Changes in Muscle Quality and Gut Microbiota of Whiteleg Shrimp (Penaeus vannamei) Within a Live Supply Chain

During farm-to-consumer transport, a live supply chain can aid in maintaining the quality of whiteleg shrimp (<i>Penaeus vannamei</i>). However, the changes in muscle quality and gut microbiota of shrimp in the live supply chain and their interactions are poorly understood. Here, we investigated the dynamics of cumulative survival, muscle quality, and gut microbiota in the key phases of the live shrimp supply chain: post-harvest, post-transport, post-respite, and simulated sales [ambient temperature (AT; 29 °C ± 0.3 °C); low temperature (LT; 23 °C ± 0.3 °C)]. The results suggest that among the various stages, the highest mortality (12%) occurred after transport, while the respite process was associated with enhanced gut-mediated stress resilience. Notably, the transport, 24 h sales, and 40 h sales stages were identified as three potential critical control points. Furthermore, the LT group exhibited an 8% higher survival rate, better quality parameters (34.9% higher hardness), increased abundance of Bacteroidetes (from 3.63% to 7.39%), and a reduced F: B ratio. Correlation analysis identified <i>Xanthomonadales</i> and <i>Oscillospirales</i> as potential biomarkers for maintaining quality, positively linked to survival, muscle hardness, and brightness. Our findings provide valuable insights into optimizing control strategies and microbial biomarkers for enhancing muscle quality in live supply chains and aquaculture.