Cortisol-induced signatures of stress in the fish microbiome

Stress experienced in intensive aquaculture can compromise fish growth, condition and immunity. Microbiome disruption may contribute to these adverse health effects, but little is known about how stress affects fish microbial communities. Here, we specifically examined the effects of stress-induced cortisol production on the fish microbiome. We exposed juvenile Atlantic salmon to a mild confinement stressor for two weeks. We then measured cortisol in the plasma, skin-mucus and faeces, and characterised the skin and faecal microbiome. Faecal and skin cortisol concentrations increased in fish exposed to confinement stress, and were positively correlated with plasma cortisol. Elevated faecal cortisol was associated with pronounced changes in the diversity and structure of the faecal microbiome. In particular, we identified a marked decline in probiotic Lactobacillales (Carnobacterium sp.) and an increase in pro-inflammatory and pathogenic taxa within the classes Clostridia and Gammaproteobacteria. In contrast, skin-mucus cortisol concentrations were lower and not associated with any detectable changes in the skin microbiome. Our results demonstrate that cortisol disrupts the gut microbiome, which may, in turn, contribute to the adverse effects of stress on fish health. They also highlight the value of using non-invasive faecal samples to monitor stress, including simultaneous determination of cortisol and stress-responsive bacteria.