Multi-region sampling of the human small intestine using an ingestible device
Fu, B.; DeSchepper, L. B.; Sun, J.; McKeithen-Mead, S. A.; Kapili, B.; Ochoa-Andersen, P.; Spencer, S. P.; Fardeen, T.; Ricardo, M.; El Kamari, V.; Sinha, S.; Relman, D. A.; Grembi, J. A.; Shalon, D.; Estrela, S.; Huang, K. C.
Show abstract
The human small intestine (SI) plays a central role in nutrient processing, host-microbe interactions, and immune regulation, yet remains poorly characterized due to the lack of minimally disruptive sampling methods. Here, we present a protocol for deploying, recovering, and analyzing samples collected using an ingestible device that enables multi-region, lumen-targeted SI sampling during normal digestion. The device incorporates a ~30-cm collapsible tube wound into pH- or time-responsive layers that sequentially unfurl in situ, typically capturing three spatially ordered samples with high yield and reliable retrieval. This protocol outlines study design, participant handling, device recovery, contamination control, and standardized workflows for analyses, including cell quantification, culturomics, sequencing, and metabolomics. We further describe benchmarking approaches for evaluating spatial resolution and strategies for assay prioritization when sample volume is limiting. By reducing participant burden and facilitating integration with stool, saliva, and clinical metadata, this approach enables longitudinal and large-cohort studies linking SI microbial ecology and host physiology to human health.
Matching journals
The top 8 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Optimised methods for the targeted surveillance of extended-spectrum beta-lactamase producing Escherichia coli in human stool 94%
- High-throughput single-cell isolation of Bifidobacterium strains from the gut microbiome 94%
- Machine-learning based detection of adventitious microbes in T-cell therapy cultures using long read sequencing 94%
Similar papers in this journal
- Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling 94%
- A ligated intestinal loop mouse model protocol to study the interactions of Clostridioides difficile spores with the intestinal mucosa during aging. 93%
- High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing 92%
Similar papers in this journal
- Longitudinal and Quantitative Fecal Shedding Dynamics of SARS-CoV-2, Pepper Mild Mottle Virus and CrAssphage 94%
- Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation 93%
- Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria 92%
Similar papers in this journal
- Capturing actively produced microbial volatile organic compounds from human associated samples with vacuum assisted sorbent extraction 91%
- Mechanical Dissociation of Tissues for Single Cell Analysis Using a Simple Motorized Device 91%
- Application of monolayer graphene to cryo-electron microscopy grids for high-resolution structure determination 90%
Similar papers in this journal
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.