Gut microbiota serve vital roles in various aspects of animal life, including development of the immune system, influence on host physiology, as well as maintenance of peripheral organ systems (e.g. adipocytes, bone). Thus, disruption of gut homeostasis can influence the onset of diseases such as metabolic and neural disorders, cancer, gastrointestinal infections and chronic inflammation. A stable microbiota within host mucus must contend with host responses as well as various types of exogenous factors, including other microbes and viruses (e.g., bacteriophage) that infect them.
Very little is known about how the host both influences and is influenced by the bacteria-phage dynamics that occur within the gut ecosystem. The urochordate Ciona intestinalis, when reared germ-free (GF), represents a powerful model system for elucidating these dynamics. Ciona digestive tract represents a simplification of the gut environment and its transparent juveniles also facilitate investigations of microbe impacts on formation of mucosal barriers. In this study, GF Ciona were colonized by previously defined members of the gut microbiome with and without exposure to strain-specific lytic phage. By comparing GF and conventionalized animals, we used a a combination of vital dye staining, qPCR, and histological localization of mucus content and, report on complex colonization dynamics that suggest early exposure to microbes are essential to a proper maturation of the gut and may influence long-term host behaviors to microbial encounters. The types of bacteria first encountered as well as the abundance of host-specific lytic phage may influence retention and assembly of the microbiota. With renewed interest in phage therapy, a simpler model system that facilitates our ability to dissect the role of phage and its impact in complex host-associated mucosal environments can shed light on how interspecific dynamics influence community structure and inspire future studies on gut dysbiosis.