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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Collection ID:CO002493
Collection Summary:Fifteen healthy subjects were enrolled in this study, and each swallowed at least 17 devices over the course of three days. Sample size was chosen to assess general variation across human intestinal tracts. Daily instructions included the following guidelines: record all foods and time they were consumed throughout the day; if you work out, do so in the morning; eat breakfast and lunch as usual; swallow a set of four devices three hours after lunch with up to 2/3 cup water; do not eat or drink anything for at least two hours after swallowing devices; if hungry after two hours, snack lightly (up to 200 calories); do not drink any caffeinated beverages after lunch until the next morning; collect all stool starting six hours after swallowing this set of devices until 48 hours after swallowing the next set of devices; eat dinner as usual at least six hours after lunch; swallow a set of four CapScan devices three hours after dinner with 2/3 cup water; after swallowing this set, do not eat or drink anything until the morning. Alcohol consumption and diet contents were not restricted. All ingested devices were recovered, and no adverse events were reported during the study. In total 274 capsule devices provided sufficient material for metabolomics analysis, and 225 provided sufficient volume or number of sequencing reads (>2500) for genomic analysis. Every bowel movement during the study was immediately frozen by the subject at -20 °C. Subject 1 provided additional samples for assessment of replicability and blooming. A total of 333 intestinal, and stool samples were analyzed with metabolomics methods.
Sample Type:Intestine