Using conjugative elements to manipulate bacterial communities

With the escalating threat of antibiotic resistance, controlling bacterial systems through drug intervention is becoming more challenging. Furthermore, even when antibiotics are effective, the dysbiosis caused by collateral damage from antibiotics can lead to the emergence of even more problematic bacterial infections. Although emerging technologies such as phage therapy and bacteriocins have the potential to circumvent these challenges, they also suffer from drawbacks including poor stability and immunogenicity within a mammalian host. This project explores an alternate strategy for manipulating the microbial population: using conjugative elements to genetically modify harmful bacteria. Conjugative elements are naturally occurring genetic entities that encode machinery necessary to facilitate their transfer between bacterial cells. In nature, these elements are often responsible for the spread of virulence factors and antibiotic resistance among bacteria. However, these undesired components can be replaced with genes engineered to specifically modulate the gene expression of targeted bacterial community members. Specifically, the virulence-causing genes of pathogens can be repressed, effectively neutralizing their potential to cause disease. Although conjugative elements have been extensively studied in the past with numerous conjugative elements having been identified in a wide range of microorganisms, we still do not understand how conjugative elements spread within complex multi-species microbial communities. Elucidating how these elements spread will not only be critical for developing conjugative-element based therapeutics but will also allow us to better understand how antibiotic resistance and virulence mechanisms spread in nature. The main focus of this study will be on how conjugative elements spread into, among, and out of Vibrio cholerae bacteria. V. cholerae is the causative agent of the diarrheal disease cholera and presents a major global health threat and a significant epidemiological burden, especially in the developing world. V. cholerae also has a robust, well-establish animal infection model making it an ideal model system for exploring alternative therapeutic strategies. In this study, the spread of conjugative elements will be characterized both within well-defined in vitro populations as well as among the complex in vivo microbial communities present during infection. Tools will also be developed to deliver specific anti-V. cholerae virulence factors into V. cholerae. Altogether, this work will serve as a first step toward specifically targeting pathogenic bacteria in multispecies microbial populations and open the door for genetically modifying in vivo microbial communities.