Characterization of genetically modified microorganisms is facilitated by long-read whole-genome sequencing
About Jolien D'aes
Jolien D’aes is a bioinformatician at Sciensano, the Belgian research institute for public and animal health. She has both wet-lab and dry-lab research experience in different fields of applied microbiology. Her main interests are microbial genomics, metagenomics, and molecular biology methods, including next-generation sequencing (NGS). Jolien's current work contributes to the development of NGS data analysis methods for detection and characterization of genetically manipulated microorganisms (GMO).
Genetically modified microorganisms (GMM) are frequently employed for manufacturing of microbial fermentation products. Although their presence in the final product is prohibited by European legislation, GMM contaminations have repeatedly been reported, raising potential public health concerns. In this case study, we used short-read sequencing and long-read Oxford Nanopore Technologies whole-genome sequencing for genomic characterization of genetically modified Bacillus strains, isolated from commercial food enzyme products. De novo hybrid assembly, complemented with additional in-depth bioinformatics investigation of long-read data, revealed a complex and unexpected genomic constitution, highlighting the added value of applying long-read sequencing for genomic analysis of GMM.