10.21228/M8RX2S
Project Title:Health benefits of dietary fiber supplementation.
Project Summary:Untargeted metabolomics to understand health benefits of dietary fiber supplementation.
Institute:Stanford University
Last Name:Lancaster
First Name:Samuel
Address:240 Pasteur Dr, BMI bldg 4400, Stanford California, 94305
Email:slancast@stanford.edu
Phone:6126004033

Subject:

Subject ID:SU002601
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Fiber Timepoint Sex
SA25137841Arabinoxylan 10 F
SA25137930Arabinoxylan 10 F
SA25138024Arabinoxylan 10 F
SA25138195Arabinoxylan 10 F
SA251382185Arabinoxylan 10 F
SA251383297Arabinoxylan 10 F
SA251384209Arabinoxylan 10 F
SA25138517Arabinoxylan 10 F
SA25138696Arabinoxylan 10 F
SA251387179Arabinoxylan 10 F
SA2513886Arabinoxylan 10 F
SA251389226Arabinoxylan 10 M
SA25139039Arabinoxylan 10 M
SA251391204Arabinoxylan 10 M
SA251392132Arabinoxylan 10 M
SA251393228Arabinoxylan 10 M
SA251394106Arabinoxylan 10 M
SA2513952Arabinoxylan 10 M
SA25139644Arabinoxylan 10 M
SA25139763Arabinoxylan 20 F
SA251398136Arabinoxylan 20 F
SA251399218Arabinoxylan 20 F
SA251400314Arabinoxylan 20 F
SA251401327Arabinoxylan 20 F
SA251402262Arabinoxylan 20 F
SA251403244Arabinoxylan 20 F
SA251404173Arabinoxylan 20 F
SA251405149Arabinoxylan 20 F
SA2514065Arabinoxylan 20 F
SA251407295Arabinoxylan 20 M
SA251408164Arabinoxylan 20 M
SA251409272Arabinoxylan 20 M
SA251410176Arabinoxylan 20 M
SA25141114Arabinoxylan 20 M
SA251412139Arabinoxylan 20 M
SA251413311Arabinoxylan 20 M
SA25141411Arabinoxylan 20 M
SA251415231Arabinoxylan 30 F
SA251416276Arabinoxylan 30 F
SA251417183Arabinoxylan 30 F
SA251418284Arabinoxylan 30 F
SA25141980Arabinoxylan 30 F
SA251420102Arabinoxylan 30 F
SA251421215Arabinoxylan 30 F
SA25142254Arabinoxylan 30 F
SA251423275Arabinoxylan 30 F
SA25142461Arabinoxylan 30 F
SA251425155Arabinoxylan 30 M
SA251426300Arabinoxylan 30 M
SA25142784Arabinoxylan 30 M
SA251428165Arabinoxylan 30 M
SA251429343Arabinoxylan 30 M
SA251430238Arabinoxylan 30 M
SA251431206Arabinoxylan 30 M
SA251432250Arabinoxylan 30 M
SA251433153Arabinoxylan Baseline F
SA251434192Arabinoxylan Baseline F
SA251435128Arabinoxylan Baseline F
SA251436211Arabinoxylan Baseline F
SA251437222Arabinoxylan Baseline F
SA251438328Arabinoxylan Baseline F
SA25143971Arabinoxylan Baseline F
SA25144055Arabinoxylan Baseline F
SA251441126Arabinoxylan Baseline F
SA251442116Arabinoxylan Baseline F
SA25144345Arabinoxylan Baseline M
SA251444287Arabinoxylan Baseline M
SA25144558Arabinoxylan Baseline M
SA251446245Arabinoxylan Baseline M
SA251447345Arabinoxylan Baseline M
SA251448320Arabinoxylan Baseline M
SA251449154Arabinoxylan Baseline M
SA251450335Arabinoxylan Baseline M
SA25145148Arabinoxylan Baseline M
SA251452279Arabinoxylan Month 1 M
SA251453158Arabinoxylan Month 1 M
SA251454325Arabinoxylan Month 2 M
SA251455263Arabinoxylan Month 2 M
SA251456273Arabinoxylan Month 3 M
SA251457271Arabinoxylan Month 3 M
SA25145887Arabinoxylan Washout D10 F
SA251459249Arabinoxylan Washout D10 F
SA251460348Arabinoxylan Washout D10 F
SA251461101Arabinoxylan Washout D10 F
SA251462180Arabinoxylan Washout D10 F
SA251463234Arabinoxylan Washout D10 F
SA251464170Arabinoxylan Washout D10 F
SA251465347Arabinoxylan Washout D10 F
SA25146626Arabinoxylan Washout D10 F
SA251467135Arabinoxylan Washout D10 F
SA251468137Arabinoxylan Washout D10 M
SA251469243Arabinoxylan Washout D10 M
SA251470292Arabinoxylan Washout D10 M
SA25147188Arabinoxylan Washout D10 M
SA251472354Arabinoxylan Washout D10 M
SA251473349Arabinoxylan Washout D10 M
SA25147451Arabinoxylan Washout D10 M
SA251475144Arabinoxylan Washout D30 M
SA251476264Arabinoxylan Washout D3 F
SA251477117Arabinoxylan Washout D3 F
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Collection:

