Metagenomic Characterization of Multiple Genetically Modified Contaminations in Commercial Microbial Fermentation Products

Overview

Journal Life (Basel)

Specialty Biology

Date 2022 Dec 23

PMID 36556336

Authors

Jolien Daes

Marie-Alice Fraiture

Bert Bogaerts

Sigrid C J de Keersmaecker

Nancy H C J Roosens

Kevin Vanneste

Affiliations

Soon will be listed here.

Abstract

Genetically modified microorganisms (GMM) are frequently employed for manufacturing microbial fermentation products such as food enzymes or vitamins. Although the fermentation product is required to be pure, GMM contaminations have repeatedly been reported in numerous commercial microbial fermentation produce types, leading to several rapid alerts at the European level. The aim of this study was to investigate the added value of shotgun metagenomic high-throughput sequencing to confirm and extend the results of classical analysis methods for the genomic characterization of unauthorized GMM. By combining short- and long-read metagenomic sequencing, two transgenic constructs were characterized, with insertions of alpha-amylase genes originating from and , respectively, and a transgenic construct with a protease gene insertion originating from , which were all present in all four investigated samples. Additionally, the samples were contaminated with up to three unculturable strains, carrying genetic modifications that may hamper their ability to sporulate. Moreover, several samples contained viable strains. Altogether these contaminations constitute a considerable load of antimicrobial resistance genes, that may represent a potential public health risk. In conclusion, our study showcases the added value of metagenomics to investigate the quality and safety of complex commercial microbial fermentation products.

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