Patients with inflammatory bowel disease (IBD) are highly susceptible to gastro-intestinal bacterial pathogens because of aberrant immune responses and therefore rely on frequent antibiotic courses throughout their illness. As a result, IBD prognosis often declines over time due to an increase in recalcitrant organisms that are antibiotic resistant and/or have increased virulence traits. These genetically-encoded traits are often carried on mobile genetic elements and exchanged between bacteria through the process of horizontal gene transfer. We have developed new methods to study this process in the microbiome. We propose to evaluate the link between inflammation and HGT in both humans and mouse models of colitis and identify interventions that may mitigate the emergence of antibiotic-resistant or recalcitrant infections.