Figure 1.

What is a microbiome? A microbiome can be defined simply as “a community of commensal, symbiotic, and pathogenic microorganisms within a body space or other environment” (Lederberg and McCray, 2001), although many varying definitions exist (Berg et al., 2020). A microbiome comprises a community of microbes including bacteria, viruses, fungi, microeukaryotic and metazoan parasites and Archaea (collectively known as the microbiota) as well as the downstream products and functionality of the microbiota. Cultured aquatic species harbor communities of microbes in the gut or gastrointestinal tract, as well as in the skin, nasal and oral cavities, gills, hemolymph, shells, integument and hepatopancreas, some of which are common across all cultured animal phyla (e.g., gills). The established microbiome composition is complex and involves not only host factors such as genotype and the host immune system, but also external environmental influences such as diet, physical parameters of culture systems, microbes in the aquatic environment and an array of water physiochemical parameters, including temperature, salinity, and dissolved oxygen. Together these parameters determine microbiome composition in host niches and these communities of commensals influence host health. Key determinants of host microbiome composition in cultured aquatic animals. Host microbiomes are determined by both environmental and host-associated factors. Environmental parameters can also reciprocally impact each other, as well as the host, particularly the microbial community within the water. Environmental parameters can be measured and, in some cases, controlled in aquaculture as can host factors such as genetics. Microbiomes occur in all cultured taxa including finfish, bivalve mollusks and crustaceans. Common microbial niches are found in a number of mucosal tissues including gut, gill and skin while others are specific to particular phyla, for example invertebrate hemolymph. Host microbiome composition itself has important implications for host health, but the functional and mechanistic pathways underlying these associations are poorly understood in aquaculture.