MS Defense Seminar of Rikki Shook

Metagenomics Workflow to Assess the Genetic Diversity of the Vibrio-Squid Symbiosis

Host-colonization sites containing low-diversity microbial populations present a unique problem when applying metagenomics approaches. For example, how does one extract information such as the number of unique genotypes and relative abundance of symbiotically relevant genes? The light organ of the Hawaiian bobtail squid (Euprymna scolopes) is colonized by multiple strains of a single, bioluminescent bacterial species, Vibrio fischeri. The strain-level diversity of V. fischeri is useful in competition for host-colonization sites, and greatly impacts the outcome of colonization experiments of the squid host. Thus, applying metagenomics to this symbiosis model system is critical to understanding the genetic factors required to compete for and colonize the host, as well as analyzing the eco-evolutionary dynamics of symbiotic associations.  This project develops a method for assessing the abundance of strains that have a gene of interest and estimate strain richness within the E. scolopes light organ. Synthetic “mock” communities with mixed proportions of six V. fischeri strains were created to test a bioinformatics pipeline optimized for use with closely related strains and then applied to a wild light organ community. Ultimately, the resulting bioinformatic workflow is adaptable and capable of determining the proportion of genomes in the sample that have genes of interest, including the type VI secretion system interbacterial weapon, and provides potential methods to determine strain richness in a light organ metagenome.