Summary of Study ST002411

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 PR001549. The data can be accessed directly via it's Project DOI: 10.21228/M8G99R 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 IDST002411
Study TitleSpatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS RP 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.
University of California, Davis
Last NameFolz
First NameJake
Address1 Shields Ave
Submit Date2022-12-16
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-01-04
Release Version1
Jake Folz Jake Folz application/zip

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Treatment ID:TR002512
Treatment Summary:The capsule sampling device (CapScan®, Envivo® Bio Inc, San Carlos, CA) consists of a one-way valve capping a hollow elastic collection bladder5 . The device is prepared for packaging by evacuating the collection bladder, folding it in half, and packaging the folded device inside a dissolvable capsule measuring 6.5 mm in diameter and 23 mm in length, onto which an enteric coating is applied. The capsule and the enteric coating prevent contamination of the collection bladder from oral-pharyngeal and gastric microbes during ingestion. When the device reaches the target pH, the enteric coating and capsule disintegrate. The target pH is pH 5.5 for type 1, pH 6 for type 2, and pH 7.5 for type 3 and type 4, with type 4 also having a time-delay coating to bias collection toward the ascending colon. After the enteric coating disintegrates, the collection bladder unfolds and expands into a tube 6 mm in diameter and 33 mm in length, thereby drawing in up to 400 µL of gut luminal contents through the one-way valve. The one-way valve maintains the integrity of the sample collected inside the collection bladder as the device moves through the colon and is exposed to stool. In this study, subjects concurrently ingested sets of 4 capsules, each with distinct coatings to target the proximal to medial regions of the small intestine (coating types 1 and 2) and more distal regions (coating types 3 and 4). After sampling, the devices were passed in the stool into specimen-collection containers and immediately frozen. After completion of sampling, the stool was thawed, and the devices were retrieved by study staff. The elastic collection bladders were rinsed in 70% isopropyl alcohol and punctured with a sterile hypodermic needle attached to a 1-mL syringe for sample removal. Samples were transferred into microcentrifuge tubes and the pH was measured with an InLab Ultra Micro ISM pH probe (Mettler Toledo). A 40-µL aliquot was spun down for 3 min at 10,000 rcf, and its supernatant was used for metabolomics analysis. The rest of the sample was frozen until being thawed for DNA extraction.