Summary of Study ST002075

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 PR001315. The data can be accessed directly via it's Project DOI: 10.21228/M8R11F 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 IDST002075
Study TitleProfiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device (Part 2)
Study Summary15 Subjects were sampled using ingestible sampling device. Device sampled regions of the small intestine depending on design of sampling device.
Institute
University of California, Davis
Last NameFolz
First NameJacob
Address451 Health Sciences Drive
Emailjfolz@ucdavis.edu
Phone(530) 752-8129
Submit Date2022-02-02
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-12-15
Release Version1
Jacob Folz Jacob Folz
https://dx.doi.org/10.21228/M8R11F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001315
Project DOI:doi: 10.21228/M8R11F
Project Title:Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device
Project Summary:15 human subjects were sampled using ingestible sampling device to sample different regions of the small intestine using different types of capsules (Capsule Type 1 to 4). Stool was also analyzed.
Institute:University of California, Davis
Last Name:Folz
First Name:Jacob
Address:451 Health Sciences Drive
Email:jfolz@ucdavis.edu
Phone:(530) 752-8129

Subject:

Subject ID:SU002158
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 Treatment
SA1959581978Capsule Type 1
SA1959591546Capsule Type 1
SA1959601475Capsule Type 1
SA1959611550Capsule Type 1
SA1959621479Capsule Type 1
SA1959631936Capsule Type 1
SA1959641486Capsule Type 1
SA1959651973Capsule Type 1
SA1959661542Capsule Type 1
SA1959671470Capsule Type 1
SA1959681932Capsule Type 1
SA1959691558Capsule Type 1
SA1959701458Capsule Type 1
SA1959711457Capsule Type 1
SA1959721559Capsule Type 1
SA1959731988Capsule Type 1
SA1959741462Capsule Type 1
SA1959751538Capsule Type 1
SA1959761466Capsule Type 1
SA1959771985Capsule Type 1
SA1959781982Capsule Type 1
SA1959791970Capsule Type 1
SA1959801507Capsule Type 1
SA1959811506Capsule Type 1
SA1959821526Capsule Type 1
SA1959831962Capsule Type 1
SA1959841508Capsule Type 1
SA1959851957Capsule Type 1
SA1959861953Capsule Type 1
SA1959871949Capsule Type 1
SA1959881522Capsule Type 1
SA1959891502Capsule Type 1
SA1959901945Capsule Type 1
SA1959911494Capsule Type 1
SA1959921491Capsule Type 1
SA1959931940Capsule Type 1
SA1959941533Capsule Type 1
SA1959951966Capsule Type 1
SA1959961944Capsule Type 1
SA1959971530Capsule Type 1
SA1959981498Capsule Type 1
SA1959991561Capsule Type 1
SA1960001929Capsule Type 1
SA1960011920Capsule Type 1
SA1960021909Capsule Type 1
SA1960032011Capsule Type 1
SA1960041425Capsule Type 1
SA1960051906Capsule Type 1
SA1960062008Capsule Type 1
SA1960071437Capsule Type 1
SA1960081436Capsule Type 1
SA1960091435Capsule Type 1
SA1960101917Capsule Type 1
SA1960112014Capsule Type 1
SA1960121417Capsule Type 1
SA1960132017Capsule Type 1
SA1960141414Capsule Type 1
SA1960151413Capsule Type 1
SA1960161418Capsule Type 1
SA1960171914Capsule Type 1
SA1960181422Capsule Type 1
SA1960192015Capsule Type 1
SA1960202016Capsule Type 1
SA1960212005Capsule Type 1
SA1960221434Capsule Type 1
SA1960231898Capsule Type 1
SA1960241897Capsule Type 1
SA1960252001Capsule Type 1
SA1960261442Capsule Type 1
SA1960271993Capsule Type 1
SA1960281902Capsule Type 1
SA1960291924Capsule Type 1
SA1960301997Capsule Type 1
SA1960311450Capsule Type 1
SA1960321446Capsule Type 1
SA1960331518Capsule Type 2
SA1960341555Capsule Type 2
SA1960351899Capsule Type 2
SA1960361527Capsule Type 2
SA1960371946Capsule Type 2
SA1960381520Capsule Type 2
SA1960391519Capsule Type 2
SA1960401915Capsule Type 2
SA1960411562Capsule Type 2
SA1960421523Capsule Type 2
SA1960431557Capsule Type 2
SA1960441925Capsule Type 2
SA1960451539Capsule Type 2
SA1960461933Capsule Type 2
SA1960471928Capsule Type 2
SA1960481937Capsule Type 2
SA1960491543Capsule Type 2
SA1960501921Capsule Type 2
SA1960511547Capsule Type 2
SA1960521537Capsule Type 2
SA1960531551Capsule Type 2
SA1960541531Capsule Type 2
SA1960551903Capsule Type 2
SA1960561918Capsule Type 2
SA1960571910Capsule Type 2
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Collection:

