# Micro-engineered capsules for spatial sampling of microbiome in vivo

> **NIH NIH R21** · TUFTS UNIVERSITY MEDFORD · 2021 · $236,310

## Abstract

Summary
Background and rationale: We are proposing exploratory research to develop and test microengineered
ingestible capsules designed to sample the content of the gastro-intestinal (GI) tract. The GI tract is known to
harbor abundant and diverse microbial communities (microbiome or microbiota) adapted to different acidity,
oxygen tension, bile concentration and other conditions found in different organs. These microbes fulfill
important metabolic functions essential to digestion and to controlling immune functions of the host. Through
the production of metabolites, these microbial communities regulate the immune response and promote the
integrity of the epithelium. Abnormal (dysbiotic) microbiomes are known to be associated with certain
conditions such as inflammation and impaired resistance to enteric infections. High-throughput sequencing and
other advanced analytical techniques enable detailed analyses of complex environments as found in the GI
tract. In contrast to the rapid development of high-throughput sequencing and other omics technologies, our
ability to non-invasively sample the GI tract is unsatisfactory. Most research uses biomolecules extracted from
feces to infer the ecology of the small and large intestine and to detect enteric pathogens. We are proposing to
develop microengineered ingestible capsules designed to sample from specific locations in the GI tract.
Sampling will be controlled using wirelessly triggered thermally actuated microvalves made from paraffin wax.
Sampling will be achieved using an embedded passive osmotic pump capable of sampling at a rate of
100~300 µL/hr without the need for electrical power. External magnetic sensor array will enable tracking of the
capsule as it moves through the GI tract due to peristalsis.
Specific Aims: The research has two Specific Aims; 1) Design, manufacture and test in vitro and ex vivo micro-
engineered ingestible capsules. Ex vivo testing will be performed in intestinal organs dissected from weaned
pigs; 2) Using the pig as a model of the human GI tract, capsule designs meeting specific in vitro and ex vivo
performance criteria will be tested in vivo. Ribosomal RNA (16S) high-throughput sequencing will be used to
profile the bacterial communities sampled by the capsule. Comparing the make-up of sampled microbiota with
those collected post-euthanasia from different sections of the pig intestine will reveal the ability of the capsules
to sample the content of specific GI organs.
Innovation: The research we are proposing aims to develop a new research tool. If successful, the technology
will enable a novel approach to studying the physiology of the GI tract and its response to perturbation
triggered by enteric infections or other conditions. The technology will facilitate the analysis of gut content
collected from various organs in a non-invasive manner. It is anticipated that further development of this
technology will lead to clinical application with improved capabilities to d...

## Key facts

- **NIH application ID:** 10088394
- **Project number:** 5R21AI144521-02
- **Recipient organization:** TUFTS UNIVERSITY MEDFORD
- **Principal Investigator:** Sameer R Sonkusale
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $236,310
- **Award type:** 5
- **Project period:** 2020-02-01 → 2024-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10088394

## Citation

> US National Institutes of Health, RePORTER application 10088394, Micro-engineered capsules for spatial sampling of microbiome in vivo (5R21AI144521-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10088394. Licensed CC0.

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