Summary of Study ST002180

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 IDST002180
Study TitleGlobal, distinctive and personal changes in molecular and microbial profiles induced by specific fibers in humans (Targeted)
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 Date2022-03-18
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-07-15
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:SU002266
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

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

mb_sample_id local_sample_id Fiber Timepoint Sex
SA20927641Arabinoxylan 10 F
SA20927730Arabinoxylan 10 F
SA20927824Arabinoxylan 10 F
SA20927995Arabinoxylan 10 F
SA209280185Arabinoxylan 10 F
SA209281297Arabinoxylan 10 F
SA209282209Arabinoxylan 10 F
SA20928317Arabinoxylan 10 F
SA20928496Arabinoxylan 10 F
SA209285179Arabinoxylan 10 F
SA2092866Arabinoxylan 10 F
SA209287226Arabinoxylan 10 M
SA20928839Arabinoxylan 10 M
SA209289204Arabinoxylan 10 M
SA209290132Arabinoxylan 10 M
SA209291228Arabinoxylan 10 M
SA209292106Arabinoxylan 10 M
SA2092932Arabinoxylan 10 M
SA20929444Arabinoxylan 10 M
SA20929563Arabinoxylan 20 F
SA209296136Arabinoxylan 20 F
SA209297218Arabinoxylan 20 F
SA209298314Arabinoxylan 20 F
SA209299327Arabinoxylan 20 F
SA209300262Arabinoxylan 20 F
SA209301244Arabinoxylan 20 F
SA209302173Arabinoxylan 20 F
SA209303149Arabinoxylan 20 F
SA2093045Arabinoxylan 20 F
SA209305295Arabinoxylan 20 M
SA209306164Arabinoxylan 20 M
SA209307272Arabinoxylan 20 M
SA209308176Arabinoxylan 20 M
SA20930914Arabinoxylan 20 M
SA209310139Arabinoxylan 20 M
SA209311311Arabinoxylan 20 M
SA20931211Arabinoxylan 20 M
SA209313231Arabinoxylan 30 F
SA209314276Arabinoxylan 30 F
SA209315183Arabinoxylan 30 F
SA209316284Arabinoxylan 30 F
SA20931780Arabinoxylan 30 F
SA209318102Arabinoxylan 30 F
SA209319215Arabinoxylan 30 F
SA20932054Arabinoxylan 30 F
SA209321275Arabinoxylan 30 F
SA20932261Arabinoxylan 30 F
SA209323155Arabinoxylan 30 M
SA209324300Arabinoxylan 30 M
SA20932584Arabinoxylan 30 M
SA209326165Arabinoxylan 30 M
SA209327343Arabinoxylan 30 M
SA209328238Arabinoxylan 30 M
SA209329206Arabinoxylan 30 M
SA209330250Arabinoxylan 30 M
SA209331153Arabinoxylan Baseline F
SA209332192Arabinoxylan Baseline F
SA209333128Arabinoxylan Baseline F
SA209334211Arabinoxylan Baseline F
SA209335222Arabinoxylan Baseline F
SA209336328Arabinoxylan Baseline F
SA20933771Arabinoxylan Baseline F
SA20933855Arabinoxylan Baseline F
SA209339126Arabinoxylan Baseline F
SA209340116Arabinoxylan Baseline F
SA20934145Arabinoxylan Baseline M
SA209342287Arabinoxylan Baseline M
SA20934358Arabinoxylan Baseline M
SA209344245Arabinoxylan Baseline M
SA209345345Arabinoxylan Baseline M
SA209346320Arabinoxylan Baseline M
SA209347154Arabinoxylan Baseline M
SA209348335Arabinoxylan Baseline M
SA20934948Arabinoxylan Baseline M
SA209350279Arabinoxylan Month 1 M
SA209351158Arabinoxylan Month 1 M
SA209352325Arabinoxylan Month 2 M
SA209353263Arabinoxylan Month 2 M
SA209354273Arabinoxylan Month 3 M
SA209355271Arabinoxylan Month 3 M
SA20935687Arabinoxylan Washout D10 F
SA209357249Arabinoxylan Washout D10 F
SA209358348Arabinoxylan Washout D10 F
SA209359101Arabinoxylan Washout D10 F
SA209360180Arabinoxylan Washout D10 F
SA209361234Arabinoxylan Washout D10 F
SA209362170Arabinoxylan Washout D10 F
SA209363347Arabinoxylan Washout D10 F
SA20936426Arabinoxylan Washout D10 F
SA209365135Arabinoxylan Washout D10 F
SA209366137Arabinoxylan Washout D10 M
SA209367243Arabinoxylan Washout D10 M
SA209368292Arabinoxylan Washout D10 M
SA20936988Arabinoxylan Washout D10 M
SA209370354Arabinoxylan Washout D10 M
SA209371349Arabinoxylan Washout D10 M
SA20937251Arabinoxylan Washout D10 M
SA209373144Arabinoxylan Washout D30 M
SA209374264Arabinoxylan Washout D3 F
SA209375117Arabinoxylan Washout D3 F
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Collection:

Collection ID:CO002259
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). Lipidomics 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:TR002278
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:SP002272
Sampleprep Summary:Lipids were extracted using a modified biphasic separation protocol with methyl tertiary-butyl ether (MTBE)(Matyash et al., 2008). Pipetting was performed using Rainin BioClean Ultra pipette tips. In 2 ml Protein LoBind Eppendorf tubes (cat# 022431102), 40 μl of neat plasma were mixed with 260 μl ice-cold MeOH and briefly vortexed to denature proteins. Next, 40 μL of an isotopically labeled standard lipid stock that approximates the blood plasma lipid composition was added to each sample (SCIEX, cat# 5040156, LPISTDKIT-101), which was prepared according to the instruction in Lipidomics Workflow Manager (LWM). The mix was briefly vortexed. Next, 1000 μL ice-cold MTBE was added after which samples were vortexed for 10 seconds followed by shaking at 4ºC for 30 min. Phase separation was induced by adding 250 μL of HPLC grade water. Samples were subsequently vortexed for 60 seconds. Next, samples were centrifuged at 16,000 g for 5 min at room temperature. 750 μL of the upper organic (MTBE) phase were transferred to a new 2 mL tube. This MTBE lipid fraction was dried down in a nitrogen blower for about 2 hours. For storage at -20ºC, 200 μL of MeOH was added to dried-down samples.

