Transcriptional REGUlation as a mediator of bacterial interactions in the microBIOME

Introduction

Bacteria from the gut microbiota constantly interact with a range of abiotic and biotic factors. Perturbations in these factors, such as nutrient depletion or exposure to exogenous microbes, require specific bacterial responses that involve tightly controlled gene expression changes. However, the transcriptional regulation mechanisms promoting such gene expression changes remain poorly understood despite their importance.

Project Overview

REGUBIOME will characterize how responses to specific biotic and abiotic stimuli are regulated at the transcriptional level in two health-associated gut bacteria: one probiotic (Lacticaseibacillus rhamnosus) and one pathobiont (Fusobacterium nucleatum, previously linked to colorectal cancer).

Methodology

This project relies on combining experimental platforms of increasing complexity to systematically characterize the responses of these two bacteria to defined biotic and abiotic factors, and to evaluate how these responses impact host health.

High-Throughput Functional Screening Tool

1. I will develop a novel high-throughput functional screening tool, coupling:
   • CRISPR interference
   • Microfluidic platforms for single-cell isolation
   • Transcriptomic profiling of isolates

By applying this tool to in vitro monocultures, I will reconstruct the first-ever gene regulatory networks in these bacteria and identify mechanisms of response to different abiotic factors.

Microfluidic Co-Culturing

2. Microfluidic co-culturing of these two strains with multiple other bacteria, coupled with metatranscriptomic profiling, will reveal the regulatory mechanisms mediating the interactions with other microbiome members.

In Vivo Work

3. Lastly, in vivo work in mouse models will shed light on how the host colonic environment impacts gene expression in these health-associated bacteria.

Conclusion

Altogether, REGUBIOME will provide proof of the importance of gut bacterial gene regulation networks to host health. Besides, by uncovering gene regulatory mechanisms in microbiome bacteria, REGUBIOME will provide novel actionable targets for microbiota modulation strategies.