Environmental and host-associated factors are the main determining factors for the salmonid gill microbiome

Gill health is a major issue in aquaculture and the role of the gill microbiome in salmonid gill health is a growing research topic. To establish the role of gill microbiota in salmonid health, it is essential to understand the importance of environmental factors and fish-associated factors in shaping the gill microbiome, while also including technical factors such as sampling method and DNA extraction methods. We addressed the relative contributions of each factor in a meta-analysis of all publicly available salmonid gill microbiome studies. We reanalyzed 20 studies containing 804 high-quality gill samples of Atlantic salmon, rainbow trout and Arctic charr to determine which factors significantly explained variation and which genera of microorganisms are associated with specific factors and followed this up with an analysis of 400 gill- and environmental samples to find gill-specific microbial signatures across studies. We found that study-specific factors are the largest explanatory factor, followed by rearing system and species, while no other factors were significant. Across studies, disease led to a significantly reduced microbial diversity. Finally, we find that salmonids share multiple core genera including beneficial nitrogen-cycle bacteria which were also widespread throughout all rearing systems. Our findings support the need for more standardized sampling and extraction methods, to minimize study-specific factors when looking for biomarkers of health or disease. However, we also show that despite most variation coming from study-specific effects, shared signatures for disease (a reduced microbial richness) and potential beneficial microorganisms can be found across salmonid gill microbiota.