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Bovine lactoferricin-lactoferrampin-encoding Lactobacillus reuteri (LR-LFCA) has been found to benefit its host by strengthening its intestinal barrier. However, several questions remain open concerning genetically engineered strains maintaining long-term biological activity at room temperature. In addition, probiotics are vulnerable to harsh conditions in the gut, such as acidity and alkalinity, and bile salts. Microencapsulation is a technique to entrap probiotic bacteria into gastro-resistant polymers to carry them directly to the intestine. We selected nine kinds of wall material combinations to encapsulate LR-LFCA by spray drying microencapsulation. The storage stability, microstructural morphology, biological activity, and simulated digestion in vivo or in vitro of the microencapsulated LR-LFCA were further evaluated. The results showed that LR-LFCA had the highest survival rate when microcapsules were prepared using a wall material mixture (skim milk, sodium glutamate, polyvinylpyrrolidone, maltodextrin, and gelatin). Microencapsulated LR-LFCA increased the stress resistance capacity and colonization abilities. In the present study, we have identified a suitable wall material formulation for spray-dried microencapsulation of genetically engineered probiotic products, which would facilitate their storage and transport.