Genetically modified microorganisms (GMM) are frequently employed for the production of microbial fermen-
; tation products such as food enzymes. Although presence of the GMM or its recombinant DNA in the final
; product is not authorized, contaminations occur frequently. Insight into the contamination source of a GMM is of
; crucial importance to allow the competent authorities to take appropriate action. The aim of this study was to
; explore the feasibility of a metagenomic shotgun sequencing approach to investigate microbial contamination in
; fermentation products, focusing on source tracing of GMM strains using innovative strain deconvolution and
; phylogenomic approaches. In most cases, analysis of 16 GMM-contaminated food enzyme products supported
; finding the same GM producer strains in different products, while often multiple GMM contaminations per
; product were detected. Presence of AMR genes in the samples was strongly associated with GMM contamination,
; emphasizing the potential public health risk. Additionally, a variety of other microbial contaminations were
; detected, identifying a group of samples with a conspicuously similar contamination profile, which suggested
; that these samples originated from the same production facility or batch. Together, these findings highlight the
; need for guidelines and quality control for traceability of these products to ensure the safety of consumers. This
; study demonstrates the added value of metagenomics to obtain insight in the microbial contamination profiles, as
; well as their underlying relationships, in commercial microbial fermentation products. The proposed approach
; may be applied to other types of microbial fermentation products and/or to other (genetically modified) pro-
; ducer strains.