ArticleFrontiers in microbiology2019
Fishing in the Soup - Pathogen Detection in Food Safety Using Metabarcoding and Metagenomic Sequencing.
Article in Frontiers in microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 66 citations in OpenAlex.
- Hunting for Helminths: short- and long-read shotgun metagenomics for helminth detection in faecal samples.PLoS neglected tropical diseases · 2026Article
- Genomic Characterization of an O-Antigen-Deficient, Hydrogen Sulfide-NegativeMicroorganisms · 2026Article
- Metagenomic analysis and proteins prediction of emerging pathogens in artisanal cheese.Molecular diversity · 2025Article
- Impact of DNA extraction, PCR amplification, sequencing, and bioinformatic analysis on food-associated mock communities using PacBio long-read amplicon sequencing.BMC microbiology · 2024Article
- Molecular and serological diagnosis of multiple bacterial zoonoses in febrile outpatients in Garissa County, north-eastern Kenya.Scientific reports · 2024Article
- Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes.PloS one · 2024Article
- Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling.Frontiers in microbiology · 2024Article
- Influence of Cellulase orMicroorganisms · 2023Article
- Tunable Magneto-Plasmonic Nanosensor for Sensitive Detection of Foodborne Pathogens.Biosensors · 2023Article
- Nanopore metatranscriptomics reveals cryptic catfish species as potential Shigella flexneri vectors in Kenya.Scientific reports · 2022Article
- ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently.BMC bioinformatics · 2022Article
- Research on safety and compliance of imported microbial inoculants using high-throughput sequencing.Frontiers in medicine · 2022Article
- The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content.Frontiers in microbiology · 2022Article
- Microbial Community, Fermentation Quality, andFrontiers in microbiology · 2022Article
- Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures.BMC genomics · 2021Article
- Deciphering Bacterial Community Structure, Functional Prediction and Food Safety Assessment in Fermented Fruits Using Next-Generation 16S rRNA Amplicon Sequencing.Microorganisms · 2021Article
- Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on theFoods (Basel, Switzerland) · 2021Article
- Isolation Procedure for CPMicroorganisms · 2021Article
- Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics usingMicrobial genomics · 2021Article
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Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In food safety the detection of food contaminations with pathogenic microorganisms is a race against time and often outpaced by error-prone epidemiological approaches. For evidence-based outbreak investigations fast and reliable techniques and procedures are required to identify the source of infection. Metagenomics has the potential to become a powerful tool in the field of modern food safety, since it allows the detection, identification and characterization of a broad range of pathogens in a single experiment without pre-cultivation within a couple of days. Nevertheless, sample handling, sequencing and data analysis are challenging and can introduce errors and biases into the analysis. In order to evaluate the potential of metagenomics in food safety, we generated a mock community containing DNA of foodborne bacteria. Herewith, we compare the aptitude of the two prevalent approaches - 16S rDNA amplicon sequencing and whole genome shotgun sequencing - for the detection of foodborne bacteria using different parameters during sample preparation, sequencing and data analysis. 16S rDNA sequencing did not only result in high deviations from the expected sample composition on genus and species level, but more importantly lacked the detection of several pathogenic species. While shotgun sequencing is more suitable for species detection, abundance estimation, genome assembly and species characterization, the performance can vary depending on the library preparation kit, which was confirmed for a naturally
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