The effect of dietary formulations and environmental factors on atlantic salmon gastrointestinal microbial community

Diet composition, husbandry and farm environments likely influence the abundance and composition of microbial communities in the GI tract of maricultured Atlantic salmon, which in turn may act as an indicator of fish health and growth rates. The aim of this study was to understand the potential influences of dietary formulations and other measurements made to GI tract microbial communities of Atlantic salmon during a feeding trial at an experimental farm. Salmon were fed four different diet formulations: 1) a standard commercial diet with normal fishmeal level (D1); 2) a low fishmeal level (D2); 3) a high protein diet with a low digestible energy (D3); and 4) a low protein diet with a high digestible energy (D4) over five sampling occasions over a 6 month interval. Microbial communities were analysed by 16S rRNA-based pyrosequencing with ~10 fish sampled per time point per diet. The results indicated that growth rates for diet D2 were overall slowest, while the other diets resulted in slightly higher growth rates. CAP and PERMANOVA indicated separation and significant differences among diet groups (p=0.003) and time of sampling (p<0.001). The results also suggested diets of high protein diet with low digestible energy, and low protein with high digestible energy, had comparatively lower levels (20-30% and 50-70%, respectively) of family Vibrionaceae compared to other diets. Moreover the abundance of Vibrionaceae, cyanobacteria and lactic acid bacteria were distinguishable among the different of diet formulation and the time of sampling. An interesting observation was the significant number of cyanobacterial reads. These reads included mainly filamentous or coccoidal forms of cyanobacteria. The overall data demonstrated dynamic salmon gastrointestinal microbial communities that were influenced by diet formulation and seasonal effects.