<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jolien D'aes</style></author><author><style face="normal" font="default" size="100%">Marie-Alice Fraiture</style></author><author><style face="normal" font="default" size="100%">Bert Bogaerts</style></author><author><style face="normal" font="default" size="100%">Yari Van Laere</style></author><author><style face="normal" font="default" size="100%">Sigrid C.J. De Keersmaecker</style></author><author><style face="normal" font="default" size="100%">Nancy Roosens</style></author><author><style face="normal" font="default" size="100%">Kevin Vanneste</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products</style></title><secondary-title><style face="normal" font="default" size="100%">Food Chemistry: Molecular Sciences</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Antimicrobial resistance</style></keyword><keyword><style  face="normal" font="default" size="100%">food enzyme</style></keyword><keyword><style  face="normal" font="default" size="100%">phylogenomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Strain-level deconvolution</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2025</style></year><pub-dates><date><style  face="normal" font="default" size="100%">June-2025</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Genetically modified microorganisms (GMM) are frequently employed for the production of microbial fermen-&lt;br&gt;
tation products such as food enzymes. Although presence of the GMM or its recombinant DNA in the final&lt;br&gt;
product is not authorized, contaminations occur frequently. Insight into the contamination source of a GMM is of&lt;br&gt;
crucial importance to allow the competent authorities to take appropriate action. The aim of this study was to&lt;br&gt;
explore the feasibility of a metagenomic shotgun sequencing approach to investigate microbial contamination in&lt;br&gt;
fermentation products, focusing on source tracing of GMM strains using innovative strain deconvolution and&lt;br&gt;
phylogenomic approaches. In most cases, analysis of 16 GMM-contaminated food enzyme products supported&lt;br&gt;
finding the same GM producer strains in different products, while often multiple GMM contaminations per&lt;br&gt;
product were detected. Presence of AMR genes in the samples was strongly associated with GMM contamination,&lt;br&gt;
emphasizing the potential public health risk. Additionally, a variety of other microbial contaminations were&lt;br&gt;
detected, identifying a group of samples with a conspicuously similar contamination profile, which suggested&lt;br&gt;
that these samples originated from the same production facility or batch. Together, these findings highlight the&lt;br&gt;
need for guidelines and quality control for traceability of these products to ensure the safety of consumers. This&lt;br&gt;
study demonstrates the added value of metagenomics to obtain insight in the microbial contamination profiles, as&lt;br&gt;
well as their underlying relationships, in commercial microbial fermentation products. The proposed approach&lt;br&gt;
may be applied to other types of microbial fermentation products and/or to other (genetically modified) pro-&lt;br&gt;
ducer strains.&lt;/p&gt;
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