Metazoans maintain complex symbiotic partnerships with microbes and are now recognized as metaorganisms with often species-specific core assemblages that can influence health and disease. In particular, microbes associated with the gut epithelium, most of which exist as dynamic, adherent (i.e., biofilm) communities, supply orders of magnitude more gene products than their respective hosts. The establishment of these communities occurs immediately upon feeding and can be structured by environment, host secretory factors, and phages (viruses that infect bacteria). Our group is developing a protochordate model system, Ciona intestinalis, to help reveal essential elements modulating the establishment and maintenance of homeostasis in mucosal environments. Despite the increased number of microbiome studies to date, remarkably little is known about the influence of phages on the structure of complex, host-associated biofilm communities. Metavirome and 16S rRNA amplicon sequencing reveals distinct viral and bacterial communities in different gut compartments (stomach, midgut, hindgut), while some are ubiquitous throughout. We have successfully isolated and cultured bacteria from each compartment, tested for presence of inducible prophages, and identified strain-specific lytic phages. In vitro assays demonstrate an increase in biofilm formation in the presence of lytic phages. Additionally, a host-derived secretory immune protein influences biofilms and may be coupled to processes inducing viral-like particles. Preliminary in vivo experiments suggest that colonization of germ-free Ciona with a core isolate and subsequent exposure to its lytic phage results in a dramatic host response to bacterial cell lysis within the gut involving extensive mucus production. Additional studies will be performed with increasingly complex bacterial and phage communities in order to resemble a more natural establishment of gut microbiomes. Ciona affords the unique opportunity to dissect each component of the symbiotic dialogue at the host-environment interface to resolve the complex tripartite dynamics involving host, bacterial, and phage interactions during colonization of mucosal surfaces.