Summary of Study ST002407

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 PR001549. The data can be accessed directly via it's Project DOI: 10.21228/M8G99R This work is supported by NIH grant, U2C- DK119886.

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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 IDST002407
Study TitleSpatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS HILIC negative data)
Study SummaryMost utilization of human diets occurs in the small intestine, which remains largely unstudied. Here, we used a novel non-invasive, ingestible sampling device to probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy subjects. We analyzed 274 intestinal samples and 60 corresponding stool homogenates by combining five metabolomics assays and 16S rRNA sequencing. We identified 1,909 metabolites, including sulfonolipids and novel bile acids. Stool and intestinal metabolomes differed dramatically. Food metabolites displayed known differences and trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract, and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites accounted for the largest inter-subject differences. Interestingly, subjects exhibited large variation in levels of bioactive fatty acid esters of hydroxy fatty acids (FAHFAs) and sulfonolipids. Two subjects who had taken antibiotics within 6 months prior to sampling showed markedly different patterns in these and other microbially related metabolites; from this variation, we identified Blautia species as most likely to be involved in FAHFA metabolism. Thus, in vivo sampling of the human small intestine under physiologic conditions can reveal links between diet, host and microbial metabolism.
Institute
University of California, Davis
Last NameFolz
First NameJake
Address1440 Wake Forest Drive, Davis, CA, 95616, USA
Emailjfolz@ucdavis.edu
Phone7155636311
Submit Date2022-12-15
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-01-04
Release Version1
Jake Folz Jake Folz
https://dx.doi.org/10.21228/M8G99R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001549
Project DOI:doi: 10.21228/M8G99R
Project Title:Spatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract
Project Summary:Most utilization of human diets occurs in the small intestine, which remains largely unstudied. Here, we used a novel non-invasive, ingestible sampling device to probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy subjects. We analyzed 274 intestinal samples and 60 corresponding stool homogenates by combining five metabolomics assays and 16S rRNA sequencing. We identified 1,909 metabolites, including sulfonolipids and novel bile acids. Stool and intestinal metabolomes differed dramatically. Food metabolites displayed known differences and trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract, and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites accounted for the largest inter-subject differences. Interestingly, subjects exhibited large variation in levels of bioactive fatty acid esters of hydroxy fatty acids (FAHFAs) and sulfonolipids. Two subjects who had taken antibiotics within 6 months prior to sampling showed markedly different patterns in these and other microbially related metabolites; from this variation, we identified Blautia species as most likely to be involved in FAHFA metabolism. Thus, in vivo sampling of the human small intestine under physiologic conditions can reveal links between diet, host and microbial metabolism.
Institute:University of California, Davis
Last Name:Folz
First Name:Jake
Address:1 Shields Ave
Email:jfolz@ucdavis.edu
Phone:7155636311

Subject:

Subject ID:SU002496
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Treatment
SA2408971978Capsule Type 1
SA2408981546Capsule Type 1
SA2408991475Capsule Type 1
SA2409001550Capsule Type 1
SA2409011479Capsule Type 1
SA2409021936Capsule Type 1
SA2409031486Capsule Type 1
SA2409041973Capsule Type 1
SA2409051542Capsule Type 1
SA2409061470Capsule Type 1
SA2409071932Capsule Type 1
SA2409081558Capsule Type 1
SA2409091458Capsule Type 1
SA2409101457Capsule Type 1
SA2409111559Capsule Type 1
SA2409121988Capsule Type 1
SA2409131462Capsule Type 1
SA2409141538Capsule Type 1
SA2409151466Capsule Type 1
SA2409161985Capsule Type 1
SA2409171982Capsule Type 1
SA2409181970Capsule Type 1
SA2409191507Capsule Type 1
SA2409201506Capsule Type 1
SA2409211526Capsule Type 1
SA2409221962Capsule Type 1
SA2409231508Capsule Type 1
SA2409241957Capsule Type 1
SA2409251953Capsule Type 1
SA2409261949Capsule Type 1
SA2409271522Capsule Type 1
SA2409281502Capsule Type 1
SA2409291945Capsule Type 1
SA2409301494Capsule Type 1
SA2409311491Capsule Type 1
SA2409321940Capsule Type 1
SA2409331533Capsule Type 1
SA2409341966Capsule Type 1
SA2409351944Capsule Type 1
SA2409361530Capsule Type 1
SA2409371498Capsule Type 1
SA2409381561Capsule Type 1
SA2409391929Capsule Type 1
SA2409401920Capsule Type 1
SA2409411909Capsule Type 1
SA2409422011Capsule Type 1
SA2409431425Capsule Type 1
SA2409441906Capsule Type 1
SA2409452008Capsule Type 1
SA2409461437Capsule Type 1
SA2409471436Capsule Type 1
SA2409481435Capsule Type 1
SA2409491917Capsule Type 1
SA2409502014Capsule Type 1
SA2409511417Capsule Type 1
SA2409522017Capsule Type 1
SA2409531414Capsule Type 1
SA2409541413Capsule Type 1
SA2409551418Capsule Type 1
SA2409561914Capsule Type 1
SA2409571422Capsule Type 1
SA2409582015Capsule Type 1
SA2409592016Capsule Type 1
SA2409602005Capsule Type 1
SA2409611434Capsule Type 1
SA2409621898Capsule Type 1
SA2409631897Capsule Type 1
SA2409642001Capsule Type 1
SA2409651442Capsule Type 1
SA2409661993Capsule Type 1
SA2409671902Capsule Type 1
SA2409681924Capsule Type 1
SA2409691997Capsule Type 1
SA2409701450Capsule Type 1
SA2409711446Capsule Type 1
SA2409721518Capsule Type 2
SA2409731555Capsule Type 2
SA2409741899Capsule Type 2
SA2409751527Capsule Type 2
SA2409761946Capsule Type 2
SA2409771520Capsule Type 2
SA2409781519Capsule Type 2
SA2409791915Capsule Type 2
SA2409801562Capsule Type 2
SA2409811523Capsule Type 2
SA2409821557Capsule Type 2
SA2409831925Capsule Type 2
SA2409841539Capsule Type 2
SA2409851933Capsule Type 2
SA2409861928Capsule Type 2
SA2409871937Capsule Type 2
SA2409881543Capsule Type 2
SA2409891921Capsule Type 2
SA2409901547Capsule Type 2
SA2409911537Capsule Type 2
SA2409921551Capsule Type 2
SA2409931531Capsule Type 2
SA2409941903Capsule Type 2
SA2409951918Capsule Type 2
SA2409961910Capsule Type 2
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Collection:

