In order to reduce antibiotic application in aquaculture, an antimicrobial peptide anti-lipopolysaccharide factor isoform 3 (ALFPm3) with highly effective inhibitory activity against pathogens was introduced to bay scallop (Argopecten irradians) using bait microalga Tetraselmis subcordiformis as a delivery system. To improve its expression and stability, a fusion of two alfpm3 genes (alfpm3–2) was inserted into an expression vector and transformed into T. subcordiformis chloroplast, followed by in vitro and in vivo functional evaluations of the antimicrobial activities of ALFPm3–2 by minimum inhibitory concentration method and bay scallop breeding experiment, respectively. The results showed that the transformants of T. subcordiformis and the purified ALFPm3–2 had significant inhibitory effects on Vibrio parahaemolyticus and Staphylococcus aureus in vitro, while feeding the transformants reduced the colonization of the two pathogens in bay scallops, which further reduced bay scallops’ mortality by 28.67 % as revealed in infection test. Furthermore, daily oral administration of ALFPm3–2 could improve the gut microbial community and reduce the inflammatory response. Combined with changes in immune factors and endotoxin, it indicated that exogenous ALFPm3–2 played antimicrobial and anti-inflammatory functions in the guts of bay scallops. Overall, this study provided strong evidence to support the oral administration of antimicrobial peptides via microalgae in aquaculture.
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