Host-Microbiota Interactions and Their Importance in Promoting Growth and Resistance to Opportunistic Diseases in Salmonids

Abstract

Salmonids are second to carps as the most important group of farmed fish, with a total annual output of over 2 million tonnes. Intensive farming practices have been developed to maximize production but at the expense of exposing farmed fish to several simultaneous stressors including frequent handling procedures, overcrowding, and poor water quality. Sanitary, prophylactic, and curative measures in an intensive farming environment are commonly used to compensate for the immune impairment that results from an over-elicited stress response. This can disrupt global interactions between the host and its microbial flora (i.e., microbiota) that play a key role in maintaining fish health in the long term. The economic importance of salmonid fish calls for a better understanding of their host-microbiota interactions to develop therapeutic tools that are less damaging for the environment and human health as well as for the fish themselves. This chapter overviews the current knowledge on factors that alter salmonid microbiomes in aquaculture and discusses the state of the art on microbial profiling and modulation, as well as current research gaps and perspectives.