Bacterial evolution during chronic inflammation and its potential for ancestral state restorative therapy

Introduction

The inflammatory environment of the intestine during IBD imposes a selection pressure that markedly differs from a healthy intestine. In our project, we study bacterial evolution during chronic inflammation, focusing on the evolutionary dynamics of pathobionts in IBD. By combining advanced genomics, imaging, and culture-based microbiology, we explore how bacteria evolve in this context.

Our phase 2 work builds on the findings from the first funding phase, where we identified adaptive mutations in bacteria that confer a selective advantage in an inflamed environment. We made three key observations: (i) evolved bacteria became more susceptible to antibiotics, (ii) their metabolism changed, and (iii) their interactions with other cells were modified. In the current funding phase, we will investigate these changes in more detail.

Furthermore, we hypothesize that the fitness costs associated with adaptation to inflammation may be exploited in a treated, non-inflamed environment to eliminate inflammation-adapted lineages, benefiting IBD patients. Ancestral replacement therapy could be a promising novel therapeutic concept for the treatment of IBD. This approach involves reintroducing high-fitness ancestral strains into the gut during the remission phase to replace the evolved, inflammation-adapted variants, which have lower fitness in this environment.

Aims

Main aims of this project are

to explore antibiotic susceptibility of evolved variants,

target metabolism and localization of evolved variants through novel imaging techniques,

to study bacteria-bacteria interactions of evolved bacteria, and

to ultimately test ancestral replacement therapy as a novel therapeutic approach for IBD.

**Fig. 2:** *Main objectives and aims of the study*.

Outlook

In the long-term, we aim to further experimentally characterize evolution during inflammation in the complex communities of IBD patients. In particular, we aim to develop humanized gnotobiotic mouse models in order to test inflammation-adapted versus ancestral traits among the bacterial strains identified in our high-resolution metagenomic analyses. This will be used to perform first proof-of-principle preclinical trials for “ancestral replacement therapy” in IBD. We envision that the imaging methods that are explored in this project will be made available routinely to the entire RU.