Summary of Study ST002409

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 IDST002409
Study TitleSpatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS RP positive 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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Collection ID:CO002491
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