Summary of Study ST002073

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.

Study ID	ST002073
Study Title	Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device
Study Summary	15 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.
Institute	University of California, Davis
Last Name	Folz
First Name	Jake
Address	451 Health Sciences Drive
Email	jfolz@ucdavis.edu
Phone	(530) 752-8129
Submit Date	2022-02-01
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2022-12-15
Release Version	1

Select appropriate tab below to view additional metadata details:

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:	SU002156
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
SA194809	BileAcid_LI_022421_Blank11	Blank
SA194810	BileAcid_LI_022421_Blank10	Blank
SA194811	BileAcid_LI_022421_Blank09	Blank
SA194812	BileAcid_LI_022421_Blank12	Blank
SA194813	BileAcid_LI_022421_Blank08	Blank
SA194814	BileAcid_LI_022421_Blank15	Blank
SA194815	BileAcid_LI_022421_Blank13	Blank
SA194816	BileAcid_LI_022421_Blank16	Blank
SA194817	BileAcid_LI_022421_Blank07	Blank
SA194818	BileAcid_LI_022421_Blank02	Blank
SA194819	BileAcid_LI_022421_Blank01	Blank
SA194820	BileAcid_LI_022421_Blank03	Blank
SA194821	BileAcid_LI_022421_Blank04	Blank
SA194822	BileAcid_LI_022421_Blank06	Blank
SA194823	BileAcid_LI_022421_Blank05	Blank
SA194824	BileAcid_HI_022421_Blank01	Blank
SA194825	BileAcid_LI_022421_Blank14	Blank
SA194826	BileAcid_HI_022421_Blank08	Blank
SA194827	BileAcid_HI_022421_Blank09	Blank
SA194828	BileAcid_HI_022421_Blank07	Blank
SA194829	BileAcid_HI_022421_Blank06	Blank
SA194830	BileAcid_HI_022421_Blank04	Blank
SA194831	BileAcid_HI_022421_Blank05	Blank
SA194832	BileAcid_HI_022421_Blank02	Blank
SA194833	BileAcid_HI_022421_Blank11	Blank
SA194834	BileAcid_HI_022421_Blank15	Blank
SA194835	BileAcid_HI_022421_Blank16	Blank
SA194836	BileAcid_HI_022421_Blank14	Blank
SA194837	BileAcid_HI_022421_Blank13	Blank
SA194838	BileAcid_HI_022421_Blank12	Blank
SA194839	BileAcid_HI_022421_Blank03	Blank
SA194840	BileAcid_HI_022421_Blank10	Blank
SA194841	BileAcid_HI_022421_1546	Capsule Type 1
SA194842	BileAcid_HI_022421_1945	Capsule Type 1
SA194843	BileAcid_LI_022421_1936	Capsule Type 1
SA194844	BileAcid_HI_022421_1949	Capsule Type 1
SA194845	BileAcid_LI_022421_1437	Capsule Type 1
SA194846	BileAcid_HI_022421_1940	Capsule Type 1
SA194847	BileAcid_LI_022421_1436	Capsule Type 1
SA194848	BileAcid_HI_022421_1936	Capsule Type 1
SA194849	BileAcid_LI_022421_1973	Capsule Type 1
SA194850	BileAcid_LI_022421_1940	Capsule Type 1
SA194851	BileAcid_LI_022421_1932	Capsule Type 1
SA194852	BileAcid_HI_022421_1953	Capsule Type 1
SA194853	BileAcid_HI_022421_1973	Capsule Type 1
SA194854	BileAcid_LI_022421_1920	Capsule Type 1
SA194855	BileAcid_LI_022421_1442	Capsule Type 1
SA194856	BileAcid_HI_022421_1978	Capsule Type 1
SA194857	BileAcid_HI_022421_1970	Capsule Type 1
SA194858	BileAcid_LI_022421_1924	Capsule Type 1
SA194859	BileAcid_HI_022421_1957	Capsule Type 1
