NSF-BSF: Developing organ-on-chip predictive models to effectively target the bacterial component of inflammatory bowel diseases

This project will investigate the role of gut microorganisms in controlling human health by focusing on microorganism interactions with the gut sugar polymer mucin. Mucin is a component of gut mucus and is very important for maintaining the integrity of the gut barrier between microorganisms and the human host. The human body needs beneficial microorganisms to help digest food and to develop the immune system, but it must keep both beneficial and pathogenic, or disease-causing, bacteria out of the bloodstream. Previous research indicates that beneficial and pathogenic bacteria secrete products to change the oxidation/reduction state of mucin. Therefore, this work will use miniaturized models of synthetic gut bacterial communities to explore gut modifications by beneficial and pathogenic bacteria in the presence of a collection of bacteria from healthy mice. The approach includes an electrochemical mucin-on-chip model and elimination of pathogens using engineered, beneficial bacteria. This work will enhance the understanding of how human health is dependent on a healthy gut microbial community and identify methods to correct gut communities that are causing disease. This project aims to investigate the uncharacterized role of invasive, pathogenic Escherichia coli (E. coli) strains in the distribution of mucin, a layer of heavily glycosylated proteins essential for maintaining the integrity of the gut barrier, and its involvement in inflammatory bowel diseases (IBD). Recent research indicates that alterations in mucin glycosylation may provide a means to differentiate between Crohn's disease and other forms of IBD. Preliminary results show that pathogenic E. coli reduces mucin while the microbiome acts as an oxidative agent. Building on these results and methodologies, a robust mucin-on-chip model will be used to investigate the role of this bacterium in the gut, both with and without an intact microbiome. Three complimentary aims will be completed to achieve mechanistic insights into mucin-bacteria interactions. Aim 1 will utilize the mucin-on-chip system as an engineered model for biofilm-mucin interactions and their outcomes. Interactions between E. coli and mucin will be identified using a specialized chip system to analyze the redox state of mucin and biofilm characteristics of various E. coli strains, compared with several probiotic strains. Aim 2 will Investigate sequence-based RNA silencing of bacterial antitoxins in mucin-associated biofilms and its impact on the fitness of the mucin and the microbial counterpart. Sequence-based interventions utilizing toxin-antitoxin (TA) systems to control the viability of E. coli before, during and after the colonization of mucin and accurately probe the response of the tissue will be developed. In Aim 3, predictor models for microbiome intervention on mucin will be engineered. To analyze the contribution of E. coli in disturbing mucin homeostasis within a complicated microbiome, the most efficient sequence-based therapies developed above in a three‐dimensional (3D) tissue model will be used. If successful, this project will provide methods for engineering microbial biofilms to treat gastrointestinal (GI) disorders. Educational activities include outreach to middle and high school science teachers to implement age-appropriate teaching materials about the microbiology of the GI tract, and the creation of an undergraduate unit operations laboratory to demonstrate a multi-species GI tract biofilm. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.