Engineering the gut microbiome of honey bees

Honey bees are critically important commercial pollinators and model systems for insect physiology and behavior. Honey bees are also suffering dramatic declines worldwide due to many factors, including agricultural practices, parasites, and pesticide use. These bees house a simple, conserved gut microbiome that is important for their health. Can we use this gut microbiome to protect bees in new ways? Synthetic biology combines recombinant DNA technology and rational design principles to redesign biological processes. Microbiome engineering applies synthetic biology and engineering principles to microbial communities to improve or expand their functions. Because of their agricultural importance, history as a model organism, and simple gut microbiome, honey bees are a promising testbed for the nascent field of microbiome engineering. In Chapter 1 I provide a brief introduction to the host-associated microbiomes, honey bees, and synthetic biology. In Chapter 2, I develop broad-host-range tools for genetic manipulation of bacteria from honey bees and show that genetically engineered bacteria can recolonize and function in bees. This lays the groundwork for follow-on efforts to both study and further engineer the bee gut microbiome. In Chapter 3, I describe the application of these genetic tools to engineer core microbiome member Snodgrassella alvi to produce double-stranded RNA (dsRNA) and thereby induce RNA-interference (RNAi) in bees. Activating RNAi enables bee researchers to study specific bee genes. In the future this technique may be used to protect honey bee hives from viruses and parasitic mites. In Chapter 4, I describe a computational approach for designing and evaluating defined bacterial communities and discuss using these defined communities in honey bees. These chapters together demonstrate how the bacterial community native to an organism can be modified and address several technical limitations of microbiome engineering in honey bees. Finally, I discuss the next steps for continuing this work.