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), a condition marked by chronic relapse. Analysing gene expression in luminal bacteria helps monitor the gut environment and assess the probiotic effects. However, the complexity of the microbiota poses a challenge. We examined the gene expression of Escherichia coli in the intestines of IBD mouse models in the context of a native gut microbiota. We adopted 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 before IBD induction yielded E. coli gene expression profiles resembling controls despite worsened colitis. Conclusively, altered E. coli gene expression in the inflamed gut may reflect environmental changes driven by interactions between inflammation and microbiota. These findings suggest that bacterial gene expression adapts dynamically to the gut environment, which is shaped by host inflammatory responses and microbiota interactions. These results have implications for developing non-invasive diagnostic bacteria for gut inflammation.