Development of a rapid SNP-typing assay to differentiate Bifidobacterium animalis subsp. lactis strains used in probiotic-supplemented dairy products

Differentiation of B. animalis subsp. lactis (BAL) strains used in probiotic-supplemented dairy products has been historically difficult and time-consuming. We describe a minisequencing assay targeting six single nucleotide polymorphisms (SNPs) that allow differentiation BAL strains. We target all six SNPs simultaneously starting from a single multiplex PCR reaction prior to minisequencing, thus saving reagents and time. This approach provides a simple, rapid, flexible SNP-based subtyping method that can be used in research laboratories, clinical trials evaluating the efficacy of B. animalis subsp. lactis, or in commercial products in order to identify commercial strains utilized in the industry.