Lactic acid bacteria (LAB) have beneficial effects on aquatic animals, improving their immune system and intestinal microbiota. Nevertheless, the probiotic effects of LAB on the Manila clam Ruditapes philippinarum remain poorly understood. Herein, the effects of administering Lactobacillus plantarum at final doses of 1 × 105 CFU/L (T5 group), 1 × 107 CFU/L (T7 group), and 1 × 109 CFU/L (T9 group) in the rearing water for eight weeks were evaluated for the antioxidant capacity, non-specific immunity, resistance to Vibrio parahaemolyticus infection, and intestinal microbiota of R. philippinarum. The rearing water without the addition of L. plantarum served as a control. The results showed that the T7 and T9 groups demonstrated a significant elevation in the disease resistance of clams against V. parahaemolyticus, in the activities of alkaline phosphatase and lysozyme in the hepatopancreas, and in the expression of antioxidant- and immune-related genes, including SOD, GPx, and GST. Meanwhile, the T7 group showed a significant enhancement in superoxide dismutase and catalase activities and CAT expression, while the T9 group experienced a remarkable elevation in reduced glutathione content. Only catalase activity was markedly elevated in the T5 group. The expression of SOD, CAT, GPx, and GST was significantly elevated in three treatment groups following the V. parahaemolyticus challenge. The T7 group exhibited a significant increase in intestinal microbiota richness. Significant increases were noted in Firmicutes abundance across all three treatment groups and in Actinobacteriota in the T5 and T7 groups. Additionally, the opportunistic pathogen Escherichia-Shigella abundance significantly decreased in three treatment groups. Furthermore, administration of 1 × 107 CFU/L L. plantarum enhanced the stability of the intestinal microecosystem, whereas a dose of 1 × 109 CFU/L might have a negative effect. The application of three doses of L. plantarum significantly enhanced intestinal microbiota functions related to the immune response and oxidative stress regulation, while a higher dose (1 × 109 CFU/L) might inhibit several functions. In conclusion, the application of L. plantarum in the rearing water exerted beneficial effects on the antioxidant capacity, non-specific immunity, resistance to V. parahaemolyticus, and the intestinal microbiota stability and functions of R. philippinarum. The beneficial effects of L. plantarum on R. philippinarum were dose-dependent, and the final dose of 1 × 107 CFU/L exhibited the optimal effects.
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