The importance of gut microbes for nutrition and health

Fish, like other vertebrates, are in close associations with their gut microbiota, as these microbial communities play essential roles in the host physiology, nutrition, homeostasis and disease resistance. Our knowledge of fish microbiota has grown significantly in the last two decades due to the advent of nucleic acid-based techniques, with most studies focusing on the gut, where most microbial biomass is located. Moreover, gut microbes have an important impact on host health through their involvement in biological processes such as nutrient processing, detoxification, immune modulation function, development, and mucosal tolerance. In this chapter, we aim to provide a thorough presentation on the role of the fish and shrimp gut microbiota for gut health and nutrition. We provide an overview of data from a broad range of studies, looking at core gut microbiota composition in important fish and shrimp species, describing how microbiota development occurs in fish, and discussing the role of gut microbiota on immune homeostasis, digestion, nutrient absorption and metabolism. Moreover, we describe the dietary impacts on the gut microbiota composition in light of the aquaculture feed industry trends, such as the inclusion of plant proteins, novel ingredients and prebiotics, and the effects on the use of antimicrobials. Lastly, in the last section, we present several commonly used methods to analyze microbiota composition and functionality.