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

> **NIH NIH R21** · TUFTS UNIVERSITY MEDFORD · 2021 · $159,895

## Abstract

ABSTRACT OF SUPPLEMENTAL RESEARCH
This proposal is submitted in response to PA-20-227 (Administrative Supplements for Research on Dietary
Supplements). The Specific Aims of parent award R21 AI144521 are (1) to design, fabricate and test micro-
engineered ingestible capsules for sampling the gastro-intestinal tract; (2) to test the capsules in pigs.
The parent project seeks to demonstrate the feasibility of non-invasively sampling the gastro-intestinal tract in
a realistic animal model and to validate the ingestible capsule technology. Non-invasive sampling of the
gastro-intestinal tract will advance the study of the intestinal microbiome and its beneficial functions. We are
seeking supplemental funding to leverage research conducted under the parent award to study the effect of
dietary supplements on the bacterial microbiota populating the gastro-intestinal tract. Although the intestinal
microbiota's response to various perturbations, like diet, antibiotics or inflammatory conditions has been
studied, the bulk of this research has been conducted in humans and rodents. For obvious reasons, most of
these studies rely on the analysis of fecal DNA and fecal metabolites, which do not closely mirror changes in
more proximal sections of the GI tract, like the jejunum, ileum and ascending colon. Supplemental funding
would allow us to: 1) increase the number of pigs to study the effect of 3 commonly used prebiotic
supplements (inulin, pectin, cellulose) on the microbiota populating different organs of the GI tract, 2) expand
the scope of the project beyond the bacterial microbiota to the intestinal epithelium and its transcriptional
response to diet. To non-invasively investigate the response of the intestinal epithelium to changes in diet, we
are proposing to use RNA-Seq to analyze the "exfoliome", i.e., the transcriptome of exfoliated epithelial cells
excreted in feces. To assess the quality of the exfoliome, we will compare exfoliome RNA-Seq data with RNA-
Seq data obtained from epithelial cells collected directly from different GI organs after the animal has been
sacrificed. The analysis of the pig intestinal exfoliome seeks to evaluate whether changes in enterocyte gene
expression are detectable non-invasively by sequencing fecal cDNA. Although supplementary experiments
expand the scope of the parent award to include dietary intervention, this research is not dependent on the
optimization of the ingestible capsule. Pigs used for testing the capsules will be leveraged to investigate the
following Supplemental Specific Aims: 1) to assess the impact of inulin, pectin and cellulose on the
bacterial microbiota sampled in vivo using an ingestible capsule and collected post-mortem from
different GI organs; 2) to apply RNA-Seq to evaluate the feasibility of characterizing the transcriptome
of exfoliated enterocytes from pigs fed control and test diet. Thus, supplemental experiments will use a
well-defined dietary intervention to expand the scope of the paren...

## Key facts

- **NIH application ID:** 10269448
- **Project number:** 3R21AI144521-02S1
- **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:** $159,895
- **Award type:** 3
- **Project period:** 2020-02-01 → 2024-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10269448

## Citation

> US National Institutes of Health, RePORTER application 10269448, Micro-engineered capsules for spatial sampling of microbiome in vivo (3R21AI144521-02S1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10269448. Licensed CC0.

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