HOST AND ENVIRONMENTAL MICROBIOMES - WHAT CAN THEY TELL US ABOUT DISEASE OUTBREAKS?

The aquatic environment in which fish live has a direct impact on their health and vitality. Aquatic ecosystems, both for aquacultured and wild fish, are increasingly altered by climate change, anthropogenic stressors, and other environmental changes. Such changes and stressors impact not only fish, but also the microbiota, or microbial communities that live in the aquatic environment and on or in the host species. It is well documented in human medicine that small alterations in the human microbiome can have significant impacts on health, leading to obesity, rheumatoid arthritis, and liver disease, for example. However, the importance of microbial community (or microbiome) shifts and the associated pathogen composition on fish health remains unknown. We predict that fish, like humans, are directly impacted by changes in their skin/gill microbiome. But, unlike humans, these microbial communities are directly related to those found in the aquatic environment in which the fish live. Thus, changes in the environmental microbiome may predict disease outbreaks in fish, especially those associated with an opportunistic pathogen such as Flavobacterium psychrophilum, the causative agent of bacterial coldwater disease (CWD). Further, such shifts in the environmental microbiome may cause similar shifts in the microbiome on the host, especially gill and skin, and result in an increased pathogen prevalence and subsequent morbidity. In this study we use diagnostic metagenetics to monitor the environmental (water) and host (gill, skin) microbiome in a population of aquaculture-reared steelhead trout before, during, and after a BCWD outbreak. This provides the ability to characterize and quantify specific pathogens and also entire microbiomes. As a monitoring tool, this technique can identify key changes in presence/absence of pathogens combined with the associated changes in the microbial community structure leading to a population level disease state in captive reared fish. Such tools will advance our ability to monitor, manage, and perhaps even prevent disease outbreaks in aquaculture.