ArticleBMC biotechnology2015
Use of next generation sequencing data to develop a qPCR method for specific detection of EU-unauthorized genetically modified Bacillus subtilis overproducing riboflavin.
Article in BMC biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products.Food chemistry. Molecular sciences · 2025Article
- Pilot market surveillance of GMM contaminations in alpha-amylase food enzyme products: A detection strategy strengthened by a newly developed qPCR method targeting a GMFood chemistry. Molecular sciences · 2024Article
- Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria.BMC genomics · 2023Article
- Metabolic Engineering ofMicroorganisms · 2023Review
- Retrospective surveillance of viableFrontiers in microbiology · 2023Article
- Strategies to Increase the Production of Biosynthetic Riboflavin.Molecular biotechnology · 2021Review
- A shotgun metagenomics approach to detect and characterize unauthorized genetically modified microorganisms in microbial fermentation products.Food chemistry. Molecular sciences · 2021Article
- Selected Instrumental Techniques Applied in Food and Feed: Quality, Safety and Adulteration Analysis.Foods (Basel, Switzerland) · 2021Review
- Identification of an unauthorized genetically modified bacteria in food enzyme through whole-genome sequencing.Scientific reports · 2020Article
- Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus.Scientific reports · 2020Article
- EFSA statement on the risk posed to humans by a vitamin BEFSA journal. European Food Safety Authority · 2019Article
- Molecular characterization of an unauthorized genetically modified Bacillus subtilis production strain identified in a vitamin BFood chemistry · 2017Article
- Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products.Analytical and bioanalytical chemistry · 2016Review
Corrections and comments
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundRecently, the presence of an unauthorized genetically modified (GM) Bacillus subtilis bacterium overproducing vitamin B2 in a feed additive was notified by the Rapid Alert System for Food and Feed (RASFF). This has demonstrated that a contamination by a GM micro-organism (GMM) may occur in feed additives and has confronted for the first time,the enforcement laboratories with this type of RASFF. As no sequence information of this GMM nor any specific detection or identification method was available, Next GenerationSequencing (NGS) was used to generate sequence information. However, NGS data analysis often requires appropriate tools, involving bioinformatics expertise which is not alwayspresent in the average enforcement laboratory. This hampers the use of this technology to rapidly obtain critical sequence information in order to be able to develop a specific qPCRdetection method.
methodsData generated by NGS were exploited using a simple BLAST approach. A TaqMan® qPCR method was developed and tested on isolated bacterial strains and on the feed additive directly.
resultsIn this study, a very simple strategy based on the common BLAST tools that can be used by any enforcement lab without profound bioinformatics expertise, was successfully used toanalyse the B. subtilis data generated by NGS. The results were used to design and assess a new TaqMan® qPCR method, specifically detecting this GM vitamin B2 overproducing bacterium. The method complies with EU critical performance parameters for specificity, sensitivity, PCR efficiency and repeatability. The VitB2-UGM method also could detect the B. subtilis strain in genomic DNA extracted from the feed additive, without prior culturing step.
conclusionsThe proposed method, provides a crucial tool for specifically and rapidly identifying this unauthorized GM bacterium in food and feed additives by enforcement laboratories. Moreover, this work can be seen as a case study to substantiate how the use of NGS data can offer an added value to easily gain access to sequence information needed to develop qPCR methods to detect unknown andunauthorized GMO in food and feed.
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