# Tunable therapeutic modulation of the gut microbiome by engineered probiotics

> **NIH NIH R01** · WASHINGTON UNIVERSITY · 2021 · $691,776

## Abstract

ABSTRACT
Engineered probiotics represent a powerful tool with which to ‘knock-in’ gene functions and pathways into the
gut microbiome, alter the structure of the gut microbiome to test hypotheses regarding community architecture
and disease, and to deliver therapeutics. However, known probiotics fail to persist in the gut due to colonization
resistance by the gut microbiota, limiting their value as either research or therapeutic tools. Further, controlled
delivery of therapeutics and other gene products by engineered probiotics is limited by a lack of robust and
tunable synthetic biology tools for the complex in vivo environment. The rationale for the proposed research is
that the promise of probiotic therapies is currently limited by poor persistence and a lack of robust engineering
tools. The central motivation for this proposal is to understand the host and microbial mechanisms governing
probiotic integration and develop tools to engineer probiotic therapies. Guided by strong preliminary data, this
interdisciplinary proposal will pursue three specific aims: to 1) identify determinants of probiotic colonization in
the gut, 2) design and optimize gut-relevant biosensor and expression circuits, and 3) demonstrate the efficacy
of in vivo delivery of a phenylketonuria (PKU) therapeutic by an enhanced probiotic colonizer.
 The first aim of this proposal is to optimize and identify mechanisms of probiotic colonization, testing the
hypothesis that probiotic gut colonization is enhanced and tunable by modulating expression of
colonization factors selected from fecal metagenomes. In particular, we will select for durable colonizers
from probiotics expressing an exhaustive combinatorial library of colonization factors driven by in vivo
characterized promoters. The second aim is to develop synthetic biology tools for tunable gene expression
control and biocontainment of engineered probiotics, testing the hypothesis that combining sensors for
temperature, pH, bile acids, and short chain fatty acids will enable spatial control over gene expression
along the gastrointestinal tract. The third aim is to demonstrate that the engineered probiotic chassis can
reliably deliver therapeutics to the gut, testing the hypothesis that our engineered probiotic can stably
deliver phenylalanine-ammonia lyase (Pal2) in a murine model of PKU to decrease serum phenylalanine.
 This proposal is innovative because our integrated and complementary research team will improve
understanding of probiotic therapies at both basic science and translational levels. The proposed experiments
are significant in that they will 1) improve our understanding of the genetic elements and microbial interactions
governing gastrointestinal colonization, 2) generate and optimize synthetic biology tools for in vivo circuit control
that will be modular and widely applicable to probiotic engineering, and 3) explore the efficacy of an alternative,
continual-delivery therapeutic for PKU. The proposed rese...

## Key facts

- **NIH application ID:** 10207474
- **Project number:** 5R01AT009741-04
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** Gautam Dantas
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $691,776
- **Award type:** 5
- **Project period:** 2018-08-10 → 2023-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10207474

## Citation

> US National Institutes of Health, RePORTER application 10207474, Tunable therapeutic modulation of the gut microbiome by engineered probiotics (5R01AT009741-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10207474. Licensed CC0.

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