Combined analysis:

Analysis ID AN003570 AN003571
Analysis type MS MS
Chromatography type Flow induction analysis Flow induction analysis
Chromatography system Shimazdu LC-30AD Shimazdu LC-30AD
Column none none
MS Type ESI ESI
MS instrument type QTRAP QTRAP
MS instrument name ABI Sciex 5500 QTrap ABI Sciex 5500 QTrap
Ion Mode UNSPECIFIED UNSPECIFIED
Units nmol/g nmol/g

Chromatography:

Chromatography ID:CH002640
Chromatography Summary:The Lipidyzer (SCIEX), a QTRAP system with SelexION ion mobility, was used for targeted profiling as described previously (Contrepois et al., 2018).DMS separates lipids based on the principle that each lipid class has a different head group dipole moment and thus mobility in the DMS aperture (Schneider et al., 2010).
Instrument Name:Shimazdu LC-30AD
Column Name:none
Flow Rate:8 μL/min
Solvent A:50% dichloromethane/50% methanol; 10 mM ammonium acetate
Chromatography Type:Flow induction analysis

MS:

MS ID:MS003327
Analysis ID:AN003570
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:QTRAP
MS Type:ESI
MS Comments:The Lipidyzer (SCIEX), a QTRAP system with SelexION ion mobility, was used for targeted profiling as described previously (Contrepois et al., 2018). In brief, flow injection analysis was performed with a LC-30AD (Shimazdu) operating at 8 μL/min (50 μL injection volume) using a running solution that consisted of 10 mM ammonium acetate in dichloromethane:MeOH (50:50). DMS separates lipids based on the principle that each lipid class has a different head group dipole moment and thus mobility in the DMS aperture (Schneider et al., 2010). The lipid molecular species were identified and quantified using multiple reaction monitoring (MRM) and positive/negative switching. Two acquisition methods were employed covering 10 lipid classes across positive and negative mode. Method 1 had SelexION voltages turned on while Method 2 had SelexION voltages turned off. Method 1 employed an isocratic flow of 8 μL/min for 7.9 min, followed by a 2 minute wash at 30 μL/min. Method 2 employed an isocratic flow of 8 μL/min for 6 minutes, followed by 2 minute wash at 30 μL/min. Each lipid was acquired throughout 20 cycles. Lipid classes targeted in positive mode: SM, DAG, CE, CER, and TAG. Lipid classes targeted in negative mode: LPE, LPC, PC, PE, and FFA. Lipids were quantified using the LWM software, which compares endogenous lipids to the known concentrations of structurally most similar spiked-in lipid standards and reports all detected lipids in nmol/g. Data analysis. Data were downloaded from the Lipidyzer LWM and merged and processed in R. In brief, Excel files (LWM output) were read with the “loadWorkbook” package. From all samples, lipid concentrations determined in a blank control (sample processed in parallel without the addition of cells) were subtracted to correct for background signals. The data set was further filtered accepting only lipid species that detected in at least 25% of all samples. Missing values were imputed by drawing from a random distribution.
Ion Mode:UNSPECIFIED
  
MS ID:MS003328
Analysis ID:AN003571
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:QTRAP
MS Type:ESI
MS Comments:The Lipidyzer (SCIEX), a QTRAP system with SelexION ion mobility, was used for targeted profiling as described previously (Contrepois et al., 2018). In brief, flow injection analysis was performed with a LC-30AD (Shimazdu) operating at 8 μL/min (50 μL injection volume) using a running solution that consisted of 10 mM ammonium acetate in dichloromethane:MeOH (50:50). DMS separates lipids based on the principle that each lipid class has a different head group dipole moment and thus mobility in the DMS aperture (Schneider et al., 2010). The lipid molecular species were identified and quantified using multiple reaction monitoring (MRM) and positive/negative switching. Two acquisition methods were employed covering 10 lipid classes across positive and negative mode. Method 1 had SelexION voltages turned on while Method 2 had SelexION voltages turned off. Method 1 employed an isocratic flow of 8 μL/min for 7.9 min, followed by a 2 minute wash at 30 μL/min. Method 2 employed an isocratic flow of 8 μL/min for 6 minutes, followed by 2 minute wash at 30 μL/min. Each lipid was acquired throughout 20 cycles. Lipid classes targeted in positive mode: SM, DAG, CE, CER, and TAG. Lipid classes targeted in negative mode: LPE, LPC, PC, PE, and FFA. Lipids were quantified using the LWM software, which compares endogenous lipids to the known concentrations of structurally most similar spiked-in lipid standards and reports all detected lipids in nmol/g. Data analysis. Data were downloaded from the Lipidyzer LWM and merged and processed in R. In brief, Excel files (LWM output) were read with the “loadWorkbook” package. From all samples, lipid concentrations determined in a blank control (sample processed in parallel without the addition of cells) were subtracted to correct for background signals. The data set was further filtered accepting only lipid species that detected in at least 25% of all samples. Missing values were imputed by drawing from a random distribution.
Ion Mode:UNSPECIFIED
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