Collection ID:CO002151
Collection Summary:Fifteen healthy subjects were enrolled in this study, and each swallowed 17 devices over the course of three days. All 255 ingested devices were recovered, and no adverse events were reported during the study. Of the 255 ingested devices, 17 contained mainly gas. Ten of the 238 ingested devices that did not contain large amounts of gas provided samples with >0 ng of DNA . Saliva samples were collected after evening meals and immediately frozen. Every bowel movement during the study was immediately frozen by the subject at -20 °C. Subject 1 provided additional samples for assessment of replicability and blooming.
Sample Type:Intestine

Treatment:

Treatment ID:TR002170
Treatment Summary:The capsule sampling device (CapScan®, Envivo Bio Inc, San Carlos CA) consists of a one-way valve capping a hollow elastic bladder. The device is prepared for packaging by evacuating the elastic bladder, folding it in half, and packaging the folded device inside a dissolvable capsule measuring 6.5 mm in diameter×23 mm long, onto which an enteric coating is applied. The target pH was pH 6 for type 1 and type 2 capsules, and pH 7.5 for type 3 and type 4, with type 2 and type 4 having a thicker coating to result in delayed opening. The elastic bladder then unfolds and expands into a tube 6 mm in diameter and 33 mm long, thereby drawing in ~300 µL of gut luminal contents through the one-way valve. The one-way valve maintains the integrity of the sample collected inside the bladder as the device moves through the colon and is exposed to stool.

Sample Preparation:

