Microbes rarely exist in isolation. Instead, they interact with multiple other partners in the broader context of a microbiome. Microbiomes play a large role in the health of the organisms with which they interact. Microbiomes are complex networks of organisms that frequently include bacteriophages, which are viruses that infect bacteria. Since bacteriophages, or phages, play essential roles in shaping bacterial evolution, it is imperative to understand the impact of these viruses within the context of complex microbial communities. The goal of this project is to fully characterize the mechanism(s) of phage-mediated evolution within complex microbial networks and ultimately examining these networks in an environment that mimics the human gut. The Broader Impact activities involve a phage hunting project that will involve middle school, high school and undergraduates in the discovery of new phages (this will involve a collaboration between MSU and Grinnell College). Blog posts, along with YouTube videos, will keep the community informed regarding progress in the identification of newly discovered phages. Teacher training, along with curriculum development in the K-12 classroom, are prominent components of the proposed workplan.
Some phages can "transduce", or package host genetic information, and pass it along to the next host during infection. This profoundly affects microbiome evolution by mobilizing and moving genes horizontally within the community. A recent discovery has uncovered novel evolution within Shigella phages that potentially increases genetic exchange within bacterial populations. To truly understand mechanisms of phage-mediated evolution, it is imperative to consider transduction within complex communities. This can be done by building on traditional studies of experimental microbial evolution, which solely use purified cultures and non-transducing phages, to multi-species communities that include transducing phages. The objective of this research is to determine mechanisms by which phage-mediated genetic transfer affects microbiome evolution. The first step in building these communities will be to isolate and characterize diverse Shigella phages. The PI will isolate Shigella phages from diverse environments, characterize their life cycles on different hosts, and perform experimental co-evolution studies between phages and hosts. These co-evolution experiments will initially be used to determine how phages evolve to infect new hosts. Combined, these results will help parameterize computational models, which will be used to build experimental networks with increasing complexity. The PI will determine selection pressures that influence rapid evolution to develop a predictive tool that can ultimately be applied to other bacteria:phage interactions. The PI will then experimentally test computationally predicted hypotheses using conditions that resulted in interesting and novel outcomes. Ultimately cell culture microfluidics (i.e. "Gut-on-a-Chip") will be developed to mimic a native microbiome and be used to study phage:host interactions in the context of a mammalian gut. The PI will track evolution and genetic mobility between phages and host bacteria using genetic sequencing of isolates after a population has evolved in this native, but easily-controlled, environment.
