Discovering Ecological and Evolutionary Principles Governing Microbial Community Responses to Bacteriophage Infection of a Cross-Feeding Synthetic Coculture and Implications for Phage-based Applications

Abstract

Bacterial viruses, called bacteriophage (phage), infect bacteria and alter microbial community structure. Phages are an untapped resource to manipulate agriculture and medically applicable microbial communities. Yet, we cannot predict how phage impact a microbial community. My research aims to uncover ecological and evolutionary principles governing responses of microbial communities that contain cross-feeding interactions, where one species provides nutrients to (‘feeds’) another, phage. I combine wet-lab experiments on an engineered microbial co-culture with mathematical modeling to explore aspects of phage infection that are difficult to manipulate experimentally. I use a cross-feeding bacterial co-culture with Escherichia coli (E. coli) and Salmonella enterica (S. enterica) bacterial strains. In this cross-feeding system, E. coli cannot produce methionine, but does produce acetate and galactose. E. coli is paired with S. enterica that over-produces methionine and consumes acetate and galactose that E. coli secretes. To this co-culture, I add phage that infect either species. I have asked how simple cross-feeding co-cultures respond to phage infection. In Chapter 2, I used mathematical modeling and wet-lab experiments to show that single phage infections can break the cross-feeding relationship by liberating nutrients previously sequestered in the infected bacterial cells, ultimately changing community composition, and that partial, not full, resistance was necessary for this effect. In Chapter 3, ‘cocktails’ made of two different phage suppressed community growth the longest in a novel formulation that targeted both the pathogenic bacterial species and the slowest growing cross-feeder. Mathematical modeling showed that this was a generalizable concept to all cross-feeding systems. In Chapter 4, despite impacting community structure, I found that long term co-evolution between phage and E. coli cross-feeding with S. enterica only had weak effects on rates of adaptation. Phage treatments tended to increase rates of adaptations, as predicted by the Red Queen hypothesis, and cross-feeding tended to decrease rates of adaptation, as predicted by the Red King hypothesis. Overall, this thesis helps set baseline expectations of how phage influence cross-feeding microbial communities.