Summary of Study ST002073

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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 IDST002073
Study TitleProfiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device
Study Summary15 human subjects were sample using an ingestible sampling device to target specific regions of the small intestine by using different capsule types (capsule types 1 to 4). Stool was also analyzed.
University of California, Davis
Last NameFolz
First NameJake
Address451 Health Sciences Drive
Phone(530) 752-8129
Submit Date2022-02-01
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-12-15
Release Version1
Jake Folz Jake Folz application/zip

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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
Phone:(530) 752-8129


Subject ID:SU002156
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female


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

mb_sample_id local_sample_id Treatment
SA194841BileAcid_HI_022421_1546Capsule Type 1
SA194842BileAcid_HI_022421_1945Capsule Type 1
SA194843BileAcid_LI_022421_1936Capsule Type 1
SA194844BileAcid_HI_022421_1949Capsule Type 1
SA194845BileAcid_LI_022421_1437Capsule Type 1
SA194846BileAcid_HI_022421_1940Capsule Type 1
SA194847BileAcid_LI_022421_1436Capsule Type 1
SA194848BileAcid_HI_022421_1936Capsule Type 1
SA194849BileAcid_LI_022421_1973Capsule Type 1
SA194850BileAcid_LI_022421_1940Capsule Type 1
SA194851BileAcid_LI_022421_1932Capsule Type 1
SA194852BileAcid_HI_022421_1953Capsule Type 1
SA194853BileAcid_HI_022421_1973Capsule Type 1
SA194854BileAcid_LI_022421_1920Capsule Type 1
SA194855BileAcid_LI_022421_1442Capsule Type 1
SA194856BileAcid_HI_022421_1978Capsule Type 1
SA194857BileAcid_HI_022421_1970Capsule Type 1
SA194858BileAcid_LI_022421_1924Capsule Type 1
SA194859BileAcid_HI_022421_1957Capsule Type 1
SA194860BileAcid_LI_022421_1929Capsule Type 1
SA194861BileAcid_HI_022421_1962Capsule Type 1
SA194862BileAcid_HI_022421_1966Capsule Type 1
SA194863BileAcid_HI_022421_1550Capsule Type 1
SA194864BileAcid_LI_022421_1970Capsule Type 1
SA194865BileAcid_HI_022421_1906Capsule Type 1
SA194866BileAcid_HI_022421_1902Capsule Type 1
SA194867BileAcid_LI_022421_1962Capsule Type 1
SA194868BileAcid_HI_022421_1898Capsule Type 1
SA194869BileAcid_LI_022421_1917Capsule Type 1
SA194870BileAcid_LI_022421_1434Capsule Type 1
SA194871BileAcid_LI_022421_1953Capsule Type 1
SA194872BileAcid_HI_022421_1917Capsule Type 1
SA194873BileAcid_LI_022421_1957Capsule Type 1
SA194874BileAcid_HI_022421_1909Capsule Type 1
SA194875BileAcid_HI_022421_1897Capsule Type 1
SA194876BileAcid_LI_022421_1949Capsule Type 1
SA194877BileAcid_HI_022421_1558Capsule Type 1
SA194878BileAcid_LI_022421_1966Capsule Type 1
SA194879BileAcid_HI_022421_1932Capsule Type 1
SA194880BileAcid_LI_022421_1944Capsule Type 1
SA194881BileAcid_LI_022421_1945Capsule Type 1
SA194882BileAcid_HI_022421_1929Capsule Type 1
SA194883BileAcid_HI_022421_1924Capsule Type 1
SA194884BileAcid_LI_022421_1435Capsule Type 1
SA194885BileAcid_HI_022421_1561Capsule Type 1
SA194886BileAcid_HI_022421_1559Capsule Type 1
SA194887BileAcid_HI_022421_1914Capsule Type 1
SA194888BileAcid_LI_022421_1898Capsule Type 1
SA194889BileAcid_LI_022421_1533Capsule Type 1
SA194890BileAcid_LI_022421_1466Capsule Type 1
SA194891BileAcid_LI_022421_1530Capsule Type 1
SA194892BileAcid_LI_022421_1526Capsule Type 1
SA194893BileAcid_LI_022421_1538Capsule Type 1
SA194894BileAcid_LI_022421_1542Capsule Type 1
SA194895BileAcid_LI_022421_1458Capsule Type 1
SA194896BileAcid_LI_022421_1550Capsule Type 1
SA194897BileAcid_LI_022421_1546Capsule Type 1
SA194898BileAcid_LI_022421_1462Capsule Type 1
SA194899BileAcid_LI_022421_1522Capsule Type 1
SA194900BileAcid_LI_022421_1470Capsule Type 1
SA194901BileAcid_LI_022421_1498Capsule Type 1
SA194902BileAcid_LI_022421_1494Capsule Type 1
SA194903BileAcid_LI_022421_1491Capsule Type 1
SA194904BileAcid_LI_022421_1486Capsule Type 1
SA194905BileAcid_LI_022421_1479Capsule Type 1
SA194906BileAcid_LI_022421_1502Capsule Type 1
SA194907BileAcid_LI_022421_1475Capsule Type 1
SA194908BileAcid_LI_022421_1508Capsule Type 1
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Collection ID:CO002149
Collection Summary:Fifteen healthy subjects were enrolled in this study, and each swallowed at least 17 devices over the course of three days. Capsules were retrieved from stool. Every bowel movement during the study was immediately frozen by the subject at -20 °C.
Sample Type:Intestine


