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The present study was conducted to isolate and identify bifidobacterial species with probiotic properties from the faeces of breast fed infants and its incorporation in the preparation of a nutraceutical whey based malt food. Identification of isolates to the genus was based on phenotypic characteristics like the unique pleomorphic morphology and carbohydrate fermentation profile. Molecular tools like 16S rDNA targeted genus and species specific mPCR primers were used for confirmation. A total of 4 isolates were identified namely B. longum (IB10 and IB12) B. breve (IB39) and B. bifidum (IB42). Subsequently the nucleotide sequences of the identified species were submitted to the GenBank for acquisition of accession number. The identified species were screened for probiotic properties like bile tolerance, antimicrobial property.