SA194860	BileAcid_LI_022421_1929	Capsule Type 1
SA194861	BileAcid_HI_022421_1962	Capsule Type 1
SA194862	BileAcid_HI_022421_1966	Capsule Type 1
SA194863	BileAcid_HI_022421_1550	Capsule Type 1
SA194864	BileAcid_LI_022421_1970	Capsule Type 1
SA194865	BileAcid_HI_022421_1906	Capsule Type 1
SA194866	BileAcid_HI_022421_1902	Capsule Type 1
SA194867	BileAcid_LI_022421_1962	Capsule Type 1
SA194868	BileAcid_HI_022421_1898	Capsule Type 1
SA194869	BileAcid_LI_022421_1917	Capsule Type 1
SA194870	BileAcid_LI_022421_1434	Capsule Type 1
SA194871	BileAcid_LI_022421_1953	Capsule Type 1
SA194872	BileAcid_HI_022421_1917	Capsule Type 1
SA194873	BileAcid_LI_022421_1957	Capsule Type 1
SA194874	BileAcid_HI_022421_1909	Capsule Type 1
SA194875	BileAcid_HI_022421_1897	Capsule Type 1
SA194876	BileAcid_LI_022421_1949	Capsule Type 1
SA194877	BileAcid_HI_022421_1558	Capsule Type 1
SA194878	BileAcid_LI_022421_1966	Capsule Type 1
SA194879	BileAcid_HI_022421_1932	Capsule Type 1
SA194880	BileAcid_LI_022421_1944	Capsule Type 1
SA194881	BileAcid_LI_022421_1945	Capsule Type 1
SA194882	BileAcid_HI_022421_1929	Capsule Type 1
SA194883	BileAcid_HI_022421_1924	Capsule Type 1
SA194884	BileAcid_LI_022421_1435	Capsule Type 1
SA194885	BileAcid_HI_022421_1561	Capsule Type 1
SA194886	BileAcid_HI_022421_1559	Capsule Type 1
SA194887	BileAcid_HI_022421_1914	Capsule Type 1
SA194888	BileAcid_LI_022421_1898	Capsule Type 1
SA194889	BileAcid_LI_022421_1533	Capsule Type 1
SA194890	BileAcid_LI_022421_1466	Capsule Type 1
SA194891	BileAcid_LI_022421_1530	Capsule Type 1
SA194892	BileAcid_LI_022421_1526	Capsule Type 1
SA194893	BileAcid_LI_022421_1538	Capsule Type 1
SA194894	BileAcid_LI_022421_1542	Capsule Type 1
SA194895	BileAcid_LI_022421_1458	Capsule Type 1
SA194896	BileAcid_LI_022421_1550	Capsule Type 1
SA194897	BileAcid_LI_022421_1546	Capsule Type 1
SA194898	BileAcid_LI_022421_1462	Capsule Type 1
SA194899	BileAcid_LI_022421_1522	Capsule Type 1
SA194900	BileAcid_LI_022421_1470	Capsule Type 1
SA194901	BileAcid_LI_022421_1498	Capsule Type 1
SA194902	BileAcid_LI_022421_1494	Capsule Type 1
SA194903	BileAcid_LI_022421_1491	Capsule Type 1
SA194904	BileAcid_LI_022421_1486	Capsule Type 1
SA194905	BileAcid_LI_022421_1479	Capsule Type 1
SA194906	BileAcid_LI_022421_1502	Capsule Type 1
SA194907	BileAcid_LI_022421_1475	Capsule Type 1
SA194908	BileAcid_LI_022421_1508	Capsule Type 1

Showing page 1 of 9 Results: 1 2 3 4 5 Next Last Showing results 1 to 100 of 818

Collection:

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:

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.

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 Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	Thermo TSQ Vantage
Ion Mode	NEGATIVE
Units	ng/mL

Chromatography:

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:

MS ID:	MS003147
Analysis ID:	AN003380
Instrument Name:	Thermo TSQ Vantage
Instrument Type:	Triple quadrupole
MS Type:	ESI
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.
Ion Mode:	NEGATIVE