Treatment ID:TR002168
Treatment Summary:Capsule types 1 to 4 were designed to sample the upper, middle, middle, and distal small intestine respectively. Stool samples were analyzed alongside samples from capsules.

Sample Preparation:

Sampleprep ID:SP002162
Sampleprep Summary:Supernatants from intestinal samples were extracted using a modified 96-well plate biphasic extraction. 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 consisting 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. Multiple dilutions were prepared for bile acid analysis as follows. The dried samples described above were dissolved in 60 µL of bile acid-run solvent (1:1 acetonitrile/ methanol (v/v) containing 6 isotopically labeled bile acid standards at 100 ng/mL) via 30 s of vortexing and 5 min of shaking on an orbital shaker. From this plate, 5 µL were transferred to a new 96-well plate and combined with 145 µL of bile acid-run solvent. Both dilutions were analyzed for all samples, and samples that still presented bile acids above the highest concentration of the standard curve (1500 ng/mL) were diluted 5:145 once more and re-analyzed. A 9-point standard curve that ranged from 0.2 ng/mL to 1500 ng/mL was used with all samples. The standard curve solutions were created by drying bile acid standard solutions to achieve the desired mass of bile acid standards and then dissolved in bile acid-run solvent. Three standard-curve concentration measurements were analyzed after every 20 samples during data acquisition along with one method blank. Approximately 4 mg (±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 AN003380
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Waters Acquity BEH C18 (100 x 2mm,1.7um)
MS instrument type Triple quadrupole
MS instrument name Thermo TSQ Vantage
Units ng/mL


Chromatography ID:CH002498
Chromatography Summary:Samples were analyzed using a Thermofisher Vanquish UHPLC system coupled to a Thermofisher TSQ Altis triple-quadrupole mass spectrometer. An Aquity BEH C18 column (1.7 µm, 2.1 mm×100 mm) with guard column Acquity BEH C18 (1.7 µm, 2.1 mm×5 mm) was used for chromatographic separation with mobile phases of A: LC-MS-grade water with 0.1% formic acid, and B: LC-MS-grade acetonitrile with 0.1% formic acid with a flow rate of 400 µL/min and column temperature of 50 °C. The gradient began at 20% B for 1 min, then shifted to 45% B between 1 and 11 min, then to 95% B between 11 and 14 min, then to 99% B between 14 and 14.5 min, 99% B was maintained until 15.5 min, then transitioned from 99% B to 20% B between 15.5 and 16.5 min, and maintained at 20% B until 18 min. Injection volume was 5 µL and MRM scans were collected for all bile acids and internal standards.
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH C18 (100 x 2mm,1.7um)
Column Temperature:50
Flow Gradient:The gradient began at 20% B for 1 min, then shifted to 45% B between 1 and 11 min, then to 95% B between 11 and 14 min, then to 99% B between 14 and 14.5 min, 99% B was maintained until 15.5 min, then transitioned from 99% B to 20% B between 15.5 and 16.5 min, and maintained at 20% B until 18 min.
Flow Rate:400 uL/min
Sample Injection:5 ul
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid
Chromatography Type:Reversed phase


MS ID:MS003147
Analysis ID:AN003380
Instrument Name:Thermo TSQ Vantage
Instrument Type:Triple quadrupole
MS Comments:MRM scans were imported to Skyline58 software. Skyline performed peak integration for all analytes with given mass transitions and retention time windows (Table S2). The chromatogram for each analyte was manually checked to confirm correct peak integration. Peak area was exported for all analytes. Bile acid chemical structures were removed if there was not a convincing chromatographic peak observed in ≥1 sample. The ratio of analyte to its closest eluting internal standard was calculated and used for quantification. A linear model was fitted to standard curve points for each bile acid (R2>0.995 for all bile acids) and the model was applied to all samples and blanks to calculate concentrations. The average concentration reported for method blanks was subtracted from sample concentrations. Since multiple dilutions were analyzed for each sample, the measurement closest to the center of the standard curve (750 ng/mL) was used. Zero values were imputed with a concentration value between 0.001 and 0.1 ng/mL. Concentrations were reported as ng/mL for intestinal sample liquid supernatant, and ng/g for wet stool.