# Microbial Engineering to Control the Structure and Function of the Gut Microbiome.

> **NIH NIH R35** · UNIVERSITY OF CHICAGO · 2023 · $410,000

## Abstract

Microbial Engineering to Control the Structure and Function of the Gut Microbiome
SUMMARY
The human microbiota, the collection of microbes that live on and in the body, is fully integrated with human
physiology and has been extensively implicated in health and disease. As with all microbial communities, the
summation of environmental, interbacterial, and interkingdom interactions governs both the composition and
function of the microbiota. To date, top-down approaches have been largely used to study microbiome
function, using multi-omics techniques to draw correlations between microbial taxa, genes, and metabolites
with functional properties in different environmental conditions. While these studies contribute a rich set of
hypotheses, bottom-up approaches are required to causally pinpoint the molecular mechanisms through which
microbes interact with their environment, one another, and the host. Synthesis of these mechanistic studies
can further enable predictive models that can be leveraged to engineer microbiomes. Through the
development and application of novel technologies, the research program described herein aims to predictively
engineer ecological responses and metabolic functions in the gut microbiome. A defined microbial community
that mirrors the phylogenetic and functional diversity of natural communities will be used as a testbed to model
the emergent phenomena that arise as a result of interbacterial interactions. Using inspiration from natural
microbial communities to fuel synthetic biology approaches, we will create new tools to allow for genetic
manipulation and expression control in previously intractable gut symbionts. These genetic tools will be applied
to link microbial genes and associated functions with emergent properties of microbial communities, including
resilience to environment perturbations and metabolic networks in the mouse gut. These studies will provide an
experimental framework to pursue investigations into the core functions that structure microbial communities
and to establish design rules for rational microbiome engineering.

## Key facts

- **NIH application ID:** 10677794
- **Project number:** 5R35GM147478-02
- **Recipient organization:** UNIVERSITY OF CHICAGO
- **Principal Investigator:** Mark Mimee
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $410,000
- **Award type:** 5
- **Project period:** 2022-08-05 → 2027-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10677794

## Citation

> US National Institutes of Health, RePORTER application 10677794, Microbial Engineering to Control the Structure and Function of the Gut Microbiome. (5R35GM147478-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10677794. Licensed CC0.

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