Escherichia coli gene expression is influenced more by gut environmental changes from inflammation and microbiota modulation than by colitis severity

Modulation of the gut microbiota has emerged as a promising diagnostic and therapeutic approach for inflammatory bowel disease (IBD), which is characterizes by chronic relapse. Analysing gene expression in luminal bacteria helps monitor the gut environment and assess the effects of probiotics. However, the complexity of the microbiota poses significant challenges. In this study, we analysed the gene expression of Escherichia coli in the intestines of IBD mouse models in the context of a native gut microbiota. We employed a reporter E. coli expressing reverse transcriptase-Cas1 fusion protein and Cas2 to record transcript data on plasmids as short oligonucleotides. Gene expression profiles differed between IBD models and controls and varied with the type of inflammatory trigger and time point. However, pre-feeding Lactobacillus crispatus prior to IBD induction resulted in E. coli gene expression profiles resembling those of controls despite exacerbation of colitis. In conclusion, altered E. coli gene expression in the inflamed gut may reflect environmental changes driven by interactions between inflammation and the microbiota. These findings suggest that bacterial gene expression adapts dynamically to the gut environment, which is shaped by host inflammatory responses and the interactions with the microbiota. These results have implications for the development of non-invasive bacterial diagnostics for gut inflammation.