Transcriptome and 16S rRNA Amplicon Sequencing Analysis of Nutrition Metabolism in Silver Pomfret at Varying Flow Rates

Silver pomfret (Pampus argenteus), a highly valued marine fish, faces challenges in aquaculture due to its sensitivity to environmental conditions. Recirculating aquaculture system (RAS) is likely to become a primary indoor cultivation method for silver pomfret in the future, so studying hydrodynamic characteristics at varying flow rates in silver pomfret RAS is crucial and has far-reaching implications for both aquaculture practices and economic returns. This study investigated the effects of water flow rates (low: 400 L/h, moderate: 600 L/h, high: 800 L/h) on the growth performance, nutritional metabolism, and gut microbiota of silver pomfret over an 8-week period. Transcriptome and 16S rRNA sequencing revealed that the moderate-flow-rate group exhibited superior growth performance, with enhanced expression of genes related to protein synthesis (HYOU1, PDIA6, ITGA11) and redox regulation (GLUL, DUSP1, GST). Additionally, the moderate flow rate promoted gut microbial diversity and stability, with higher abundances of fermentation- and chemoheterotrophy-related functions, suggesting improved nutrient metabolism. In contrast, high flow rates induced anaerobic metabolism, leading to lactate accumulation and reduced growth. These findings demonstrate that a moderate flow rate of 600 L/h optimizes silver pomfret aquaculture by enhancing growth, metabolic efficiency, and microbial health, providing a foundation for sustainable large-scale farming practices.