UC Irvine

Bacterial biofilms cause persistent and deadly infections in medical settings, which are resistant to conventional antibiotic doses. Medical biofilms are often multi-species communities of bacteria which are maintained through chemical signaling and metabolite exchange. An improved understanding of the interactions between bacteria governing community behavior will facilitate the discovery of drug targets for biofilm prevention and eradication. In this thesis, I describe coculture interactions between different species of bacteria and a method to track metabolic states of bacteria in different environments.

One example of such coculture interactions is illustrated in the competition for iron in an in vitro infection model. Salmonellaenterica serovar Typhimurium (STm) causes acute infections in the gut, but STm infections are abolished in coculture with a probiotic bacterium, Escherichia coli Nissle (EcN). EcN outcompetes STm in the gut via a class of bactericidal compounds, called microcins, which are conjugated to iron scavenging siderophore molecules. In vitro biofilm models show that STm uses EcN siderophores to acquire iron, and that siderophore conjugation is an anti-cheating strategy employed by EcN to outcompete STm for nutrients.

In another example of novel coculture interactions, E. coli and Pseudomonas aeruginosa have competitive interactions governing biofilm establishment and dispersal. The E. coli biofilm dispersal is triggered by P. aeruginosa quorum sensing (QS) compounds. However, E. coli biofilms grown on periodic microcturctures, resembling the stomach micro-villi, are shown to modulate this pathway by metabolite accumulation in engineered microenvironments. Substrate structures induce changes in E. coli biofilm morphology, which in turn increase the concentration of indole, a constitutively produced metabolite within the biofilm. Moreover, the monoculture biofilms grown on microstructured substrates are significantly more susceptible to antibiotics than monocultures on flat substrates. FLIM is a label free, non-invasive technique and has immense potential for use as a means to probe interactions in microbial communities. Fluorescence lifetime imaging microscopy (FLIM), demonstrates that this increased antibiotic susceptibility is due to changes in cellular metabolism induced by an altered microenvironment. The research in this thesis demonstrates more long term and permanent strategies for biofilm infections and will provide guidelines and inspiration for improved diagnostics, and treatments for biofilm infections.