Cortisol stress response is linked to changes in the diversity and structure of the Atlantic salmon faecal microbiome

The intensification of aquaculture is often associated with increased levels of stress in farmed fish, which adversely impact health and welfare. Cortisol stress response is known to affect fish physiology and immunity, but impacts on the microbiome are unknown. We therefore aimed to examine the effects of cortisol on the skin and gut microbiome of juvenile Atlantic salmon, following exposure to a mild, aquaculture-relevant, confinement stressor. We measured cortisol directly in the skin mucus and faeces, as well as plasma, and characterised the matched skin and faecal microbiome of individual fish. Although there was no clear relationship between skin cortisol concentration and the skin microbiome, we identified a very distinctive relationship between measured cortisol concentration and microbiome diversity and structure in the faeces. This included a clear inhibition of lactic acid bacteria and promotion of pro-inflammatory and pathogenic taxa. Given the fundamental influence of microbiota and their metabolites on many aspects of host health, this suggests that cortisol-mediated disruption of the intestinal microbiome is likely to contribute to the adverse effects of stress on immune function and disease resistance.