Longitudinal sampling of the rainbow trout (Oncorhynchus mykiss) microbiome reveals effects of dietary cecropin A and Yersinia ruckeri infection

The tradeoffs between use of antimicrobials and microbiome health are not well understood. Recent studies have demonstrated the power of the fish microbiome to promote disease resistance. At the same time, a parallel body of research shows the promise of new generation of treatments based on antimicrobial peptides (AMP). In this study we examine how the insect AMP cecropin A affects the rainbow trout (Oncorhynchus mykiss) microbiome in the presence or absence of infection challenge with Yersinia ruckeri. We reveal that supplementation of the diet with cecropin A gives rise to a distinct gut microbiome, and that cecropin A appears to increase trout susceptibility to colonization by Y. ruckeri. Additionally, our data shed new light on an emerging mutualistic relationship between the salmonid host and a member of the genus Mycoplasma. Decreased relative abundance of Mycoplasma sp. in the microbiome has been correlated to disease state; unravelling the nature of this relationship is a key step for advancing microbiome-based health strategies for aquaculture.