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MB Sample ID: SA240906
Local Sample ID: | 1470 |
Subject ID: | SU002496 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
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Subject:
Subject ID: | SU002496 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
1470 | SA240906 | FL030298 | Capsule Type 1 | Treatment |
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 |