Abstract

The human gut is a heterogeneous environment. Diseases like inflammatory bowel disease (IBD) modify the physical properties of the gut, such as osmolality. These changes are thus desirable biomarkers for personalized diagnosis and treatment. Current diagnostic tools are invasive and insufficient to precisely detect changes of the physical environment. Likewise, disease heterogeneity hinders final diagnosis, showing the importance of creating personalized and sensitive diagnostic tools. For these reasons, its necessary to develop clinically relevant technologies that can safely and accurately report on these physical changes across different regions of the human gut. Extensive research on the human microbiome has revealed that microbes are able to sense shifts in the gut’s physical properties, making them strong candidates to report on these novel biomarkers. Furthermore, advances in synthetic biology have allowed the creation of microbial whole-cell biosensors that robustly report disease biomarkers in the human gut. Therefore, this thesis shows the potential of the probiotic strain Escherichia coli Nissle 1917 (EcN) as a chassis for gut osmolality biosensors. Here, RNA-seq and differential gene expression analysis were used to filter and compare genes that strongly and exclusively respond to different osmolality levels relative to general stress conditions. It was found that five promoters met the conditions, nevertheless, there was cross-reactivity within levels of osmolality and with other general stress conditions. Interestingly, some of the selected promoters had not been shown to react to elevated osmolality conditions, hinting at differences between EcN and other E. coli strains. Based on this, further experimentation is necessary to validate the activity of these promoters in the conditions of interest. Taken together, this work provides a starting point for gut osmolality biosensors using the probiotic strain EcN, providing more options for building biosensors of gut biomarkers.