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Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial

Jolien D'aes1, Marie-Alice Fraiture1, Bert Bogaerts1

  • 1Sciensano, Transversal activities in Applied Genomics (TAG), J. Wytsmanstraat 14, 1050 Brussels, Belgium.

Life (Basel, Switzerland)
|December 23, 2022
PubMed

Insights

Metagenomic sequencing identified unauthorized genetically modified microorganisms (GMM) and Bacillus contaminants in commercial fermentation products. This highlights the risk of antimicrobial resistance genes and the value of advanced sequencing for product safety.

Area of Science:

  • Microbiology
  • Genomics
  • Food Science

Background:

  • Genetically modified microorganisms (GMM) are widely used in industrial fermentation for products like enzymes and vitamins.
  • Unauthorized GMM contamination in commercial fermentation products has led to regulatory concerns and recalls.
  • Classical analysis methods may not fully characterize complex GMM contaminations.

Purpose of the Study:

  • To evaluate the utility of shotgun metagenomic high-throughput sequencing for identifying and characterizing unauthorized GMM in commercial fermentation products.
  • To compare metagenomic sequencing with traditional analytical techniques for genomic characterization of contaminants.
  • To assess the safety implications of identified GMM and other microbial contaminants.

Main Methods:

  • Utilized a combination of short-read and long-read shotgun metagenomic sequencing.
  • Analyzed four commercial microbial fermentation product samples for GMM presence and genetic constructs.
  • Investigated the genomic characteristics of contaminating microbial strains, including Bacillus species.

Main Results:

  • Successfully identified and characterized three distinct transgenic constructs containing alpha-amylase and protease genes from Bacillus species.
  • Detected contamination by up to three unculturable Bacillus strains, some with genetic modifications affecting sporulation.
  • Quantified a significant load of antimicrobial resistance genes associated with the identified contaminants, posing a potential public health risk.

Conclusions:

  • Shotgun metagenomic sequencing provides significant added value for comprehensive quality and safety assessment of complex fermentation products.
  • Metagenomics enables detailed genomic characterization of unauthorized GMM and other microbial contaminants, surpassing limitations of classical methods.
  • The presence of GMM and associated antimicrobial resistance genes underscores the need for robust detection and safety monitoring in food production.
Keywords:
Bacillusfood enzymegenetically modified microorganisms (GMM)hybrid genome assemblymetagenomic shotgun sequencing

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