| Summary: | It is well known that gut bacteria can play key roles in host health and changes in microbiome diversity and compositions have been associated with diet, disease development and the environment the host encounters. The gastrointestinal microbiota of mammals has been studied extensively and significant progress has been made in the same area for aquacultured finfish. However, there are still gaps in knowledge around how the finfish microbiome is associated with health and productivity, particularly in a commercial aquaculture setting. The aims of this Thesis were to characterise the bacterial constituents of Tasmanian Atlantic salmon (Salmo salar) microbiomes to 1) assess the impact of time from feeding on measurement and quantification of gut microbiota composition and determine the effectiveness of the faecal scoring method as a rapid way to assess digestive status; 2) examine the effect of the early life production cycle and rearing environment on the composition of host-associated microbiomes; and 3) investigate the efficacy of prebiotic feed supplementation in amelioration of pathomorphological changes caused by soybean meal on the gastrointestinal tract, and the impact on digesta-associated microbiota and growth performance. A faecal score system was originally developed as an indicator of summer stress by using digestive status as a measure of “gut health” and is currently used on salmon farms in Tasmania, Australia. Although faecal scoring is widely employed as a means to assess digestive status in different animal species as well as humans the specific relationship between faecal score and gut microbiome is still poorly understood in Atlantic salmon, as are the potential confounding effects of inconsistent timing of scoring post feed. We assessed the impacts of time of sampling in relation to last feeding on both faecal scores and gut microbiota composition in adult Atlantic salmon. Two marine cohorts in different seasons (summer and winter) were sampled over a 24 hour period and comparisons were made ...
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