Over recent years, it has become increasingly apparent how important the microbiome is to human health and disease. But relatively little is known about the molecular mechanisms employed by symbiotic bacteria to stably colonize the gut, as they are difficult to experimentally study in isolation. At the California Academy of Science’s Steinhart Aquarium, we are currently developing the Siphamia-Photobacterium symbiosis as a simple binary model to disentangle the complexities underlying gut-associated vertebrate-bacteria associations. We recently assembled the genome of Siphamia tubifer, unlocking the potential for exciting new research projects addressing the molecular mechanisms that regulate the symbiosis.