The Atlantic salmon aquaculture industry in Australia is of great importance due to the increased demand for fish and/or fish products, however outbreaks of disease, in particular gastrointestinal (GI) disruptions, can result in underweight fish and increased mortalities, leaving the industry with severe financial losses. The gut microbiota of salmon in other countries has been characterised previously revealing a dominance of Gram-negative bacteria such as Vibrio, Pseudomonas and Aeromonas species as well as Gram-positive bacteria, eg. lactic acid bacteria (LAB) important for GI health. The composition and change in the GI microbiota in Tasmanian Atlantic salmon has not been investigated, particularly in response to seasonal and diet variations. As the study of such changes often requires lengthy and expensive feed trials, the use of in vitro fermentation models, in particular a semi-continuous model, may offer an alternative. This thesis examined the changes in the bacterial composition of farmed Tasmanian Atlantic salmon in response to seasonal variations and different commercial diets, as well as varying fishmeal (FM) inclusion levels. This study also investigated the prevalence and persistence of some of the potential fish pathogens, the functional status, overall metabolic capacity (MC) as well as virulence genes (VGs) present in the gut microbiota of these fish. A semi-continuous fermentation model was also established as an in vitro tool to assess the impact of diet components on the microbiota of Atlantic salmon. Lastly this thesis identified LAB strains, isolated from healthy salmon, and characterised these against the existing selection criteria of a potential probiotic.
Submitted in the fulfilment of the requirements of the degree of Doctor of Philosophy, University of the Sunshine Coast, 2015.