Sampleprep ID:SP002164
Sampleprep Summary:Supernatants from intestinal samples were extracted using a modified 96-well plate biphasic extraction63. Samples in microcentrifuge tubes were thawed on ice and 10 µL were transferred to wells of a 2-mL polypropylene 96-well plate in a predetermined randomized order. A quality control (QC) sample consisteing of a pool of many intestinal samples from pilot studies was used to assess analytical variation. QC sample matrix (10 µL) and blanks (10 µL of LC-MS grade water) were included for every 10th sample. One hundred seventy microliters of methanol containing UltimateSPLASH Avanti Polar Lipids (Alabaster, Alabama) as an internal standard were added to each well. Then 490 µL of methyl-tert-butyl-ether (MTBE) containing internal standard Cholesterol Ester 22:1 were added to each well. Plates were sealed, vortexed vigorously for 30 s, and shaken on an orbital shaking plate for 5 min at 4 °C. The plate was unsealed and 150 µL of cold water were added to each well. Plates were re-sealed, vortexed vigorously for 30 s, and centrifuged for 12 min at 4000 rcf and 4 °C. From the top phase of the extraction wells, two aliquots of 180 µL each were transferred to new 96-well plates, and two aliquots of 70 µL each from the bottom phase were transferred to two other new 96-well plates. Plates were spun in a rotary vacuum until dry, sealed, and stored at -80 °C until LC-MS/MS analysis. One of the 96-well plates containing the aqueous phase of extract was dissolved in 35 µL of HILIC-run solvent (8:2 acetonitrile/ water, v/v). Five microliters were analyzed using non-targeted HILIC LC-MS/MS analysis. Immediately after HILIC analysis, the 96-well plates were spun in a rotary vacuum until dry, sealed, and stored at -80 °C until targeted bile acid analysis. Approximately 4±1 mg of wet stool were transferred to 2-mL microcentrifuge tubes. Twenty microliters of QC mix were added to microcentrifuge tubes for QC samples. Blank samples were generated using 20 µL of LC-MS grade water. To each tube, 225 µL of ice-cold methanol containing internal standards (as above) were added, followed by 750 µL of ice-cold MTBE with CE 22:1. Two 3-mm stainless-steel grinding beads were added to each tube and tubes were processed in a Geno/Grinder automated tissue homogenizer and cell lyser at 1500 rpm for 1 min. One hundred eighty-eight microliters of cold water were then added to each tube. Tubes were vortexed vigorously and centrifuged at 14,000 rcf for 2 min. Two aliquots of 180 µL each of the MTBE layer and two aliquots of 50 µL each of the lower layer were transferred to four 96-well plates, spun in a rotary vacuum until dry, sealed, and stored at -80 °C until analysis with the intestinal samples. Stool samples were analyzed using HILIC non-targeted LC-MS/MS and diluted in an identical manner to intestinal samples as described above. Stool samples were analyzed in a randomized order after intestinal samples.

Combined analysis:

Analysis ID AN003382
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Vanquish
Column Waters Acquity UPLC BEH amide,(150 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE
Units peak height

Chromatography:

Chromatography ID:CH002500
Chromatography Summary:Data acquisition : 3 µL sample aliquots were injected on a Waters Acquity UPLC BEH Amide column (150 mm length × 2.1 mm id; 1.7 μm particle size) maintained at 45°C. A Waters Acquity VanGuard BEH Amide pre-column (5 mm × 2.1 mm id; 1.7 μm particle size) was used as guard column. Mobile phase A was 100% LC-MS grade water with 10 mM ammonium formate and 0.125% formic acid and mobile phase B was 95:5 v/v acetonitrile:water with 10 mM ammonium formate and 0.125% formic acid. Gradient was started at 100% (B) for 2 min, 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min and isocratic until 16.75 min. The column flow was 0.4 mL/min. Vanquish UHPLC system (ThermoFisher Scientific) was used.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity UPLC BEH amide,(150 x 2.1mm,1.7um)
Flow Gradient:Gradient was started at 100% (B) for 2 min, 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min and isocratic until 16.75 min.
Flow Rate:0.4 mL/min
Solvent A:100% water; 0.125% formic acid; 10 mM ammonium formate
Solvent B:95% acetonitrile/5% water 0.125% formic acid; 10 mM ammonium formate
Chromatography Type:HILIC

MS:

MS ID:MS003149
Analysis ID:AN003382
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:A Thermo Q-Exactive HF Orbitrap MS instrument was operated in positive and negative ESI mdoes respectively with the following parameters: mass range 60−900 m/z; spray voltage 3.6kV (ESI+) and −3kV (ESI−), sheath gas (nitrogen) flow rate 60 units; auxiliary gas (nitrogen) flow rate 25 units, capillary temperature 320 ◦C, full scan MS1 mass resolving power 60,000, data-dependent MSMS (dd-MSMS) 4 scans per cycle, normalized collision energy at 20%, 30%, and 40%, dd-MSMS mass resolving power 15,000. Thermo Xcalibur 4.0.27.19 was used for data acquisition and analysis. Instruments was tuned and calibrated by manufacturer’s recommendations. MSDIAL was used for data processing. Conjugated bile acid peak height was converted to relative concentration in ng/mL by comparing to targeted bile acid dataset ST002073.
Ion Mode:POSITIVE
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