Collection ID:CO002594
Collection Summary:The study is a longitudinal, randomized crossover design in which 18 consented participants (8 men and 10 women) had their diets periodically supplemented with two fibers, arabinoxylan (AX) and long-chain inulin, and a mixture of fibers consisting of equal parts AX, LCI, acacia gum, glucomannans, and resistant starch. Participants were randomized to consume either AX or LCI first, and the mixed fibers were always administered last. For each of the fiber cycles, blood, urine and stool samples were collected at seven timepoints: baseline, end of week one, end of week two, end of week three, day 3 after end of supplementation and day 10 after end of supplementation. Blood was fractionated into plasma, serum and peripheral blood mononucleotide cells (PBMCs). Metabolomics was performed on the plasma fraction of the blood. Once all samples were in the correct aliquots, they were stored at -80C. Samples were only thawed when prepared for analysis for each of the respective omics assay which were all performed within 5 years of collecting the samples.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR002613
Treatment Summary:Participants went through 3 cycles of fiber supplementation, each cycle was three weeks long with weekly increasing doses of 10 g/day during the first week, 20g/day during the second week and 30 g/day during the third week. Randomized for the first two cycles, fibers tested were chicory inulin (99%>5 dp; range 2-60dp; average >23 dp) and arabinoxylan (psyllium husks powder Now Foods) and a mix of 5 fibers during the third cycle. The fiber mix included equal amounts of inulin, arabinoxylan, glucomannan (Now Foods), resistant starch (Hi Maize from Honeyville), and acacia fiber (Now Foods). Washout period between the cycles was from 6-10 weeks. Fiber was provided in 10 g sachets and participants were instructed to resuspend content of the sachet in at least 8 oz of water and drink one with breakfast for the first week, one with breakfast and one with dinner during the second week, and one with each meal (breakfast, lunch and dinner) during the third week.

Sample Preparation:

Sampleprep ID:SP002607
Sampleprep Summary:We performed an untargeted metabolomics using a platform, previously described in Contrepois et al., 2015 (Contrepois et al., 2015) to profile plasma extracted metabolites. Samples were thawed and 100 μL of plasma was transferred into a 2mL Protein Lobind Eppendorf tube. In order to precipitate and remove proteins, 400 μL of 1:1:1 methanol:acetonitrile:acetone solution, including 17 internal standards to control for extraction efficiency and evaluate LC-MS performance, was added to each plasma sample while on a cold plate. Samples were placed on the vortex shaker for 15 minutes at 4C then placed at -20C for two hours to allow for sufficient protein precipitation. Samples were centrifuged at 10,000 rpm for 10 min at 4C and the supernatant (metabolite extract) from each sample was carefully removed and placed in a new 2mL Protein Lobind Eppendorf tube. Samples were placed in the turbovap, evaporated to dryness under nitrogen and stored at -80C. Before analysis on the MS, samples were reconstituted in 100 μL 1:1 methanol:water solution and vortexed for 30s, placed in a bath sonicator for 30s and incubated on ice for 30s. This process was repeated 3 times for all samples and were centrifuged at 10,000 rpm for 10 min at 4C. The supernatant of each of these was then transferred to MS tubes and stored at -20C until ran on the mass spectrometer.

Combined analysis:

Analysis ID AN004115 AN004116 AN004117 AN004118
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish Thermo Dionex Ultimate 3000 RS Thermo Dionex Ultimate 3000 RS
Column SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um) SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um) Agilent Zorbax SBaq (2.1 x 50 mm, 1.8 um) Agilent Zorbax SBaq (2.1 x 50 mm, 1.8 um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Area Area Area Area

Chromatography:

