Beneficial partnerships with bacteria are essential for the well-being of all of life on Earth, shaping health and fitness, ecosystem functioning, and even food security. Despite how dependent we are on these symbioitc associations; little is known regarding how hosts initially identify and select specific microbial partners from the complex communities in their surrounding environment. This is especially true at the finest scales, where hosts must distinguish between highly similar species or genetically distinct strains of the same species. This project addresses this challenge using the Siphamia- Photobacterium mandapamensis symbiosis as a highly tractable vertebrate-bacteria model system to investigate the molecular mechanisms that govern how animals recognize and initiate symbiosis with specific microbial partners and not others. Results will advance our understanding of how beneficial animal-microbe associations are established and maintained, with implications across a range of systems, including the vertebrate gut microbiome. This CAREER project will develop a new course-based undergraduate research experience in microbial genomics along with workshops and structured training of graduate students in cutting-edge genomic technologies, advancing national priorities in biotechnology and workforce development. The overall goal of this project is to determine the molecular mechanisms by which animal hosts recognize and selectively recruit specific microbial symbionts, with an emphasis on subspecies (strain)-level discrimination. This research uses the experimentally tractable Siphamia-Photobacterium mandapamensis symbiosis, a highly specific partnership between a coral reef fish and luminous bacterium, as a model for investigating the mechanisms underpinning host specificity. The bacterial symbiont is acquired from the seawater early in host development and housed in a specialized light organ attached to the fish’s intestine. Despite the strict species-level