Probiotics have poor gastrointestinal delivery because they lose their viability during intestinal passage. Microencapsulation has a significant effect on the survival of probiotic bacteria. This study aimed to synthesize chitosan-alginate nanoparticles and encapsulate Bacillus coagulans NBRC-12583 and Enterococcus faecium MGFR1 in alginate (Alg), chitosan (Cht) and inulin (Inu) by micro- and nano-encapsulation to investigate the viability of encapsulated strains in simulated gastrointestinal condition. The survival of free and encapsulated bacteria was studied for 120 min. The population of B. coagulans encapsulated in Cht-Alg only decreased by 0.86 log CFU, while that of E. faecium encapsulated in Cht-Alg nanoparticles only decreased by 0.27 log CFU. Treated with simulated intestinal fluid, B. coagulans and E. faecium populations decreased by 1.03 and 0.17 log CFU, respectively. E. faecium microencapsulated in Cht-Alg and Inu had a maximum encapsulation efficiency of 96.78%. E. faecium encapsulated in Cht-Alg nanoparticles and Inu was more viable than other encapsulated bacteria. Scanning electron microscopy was done to investigate the microcapsules' surface morphology, structure, internal cross-sectional view, and the zeta potential for the surface charge of Cht-Alg nanoparticles. The viability of the probiotic bacteria was enhanced significantly by microencapsulation and nanomaterial-based encapsulation within the chitosan-alginate and inulin matrix.
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