10 - The fish microbiome and its interactions with mucosal tissues

Abstract

The microbiomes of fish are complex communities comprising protists, yeasts, viruses, and members of the Bacteria and Archaea. These communities inhabit the skin, gills, and gastrointestinal (GI) tract. The abundance and composition of the organisms that comprise the microbiome are affected by a range of factors including temperature, seasonality, host genetics, and diet. Despite this, the microbiome contains core components, especially within the GI tract, which are well adapted to the selection pressures associated with the host fish species and as such these core microbes are commonly found in individuals of the same species even when reared in different locations or conditions (including wild and farmed individuals). The microbiome is important in barrier function (i.e., excluding foreign pathogens) and germ-free experiments demonstrate that fish larvae fail to develop properly in the absence of the microbiome. This is most prominent in the GI tract where the microbiome has been implicated in GI differentiation, morphology, immunity, and nutrient absorption. The mechanisms that drive these actions are partly described and various molecules that are important in the complicated processes of host-microbe cross-talk have been identified. This chapter provides a review on the current knowledge of fish microbiomes and their interactions with the fish mucosa.