Collection ID:CO002489
Collection Summary:The CapScan sampling devices (Envivo Bio Inc, San Carlos CA) were constructed with a coating designed to dissolve at a specific pH to take advantage of the pH gradient of the human intestine. After the coating dissolved, a compressed elastic bladder expanded to pull in 400 µL of luminal contents through a oneway valve. This valve remained sealed until recovery from stool. The pH coating of each capsule type Page 13/30 dissolved at pH 5.5 (type 1), 6 (type 2), or 7.5 (types 3 and 4). Type 4 also had a time delay to target the distal ileum or ascending colon. Four sampling capsules were swallowed 3 hours after lunch or dinner across 2 days (Figure 1A). Subjects were instructed to maintain their normal diet, record the time of any food or drink consumed over the testing period, and to not consume caffeinated beverages after lunch on sampling days. Detailed guidelines are provided in Supplemental Material. Stool was collected and immediately frozen at -20 °C until stool was thawed and filled capsule devices were retrieved. Liquid sample was removed from each bladder using a hypodermic needle. An aliquot of each sample was used for 16S rRNA gene sequencing while another aliquot was centrifuged at 10,000 rcf for 3 min, and the supernatant was used for metabolomics analysis.
Sample Type:Intestine

Treatment:

Treatment ID:TR002508
Treatment Summary:We aimed to comprehensively study metabolomic differences among luminal samples from the upper intestinal tract of 15 healthy subjects to better understand the extent of spatial and temporal variation and to gauge the prospects of integrating metabolome and microbiome data. Volunteers swallowed sets of 4 sampling devices per sampling timepoint. These ingestible sampling devices were comprised of a collapsed collection bladder capped by a one-way valve in a capsule treated with pH-sensitive coatings. The four types of capsules differed only in their enteric coating which dissolved at pH 5.5 (capsule 1), pH 6 (capsule 2), and pH 7.5 (capsules 3 and 4) (Figure 1A). The thickness and pH-responsiveness of the coating enabled sampling at specific locations of the intestinal tract after entry into the duodenum. The devices did not contain any electronics beyond a passive radio frequency identification chip for tracking purposes. Once the coatings dissolved, an elastic collection bladder expanded and collected up to 400 µL of luminal contents through vacuum suction. The one-way valve prevented loss of sample and contamination from downstream fluids. Stool samples were frozen at -20 °C and all capsules were recovered from the stool prior to analysis. Liquid contents were retrieved from capsules using hypodermic needles. Aliquots of the raw sample were used for 16S ribosomal RNA microbiome analyses and the supernatants from centrifugated samples were used for metabolomic studies.

Sample Preparation:

Sampleprep ID:SP002502
Sampleprep Summary:For all non-targeted analyses, 10 µL of intestinal lumen samples were subjected to a modified biphasic water, methanol, and methyl tert-butyl ether extraction 78 to separate polar and non-polar metabolites. The polar and non-polar phases were divided into multiple aliquots in 96-well plates, dried by rotary vacuum, and frozen until further analysis. Homogenized stool samples were prepared using an analogous extraction procedure with modification for bead-homogenization and extraction in microcentrifuge tubes to account for the solid nature of the sample. Targeted bile acid analysis was performed using aqueous phase of the described biphasic extraction. Targeted SCFA analysis used an acidified water and MTBE extraction followed by MTBSTFA derivatization 79 . For detailed sample preparation methods see Supplemental Material.

Combined analysis:

Analysis ID AN003924
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Vanquish
Column HILIC BEH Amide
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap
Ion Mode NEGATIVE
Units Peak Height

Chromatography:

Chromatography ID:CH002903
Instrument Name:Thermo Vanquish
Column Name:HILIC BEH Amide
Column Temperature:45
Flow Gradient:100%B to 30% B over 15 minutes
Flow Rate:400 ul/min
Solvent A:100% water; 0.1% formic acid 10mM ammonium formate
Solvent B:95% acetonitrile/5% water; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:HILIC

MS:

MS ID:MS003662
Analysis ID:AN003924
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:See associated paper
Ion Mode:NEGATIVE
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