The prevalence of SGS and other gut-related diseases is a primary cause of economic losses related to the farming of Atlantic Salmon with AGD being more significant. Maricultured Atlantic salmon in Tasmanian south-eastern waters have been frequently noted to exhibit an increased mortality during summer due to SGS. The problem is of concern to the Tasmanian aquaculture industry due to reduction in production efficiency. The aetiology of the SGS is unidentified but the fact that antibiotics can resolve the problem temporarily suggests that SGS is induced by a bacterial agent or agents. Identification of the aetiology of the disease is therefore a priority to resolve the problem. This however, requires a detailed investigation of the dynamics of microbial communities in the gut and their response to environmental factors such as temperature and diet over time as well as investigating their interaction with the gut epithelium. This has to be done not only in salmon afflicted with SGS but also in healthy salmon to determine how the protective effect of normal microflora in salmon is compromised during warm seasons allowing overgrowth of certain species of bacteria. Previous research suggests SGS may be caused by the proliferation of apparently non-pathogenic species of Vibrios or Aliivibrios. This needs to be verified and we plan to investigate this as well as investigating pathogenic potential of all bacteria that establish a close contact with the gut epithelium of salmon over time. And finally the importance of probiotic strains with potential to competitively exclude pathogenic strains in salmon’s gut and their population dynamics requires investigation as these bacteria may have an important role in prevention of the SGS.