A synbiotic composed of alginate nanoencapsulated prebiotic (pomegranate peel phytogenics) and multi-species probiotics (Lactococcus lactis, Lactobacillus plantarum, Lactobacillus paracasei, and Saccharomyces cerevisiae) has been developed as a potential eco-friendly alternative to antibiotics. The physicochemical properties of the encapsulated synbiotic were evaluated, and its gastric and storage tolerance, as well as its antioxidant and antimicrobial activity, were tested and compared to that of the non-encapsulated synbiotic (free synbiotic). The results showed that the prebiotic pomegranate peel ethanolic extract contained seven phenolic compounds, with cinnamic being the most abundant (13.26 µL/mL). Sodium alginate-CaCl2 nanocapsules were effective in encapsulating 84.06 ± 1.5% of the prebiotic’s phenolic compounds and 98.85 ± 0.57% of the probiotics. The particle size of the alginate-CaCl2 nanoencapsulated synbiotic was 544.5 nm, and the polydispersity index and zeta potential values were 0.593 and −12.3 mV, respectively. Thermogravimetric analysis showed that the alginate-CaCl2 nanoencapsulated synbiotic had high thermal stability at high temperatures, with only 2.31% of its weight being lost within the temperature range of 70–100 °C. The count of viable probiotics in the nanoencapsulated synbiotic was significantly higher than that in the free synbiotic after exposure to gastric acidity and storage for six months at room temperature. The percent inhibition values of the nanoencapsulated synbiotic and ascorbic acid (as a standard antioxidant) were comparable and significantly greater than those of the free synbiotic. The half-maximal inhibitory concentrations (IC50) of the nanoencapsulated synbiotic and ascorbic acid were significantly lower than those of the free synbiotic (3.96 ± 0.42 µg/mL and 4.08 ± 0.79 µg/mL for nanoencapsulated synbiotic and ascorbic acid, respectively, vs. 65.75 ± 2.14 µg/mL for free synbiotic). The nanoencapsulated synbiotic showed the highest significant antimicrobial activity against Escherichia coli (ATCC 8739). Both the nanoencapsulated and free synbiotics showed antimicrobial activity against Staphylococcus aureus (ATCC 6538), similar to that of gentamicin, although the nanoencapsulated synbiotic showed significantly higher inhibition activity compared to the free synbiotic. The nanoencapsulated synbiotic showed antimicrobial activity comparable to gentamicin against Pseudomonas aeruginosa (ATCC 90274), whereas the free synbiotic showed the least antimicrobial activity (p < 0.05). Both synbiotics showed significantly higher antimicrobial activity against Salmonella typhi (ATCC 6539) than gentamicin. Both synbiotics showed antifungal activity against Aspergillus niger and Aspergillus flavus, with a stronger effect observed for the nanoencapsulated synbiotic. However, the activity of both synbiotics was significantly lower than that of fluconazole (an antifungal drug).
