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Acid resistant shell-matrix microcapsules, loaded with Streptococcus thermophilus,were prepared by embedding trehalose in the matrix of chitosan-alginate microcapsules.The obtained chitosan-trehalose-alginate microcapsules were superior to chitosan-alginate microcapsules as the immobilized bacteria may have: higher freeze-drying viability and better long-term storage stability.The construction of acid resistant shell-matrix microcapsules provides a new way for the development and application of microencapsulation technology in probiotics.The viable counts of S.thermophilus in chitosan-trehalose-alginate microcapsules was 8.34±-0.30 Log CFU g-1 after freeze-drying,which was nearly 1 Log greater than that in chitosan-alginate microcapsules (7.28±0.25 Log CFU g-1).Subsequently, the two kinds of microcapsules were both treated in simulated gastric juices (pH=1.5) for 2h to evaluate the acid tolerance, the viable counts of S.thermophilus in chitosan-trehalose-alginate microcapsules reached to 6.45±0.09 Log CFU g-1, while it was merely 4.82±0.22 Log CFU g-1 in chitosan-alginate microcapsules.The stability study indicated that encapsulated S.thermophilus in chitosan-trehalose-alginate microcapsules still remained a high viability at 25℃ for 3months, achieving viable count of 7.72±0.13 Log CFU g-1, while the viable counts in chitosan-alginate microcapsules were only 4.21±0.24 Log CFU g-1.