Effects of microencapsulated antimicrobial peptides on the growth, immunity, infection resistance, gut microbiota, and gene transcriptome in Manila clam (Ruditapes philippinarum) larvae

Pathogenic infections are a major cause of high mortality rates in bivalve hatcheries. Antimicrobial peptides (AMPs), recognized for their broad-spectrum antibacterial activity and low potential to induce antibiotic resistance, have attracted increasing attention. In this study, two AMPs derived from crab and scallop were heterologously expressed in Pichia pastoris. The AMPs were then encapsulated in microcapsules for the first time and systematically assessed for their effects on growth, immunity, infection resistance, gut microbiota composition, and transcriptomic profiles in Ruditapes philippinarum larvae. The results showed that the two AMPs displayed distinct bands at ∼15 kDa and exhibited strong in vitro antibacterial activity against three Vibrio strains. Relative to the 0 mg/g control group, clams fed AMPs at 0.07 and 0.1 mg/g significantly improved performance outcomes. Specifically, at 0.07 mg/g, AMPs significantly increased survival rates by 23 %–31 %, resulting in greater total biomass. By contrast, the 0.1 mg/g dose led to a 32 % increase in individual wet weight. When challenged with Vibrio crassostreae, both doses (0.07–0.1 mg/g) improved survival by 30 %–70 % compared to the control. Additionally, compared to the unencapsulated form, microencapsulated AMPs at 0.1 mg/g increased total biomass by 47 %, individual wet weight by 29 %, and survival under V. crassostreae challenge by 40 %. Physiologically, clams fed 0.1 mg/g AMPs showed higher antioxidant and immune enzyme activities and lower malondialdehyde levels than the 0 mg/g control. Further microbiota analysis showed that AMPs at 0.1 mg/g, compared to the 0 mg/g control, enriched beneficial taxa such as Bacilli (class) and Solibacillus (genus), while suppressing pathogenic genera Vibrio and Tenacibaculum. In parallel, transcriptomic analysis revealed that AMPs downregulated genes involved in inflammation, cellular stress, and metabolic regulation, relative to the control. These findings support the application of microencapsulated AMPs as functional additives in bivalve hatchery management.