UC San Diego

Despite having traditionally been studied in isolation, the natural context of microbial growth is in the presence of other species. Research on microbes in interactive contexts has previously been challenging due to the complexity of natural microbiomes and an inability to culture non-model organisms. To address these challenges, a model microbiome based on the cheese rind has been developed. This system is of intermediate diversity and contains genetically tractable and culturable organisms, enabling mechanistic study of microbial interactions. Using species from this model microbiome, we apply cutting-edge genetic, metabolomic, and imaging techniques to investigate mechanisms of intermicrobial interactions. Chapter 1 reviews recent findings regarding intermicrobial interactions. Chapter 2 reports on the development of an RB-TnSeq library in cheese-associated bacterium Pseudomonas psychrophila and the use of this library in a three-member cheese rind model community to identify intermicrobial interactions. Chapter 3 presents the application of RB-TnSeq to the study of mechanisms related to bacterial-fungal interactions. This chapter also introduces a custom analysis pipeline developed for cross-condition RB-TnSeq comparisons. Chapter 4 describes three projects stemming from Chapter 3,which relate to an E. coli gene of unknown function, a fungal protein with potential antibiotic activity, and the application of RB-TnSeq to the study of bacterial-bacterial interactions, including the creation and characterization of an RB-TnSeq library in another cheese-associated bacterium Hafnia sp. str. JB232. Finally, Chapter 5 discusses potential future directions for this work and provides concluding remarks.