Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device (Part 2)

ABSTRACT: 15 Subjects were sampled using ingestible sampling device. Device sampled regions of the small intestine depending on design of sampling device.

ORGANISM(S): Human Homo Sapiens

TISSUE(S): Intestine

SUBMITTER: Jacob Folz

PROVIDER: ST002075 | MetabolomicsWorkbench | Wed Feb 02 00:00:00 GMT 2022

REPOSITORIES: MetabolomicsWorkbench

ACCESS DATA

Json Xml

Similar Datasets

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device

Project description:15 human subjects were sample using an ingestible sampling device to target specific regions of the small intestine by using different capsule types (capsule types 1 to 4). Stool was also analyzed.

2022-02-01 | ST002073 | MetabolomicsWorkbench

Profiling of the human intestinal microbiome and bile acids under physiologic conditions using an ingestible sampling device

Project description:The spatiotemporal structure of the human microbiome, proteome, and metabolome reflects and determines regional intestinal physiology and may have implications for disease. Yet, we know little about the distribution of microbes, their environment, and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals. To address these deficiencies, we developed and evaluated a safe, ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion and maintains the viability of microbes from these locations. The collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses revealed significant differences between microbes, phages, host proteins, and metabolites present in the intestines versus stool. Certain microbial taxa and gene classes were differentially enriched, and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundancepredicted species that altered the bile acid pool through deconjugation. Furthermore,microbially conjugated bile acids displayed amino acid-dependent trends in concentration that were not apparent in stool. Overall, non-invasive longitudinal profilingof microbes, proteins, and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in humanphysiology and disease.

2023-01-18 | PXD038906 | Pride

Spatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS RP positive data)

Project description: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.

2022-12-16 | ST002409 | MetabolomicsWorkbench

Spatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS HILIC negative data)

2022-12-15 | ST002407 | MetabolomicsWorkbench

Spatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS RP negative data)

2022-12-16 | ST002411 | MetabolomicsWorkbench

experiment_pills_2

Project description:Ingestible Osmotic Pill for In-vivo Sampling of Gut Microbiome

| PRJEB32383 | ENA

experiment_pills

Project description:Ingestible Osmotic Pill for In-vivo Sampling of Gut Microbiome

| PRJEB30052 | ENA

RNA-seq data from submiligram porcine myocardial tissue before and after myocardial infarction

Project description:We have developed an endovascular micro-endomyocardial biopsy device (Micro-EMB) with an outer diameter of 0.4 mm in order to minimize procedural risk, sampling trauma, and increase sampling specificity compared to conventional EMB. Here, we have taken micro-EMB samples from swine myocardium before, during and after myocardial infarction to detect potential gene expression responses.

2021-04-13 | GSE164962 | GEO

RNA expression analysis in a multigeneration feeding study of OF1 outbred mice

Project description:To analyze the effect of different aliments, male OF1 mice were fed ad libitum with a custom-made diet containing 33% maize derived from three cultivars containing comparable nutritional values for multiple generations. To evaluate possible effects on the gene expression in the small intestine, the jejunum of nine randomly chosen males of the F3 was sampled at the age of 7 weeks. Note that the lack of information on the time of sampling or its randomization between the experimental groups limited the value of the internal microarray data set for the context originally addressed (diet).

2013-02-20 | GSE44396 | GEO

Endovascular Device for Endothelial Cell Sampling

Project description:We have developed an endovascular catheter-based device for sampling of the endothelium, intended for RNA-seq analysis. With an outer diameter of 0.23 mm it is capable of reaching peripheral vessels for endothelial sampling, and favourably compares to other approaches with stent retrievers or similar tools. Here, we have collected samples from liver and kidney vessels from swine and performed RNA-sequencing to validate the sample quality.

2022-08-21 | GSE197756 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data