Deciphering host-gut microbiota spatio-functional plasticity in inflammation

Introduction

Over the past two decades, gut bacteria have emerged as major regulators of human health. The focus in the field thus far has been on bacterial taxonomy, with their spatial organization and functionality largely overlooked. Crohn's disease (CD) vividly portrays this spatiofunctional dimension, as it features patches of gut inflammation (skip lesions) surrounded by uninflamed regions in the same host with a clear demarcation but unknown cause.

Preliminary Data

Our preliminary data demonstrate host-microbe functional feedback loops in which bacterial strains can adapt and modify their immunomodulatory functions in response to the host. Moreover, we find functional alterations in gut bacteria of IBD patients. Thus, we hypothesize that bacterial spatio-functionality can be largely affected by host physiology and, in turn, modulate the pathophysiological state, creating a functional feedback loop.

Research Proposal

We propose to study bacterial spatiofunctional plasticity and mechanisms of host-microbe interactions in CD, and their potential causal effects on inflammation, combining microbiology, immunology, and systems biology approaches. We intend to focus on three independent yet complementary aims:

1. Characterize host-microbe spatio-functional alterations in skip lesions and assess their potential causal effects on inflammation.
2. Decipher the functional and molecular mechanisms of host-microbe feedback loops in healthy and inflamed intestines.
3. Develop a toolbox for high-resolution functional analyses of gut bacteria directly in their natural environments.

Significance of the Study

This study will address, for the first time, bacterial functional plasticity in response to host inflammation, unveiling the phenomena, its mechanism of action, and potential causal effects on gut inflammation. Such understanding can shift our perception of microbiota-host interactions, may explain contradictions in the field, point to novel contributing factors to CD and related disorders, and guide future translational studies.