Temperature-dependent phage-bacterium coexistence strategy mediates the intestinal microbial community diversity in shrimp

The diversity of intestinal bacterial communities is closely associated with host health. Phage-bacterium interactions are key determinants of this diversity, and temperature represents a critical environmental factor influencing these interactions. At elevated temperatures, pathogenic bacteria such as Vibrio parahaemolyticus ( V. parahaemolyticus ) proliferate in shrimp aquaculture systems, whereas phages with density-dependent infection dynamics fail to control bacterial populations, resulting in recurrent digestive tract diseases. In this study, a V. parahaemolyticus -T6 (VP) strain and its lytic phage (VP-T6a) were isolated from the shrimp intestine. Integrated omics analyses were employed to investigate how temperature modulates phage- V. parahaemolyticus interactions during infection and how these temperature-dependent dynamics affect intestinal microbial diversity. In vitro, VP-T6a replicated efficiently at relatively low temperatures (20°C–33°C), increasing its abundance, reducing VP density, and elevating the multiplicity of infection (MOI). However, phage-resistant VP variants emerged during co-culture with VP-T6a, preventing complete lysis of the VP population. At higher temperatures (35°C–37°C), the expression of VP-T6a packaging-related genes was suppressed after adsorption to VP, resulting in no production of progeny phages. Consequently, VP continued to replicate normally, increasing in abundance, whereas VP-T6a abundance declined, leading to a lower MOI. Within the optimal MOI range (0.001–0.01), co-cultures of VP-T6a and VP yielded the highest titers of progeny phages. In vivo, temperature also modulated VP-T6a-VP interactions within the shrimp intestine. The two temperature-dependent interaction patterns exerted distinct effects on the dominant taxa of the intestinal microbiota. Under low-temperature conditions, VP-T6a reduced the influence of VP on the microbial network, whereas this effect was absent at high temperatures. Moreover, low-temperature interaction patterns more effectively increased the contribution of deterministic processes in the shrimp intestinal bacterial community compared with high-temperature interaction patterns. This study reveals a temperature-dependent phage-bacterium coexistence strategy in the shrimp intestine that maintains a dynamic equilibrium between phages and their bacterial hosts. At elevated temperatures, phages fail to suppress V. parahaemolyticus proliferation, potentially weakening the intestinal microbiota’s resistance to exogenous invasion and thereby posing a potential risk to digestive tract health in shrimp. Video Abstract