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Yoghurt can be enriched with dietary fibre, antioxidant, vitamin C and omega 3 rich oil. In this study functional yoghurt is prepared with flaxseed oil and guava pulp and physico chemical properties were analysed between 0 day and 21 days. Significant decrease in pH and increase in titratable acidity were observed throughout the storage period. There is a mild decrease in the values of fat as well as total solids content noticed from 0 day (23.43±0.05) to 21st day (22.61±0.02 for functional yoghurt. Though the difference was not significant (P≥0.05) up to 7th day of storage and later on there is a significant (P≤0.05) difference observed on 14th and 21st day of storage. There was a static decrement in syneresis from control to other three treatments. In regard to total phenolic content, there was a significant (P≤0.05) difference observed from zero day to 21st day of storage. There was a significant (P≤0.05) decrease in the DPPH radical scavenging activity from 0 day (4.51±0.14) to 21st day (2.32±0.10) for functional yoghurt. The gradual reduction in the antioxidant property of functional yoghurt during the storage period may be attributed to physicochemical changes occur during storage period which lead to loss of both probiotics and phytochemicals.