Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM <i>Bacillus velezensis<...

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Autores principales:	Jolien D’aes, Marie-Alice Fraiture, Bert Bogaerts, Sigrid C. J. De Keersmaecker, Nancy H. C. Roosens, Kevin Vanneste
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	genetically modified microorganism (GMM) <i>Bacillus velezensis</i> food enzyme whole-genome sequencing hybrid genome assembly SNP phylogenomic analysis Chemical technology TP1-1185
Acceso en línea:	https://doaj.org/article/9bab03c5a242438386d204f7ca6fe186
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spelling	oai:doaj.org-article:9bab03c5a242438386d204f7ca6fe1862021-11-25T17:33:41ZCharacterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products10.3390/foods101126372304-8158https://doaj.org/article/9bab03c5a242438386d204f7ca6fe1862021-10-01T00:00:00Zhttps://www.mdpi.com/2304-8158/10/11/2637https://doaj.org/toc/2304-8158Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM <i>Bacillus velezensis</i> used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM <i>B. velezensis</i> isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.Jolien D’aesMarie-Alice FraitureBert BogaertsSigrid C. J. De KeersmaeckerNancy H. C. RoosensKevin VannesteMDPI AGarticlegenetically modified microorganism (GMM)<i>Bacillus velezensis</i>food enzymewhole-genome sequencinghybrid genome assemblySNP phylogenomic analysisChemical technologyTP1-1185ENFoods, Vol 10, Iss 2637, p 2637 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	genetically modified microorganism (GMM) <i>Bacillus velezensis</i> food enzyme whole-genome sequencing hybrid genome assembly SNP phylogenomic analysis Chemical technology TP1-1185
spellingShingle	genetically modified microorganism (GMM) <i>Bacillus velezensis</i> food enzyme whole-genome sequencing hybrid genome assembly SNP phylogenomic analysis Chemical technology TP1-1185 Jolien D’aes Marie-Alice Fraiture Bert Bogaerts Sigrid C. J. De Keersmaecker Nancy H. C. Roosens Kevin Vanneste Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products
description	Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM <i>Bacillus velezensis</i> used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM <i>B. velezensis</i> isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.
format	article
author	Jolien D’aes Marie-Alice Fraiture Bert Bogaerts Sigrid C. J. De Keersmaecker Nancy H. C. Roosens Kevin Vanneste
author_facet	Jolien D’aes Marie-Alice Fraiture Bert Bogaerts Sigrid C. J. De Keersmaecker Nancy H. C. Roosens Kevin Vanneste
author_sort	Jolien D’aes
title	Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products
title_short	Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products
title_full	Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products
title_fullStr	Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products
title_full_unstemmed	Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products
title_sort	characterization of genetically modified microorganisms using short- and long-read whole-genome sequencing reveals contaminations of related origin in multiple commercial food enzyme products
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/9bab03c5a242438386d204f7ca6fe186
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Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

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