Chromatography ID:CH003049
Chromatography Summary:HILIC experiments were performed using a ZIC-HILIC column 2.1x100 mm, 3.5μm, 200Å (Merck Millipore) and mobile phase solvents consisting of 10mM ammonium acetate in 50/50 acetonitrile/water (A) and 10 mM ammonium acetate in 95/5 acetonitrile/water (B).(Contrepois et al., 2015)
Instrument Name:Thermo Vanquish
Column Name:SeQuant ZIC-HILIC (100 x 2.1mm, 3.5um)
Column Temperature:40
Flow Gradient:The gradient profile used was 99%B for 2 minutes, 99-1% B over 15 minutes, 1%B for 3 minutes. 99%B for 5 minutes.
Flow Rate:.5 ml/min
Solvent A:10mM ammonium acetate in 50/50 acetonitrile/water
Solvent B:10 mM ammonium acetate in 95/5 acetonitrile/water
Chromatography Type:HILIC
  
Chromatography ID:CH003050
Chromatography Summary:RPLC experiments were performed using a Zorbax SBaq column 2.1 x 50 mm, 1.8 μm, 100Å (Agilent Technologies) and mobile phase solvents consisting of 0.06% acetic acid in water (A) and 0.06% acetic acid in methanol (B). (Contrepois et al., 2015)
Instrument Name:Thermo Dionex Ultimate 3000 RS
Column Name:Agilent Zorbax SBaq (2.1 x 50 mm, 1.8 um)
Column Temperature:60
Flow Gradient:The gradient profile used was 1% B for 1 minute, 1%-80% B over 8 minutes, 80% B for 3 minutes, 1% B for 5 minutes.
Flow Rate:.6ml/min
Solvent A:0.06% acetic acid in water
Solvent B:0.06% acetic acid in methanol
Chromatography Type:Reversed phase

MS:

MS ID:MS003862
Analysis ID:AN004115
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw data were imported into Progenesis QI 2.3 software (Water, Milford, MA, USA) to align and quantify chromatographic peaks. Data from all 4 acquisition modes (HILIC positive, HILIC negative, RPLC positive, RPLC negative) were processed independently. Using in house R code, we 1) removed noise, 2) imputed data and 3) adjusted for MS drift with time using the LOESS normalization method on pooled QCs injected every 10 injections in the sequence. We used MetID and our MS/MS data to identify 12740 metabolites with confidence levels ranging from 1-3, where 1 matches MS/MS, retention time and m/z from standards on our platform (843 metabolites), 2 has MS/MS and m/z matches from a database (395 metabolites), and 3 matches the m/z of a database (11,502).
Ion Mode:POSITIVE
  
MS ID:MS003863
Analysis ID:AN004116
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw data were imported into Progenesis QI 2.3 software (Water, Milford, MA, USA) to align and quantify chromatographic peaks. Data from all 4 acquisition modes (HILIC positive, HILIC negative, RPLC positive, RPLC negative) were processed independently. Using in house R code, we 1) removed noise, 2) imputed data and 3) adjusted for MS drift with time using the LOESS normalization method on pooled QCs injected every 10 injections in the sequence. We used MetID and our MS/MS data to identify 12740 metabolites with confidence levels ranging from 1-3, where 1 matches MS/MS, retention time and m/z from standards on our platform (843 metabolites), 2 has MS/MS and m/z matches from a database (395 metabolites), and 3 matches the m/z of a database (11,502).
Ion Mode:NEGATIVE
  
MS ID:MS003864
Analysis ID:AN004117
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw data were imported into Progenesis QI 2.3 software (Water, Milford, MA, USA) to align and quantify chromatographic peaks. Data from all 4 acquisition modes (HILIC positive, HILIC negative, RPLC positive, RPLC negative) were processed independently. Using in house R code, we 1) removed noise, 2) imputed data and 3) adjusted for MS drift with time using the LOESS normalization method on pooled QCs injected every 10 injections in the sequence. We used MetID and our MS/MS data to identify 12740 metabolites with confidence levels ranging from 1-3, where 1 matches MS/MS, retention time and m/z from standards on our platform (843 metabolites), 2 has MS/MS and m/z matches from a database (395 metabolites), and 3 matches the m/z of a database (11,502).
Ion Mode:POSITIVE
  
MS ID:MS003865
Analysis ID:AN004118
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Raw data were imported into Progenesis QI 2.3 software (Water, Milford, MA, USA) to align and quantify chromatographic peaks. Data from all 4 acquisition modes (HILIC positive, HILIC negative, RPLC positive, RPLC negative) were processed independently. Using in house R code, we 1) removed noise, 2) imputed data and 3) adjusted for MS drift with time using the LOESS normalization method on pooled QCs injected every 10 injections in the sequence. We used MetID and our MS/MS data to identify 12740 metabolites with confidence levels ranging from 1-3, where 1 matches MS/MS, retention time and m/z from standards on our platform (843 metabolites), 2 has MS/MS and m/z matches from a database (395 metabolites), and 3 matches the m/z of a database (11,502).
Ion Mode:NEGATIVE
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