Molecular characterization of an unauthorized genetically modified Bacillus subtilis production strain identified in a vitamin B2 feed additive

•Genetically modified Bacillus subtilis identified in a vitamin B2 product.•Whole genome sequencing runs are performed for characterization of the isolated strain.•Complex modifications of the genome are identified.•Four putative recombinant plasmids are characterized.•Real-time PCR methods are developed and available for testing vitamin B2 products.