Intestinal morphology and host‑ and system‑associated microbiome dynamics during short‑term fasting and refeeding of Atlantic salmon in recirculating aquaculture systems

Abstract

Short-term fasting is common in aquaculture prior to handling events, yet its impact on microbial communities and fish health remains poorly understood. We assessed the effects of a 5-day fasting period followed by refeeding on microbial dynamics in a recirculating aquaculture system (RAS), with RAS communities sampled after 5 days of refeeding and the mucosal skin and intestine microbiomes of post-smolt Atlantic salmon (Salmo salar) sampled after 6 days. The biofilter and biofilm bacterial profiles remained relatively stable throughout fasting and refeeding, unlike the water microbiome, which showed the most significant changes during refeeding, consistent with distinct microbial growth strategies under fluctuating nutrient conditions. The skin mucus microbiome shares similarities with trends in the water microbiome. No change in skin histomorphometry was observed during the fasting and refeeding periods. In contrast, distal intestinal tissue structures showed differences during the fasting period, indicating potential effects on the intestinal health of salmon. Notably, fasted fish had a higher relative abundance of Vibrio bacteria in their remaining digesta. Neither fasting or subsequent refeeding had any effect upon injury-based operational welfare indicators (OWIs) or serum cortisol levels. The study sheds light on the interactions between short-term fasting, microbial community dynamics, and Atlantic salmon health in RAS.