Summary of Study ST002409

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 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.
Institute
University of California, Davis
Last NameFolz
First NameJake
Address1 Shields Ave
Emailjfolz@ucdavis.edu
Phone7155636311
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
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:SU002498
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
SA2412501978Capsule Type 1
SA2412511546Capsule Type 1
SA2412521475Capsule Type 1
SA2412531550Capsule Type 1
SA2412541479Capsule Type 1
SA2412551936Capsule Type 1
SA2412561486Capsule Type 1
SA2412571973Capsule Type 1
SA2412581542Capsule Type 1
SA2412591470Capsule Type 1
SA2412601932Capsule Type 1
SA2412611558Capsule Type 1
SA2412621458Capsule Type 1
SA2412631457Capsule Type 1
SA2412641559Capsule Type 1
SA2412651988Capsule Type 1
SA2412661462Capsule Type 1
SA2412671538Capsule Type 1
SA2412681466Capsule Type 1
SA2412691985Capsule Type 1
SA2412701982Capsule Type 1
SA2412711970Capsule Type 1
SA2412721507Capsule Type 1
SA2412731506Capsule Type 1
SA2412741526Capsule Type 1
SA2412751962Capsule Type 1
SA2412761508Capsule Type 1
SA2412771957Capsule Type 1
SA2412781953Capsule Type 1
SA2412791949Capsule Type 1
SA2412801522Capsule Type 1
SA2412811502Capsule Type 1
SA2412821945Capsule Type 1
SA2412831494Capsule Type 1
SA2412841491Capsule Type 1
SA2412851940Capsule Type 1
SA2412861533Capsule Type 1
SA2412871966Capsule Type 1
SA2412881944Capsule Type 1
SA2412891530Capsule Type 1
SA2412901498Capsule Type 1
SA2412911561Capsule Type 1
SA2412921929Capsule Type 1
SA2412931920Capsule Type 1
SA2412941909Capsule Type 1
SA2412952011Capsule Type 1
SA2412961425Capsule Type 1
SA2412971906Capsule Type 1
SA2412982008Capsule Type 1
SA2412991437Capsule Type 1
SA2413001436Capsule Type 1
SA2413011435Capsule Type 1
SA2413021917Capsule Type 1
SA2413032014Capsule Type 1
SA2413041417Capsule Type 1
SA2413052017Capsule Type 1
SA2413061414Capsule Type 1
SA2413071413Capsule Type 1
SA2413081418Capsule Type 1
SA2413091914Capsule Type 1
SA2413101422Capsule Type 1
SA2413112015Capsule Type 1
SA2413122016Capsule Type 1
SA2413132005Capsule Type 1
SA2413141434Capsule Type 1
SA2413151898Capsule Type 1
SA2413161897Capsule Type 1
SA2413172001Capsule Type 1
SA2413181442Capsule Type 1
SA2413191993Capsule Type 1
SA2413201902Capsule Type 1
SA2413211924Capsule Type 1
SA2413221997Capsule Type 1
SA2413231450Capsule Type 1
SA2413241446Capsule Type 1
SA2413251518Capsule Type 2
SA2413261555Capsule Type 2
SA2413271899Capsule Type 2
SA2413281527Capsule Type 2
SA2413291946Capsule Type 2
SA2413301520Capsule Type 2
SA2413311519Capsule Type 2
SA2413321915Capsule Type 2
SA2413331562Capsule Type 2
SA2413341523Capsule Type 2
SA2413351557Capsule Type 2
SA2413361925Capsule Type 2
SA2413371539Capsule Type 2
SA2413381933Capsule Type 2
SA2413391928Capsule Type 2
SA2413401937Capsule Type 2
SA2413411543Capsule Type 2
SA2413421921Capsule Type 2
SA2413431547Capsule Type 2
SA2413441537Capsule Type 2
SA2413451551Capsule Type 2
SA2413461531Capsule Type 2
SA2413471903Capsule Type 2
SA2413481918Capsule Type 2
SA2413491910Capsule Type 2
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Collection:

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

Treatment:

Treatment ID:TR002510
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:SP002504
Sampleprep Summary:Extraction is carried out using a bi-phasic solvent system of cold methanol, methyl tert-butyl ether (MTBE), and water. In more detail, cold methanol (225 µL is added to a 5mg tissue sample aliquot, which is placed into a 1.5 mL Eppendorf tube. Then, 750 µL of cold MTBE is added, followed by vortexing for 10 s. and shaking for 6 min. at 4ºC. Phase separation is induced by adding 188 µL of mass spec-grade water. After vortexing for 20 s. the sample is centrifuged at 14,000 rpm for 2 min. The upper organic phase is collected in two 300 µL aliquots for lipid analysis polar layer is collected in two 125 µL aliquots for HILIC analysis. One is stored at -20ºC as a backup and the other is evaporated to dryness in a SpeedVac. Dried extracts are resuspended in acetonitrile.

Combined analysis:

Analysis ID AN003926
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column CSH C18 column (100 mm length × 2.1 mm i.d.; 1.7-µm particle size)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF-X Orbitrap
Ion Mode POSITIVE
Units peak height

Chromatography:

Chromatography ID:CH002905
Instrument Name:Thermo Vanquish
Column Name:CSH C18 column (100 mm length × 2.1 mm i.d.; 1.7-µm particle size)
Column Temperature:65
Flow Gradient:15% B from 0 to 0.6 min, 30% B by 2 min, 48% B by 2.5 min, 82% B by 11 min, 99% B from 11.5 to 12 min, and 15% B from 12.1 to 14.2 min
Flow Rate:600 ul/min
Solvent A:90% acetonitrile/10% water; 0.1% formic acid; 10 mM ammonium formate
Solvent B:80% isopropanol/20% acetonitrile; 0.1% formic acid; 10 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS003664
Analysis ID:AN003926
Instrument Name:Thermo Q Exactive HF-X Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:HESI source conditions are as follows: sheath gas flow 55, auxiliary gas flow 15, sweep gas flow 3, capillary temperature 275°C, S-lens RF level 50, auxiliary gas heater temperature 450 °C, and needle voltage 3500 V and -3500 V for positive and negative ionization mode, respectively. DDA MS/MS spectra were acquired for the top 4 ions. MS scans were collected with 60k resolving power from 120-1700 m/z, AGC target of 106 ions, and maximum accumulation time of 100 ms. MS/MS spectra were collected with 15k resolving power, 1 Da isolation window, normalized collision energy of 20, 30, 60, 2 s dynamic exclusion window, 8×103 AGC target, and 50 ms maximum accumulation time. Spectra were stored in centroid mode. Three rounds of iterative exclusion MS/MS were acquired for each pooled QC sample.
Ion Mode:POSITIVE
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