The effect of diet and environmental temperature on the faecal microbiota of farmed Tasmanian Atlantic Salmon (Salmo salar L.)

We investigated the changes in the faecal microbial population of the hindgut of farmed Atlantic salmon fed two commercial diets (A and B) over a 10‐month period. At each sampling round, hindgut contents of 40 fish (20 per diet) were pooled according to diet and cultivated on selective agar. The functional status of all microbiota was assessed against 48 substrates using the PhPlate generalized microplate, which also yielded a metabolic capacity (MC) value for each microbiota. Virulence gene profiles of each microbiota were also investigated. The number of different bacterial groups between two diets varied slightly and increased as water temperature peaked at 18.5°C during summer. This however, was associated with an increase in Vibrio numbers and a decrease in lactic acid bacterial numbers. A shift in the functional status of gut microbiota was observed as temperature increased, which was coupled with a decrease in the MC‐value of the microbiota in both diets. Of the 35 virulence genes tested from total DNA extract of the microbiota, only cdt and east1 were detected. Results indicate that temperature is the main driver of changes to the gut microbiota in farmed Tasmanian Atlantic salmon receiving these two diets.