The Use of Next Generation Sequencing for Improving Food Safety: Translation into practice

Autor: Peter McClure, Marc W. Allard, Sébastien Leuillet, Kathleen Grant, Bon Kimura, Jos M.B.M. van der Vossen, Peter Gerner-Smidt, Silin Tang, Mitsuru Katase, Samuel Chaffron, Lay Ching Chai, Anett Winkler, John W. Chapman, Yinghua Xiao, Balamurugan Jagadeesan
Přispěvatelé: Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, Laboratoire des Sciences du Numérique de Nantes (LS2N), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Bioinformatique (COMBI), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Dyslipoproteinémies et athérosclerose : Génétique, métabolisme et thérapeutique, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR14-Institut National de la Santé et de la Recherche Médicale (INSERM), Public Health England [London]
Jazyk: angličtina
Rok vydání: 2018
Předmět:
Food Safety
Food industry
Computer science
Food safety and quality
Context (language use)
Computational biology
Polymorphism
Single Nucleotide
Microbiology
Article
DNA sequencing
03 medical and health sciences
[SDV.EE.ECO]Life Sciences [q-bio]/Ecology
environment/Ecosystems
Next generation sequencing
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Genomics [q-bio.GN]
Food Industry
ComputingMilieux_MISCELLANEOUS
030304 developmental biology
2. Zero hunger
Whole genome sequencing
0303 health sciences
030306 microbiology
business.industry
Computational Biology
High-Throughput Nucleotide Sequencing
[SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Molecular Networks [q-bio.MN]
Genomics
Sequence Analysis
DNA
Food safety
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Metagenomics
Implementation
Practice Guidelines as Topic
Food Microbiology
Metabarcoding
Multilocus sequence typing
Data sharing
Identification (biology)
[SDE.BE]Environmental Sciences/Biodiversity and Ecology
business
Multilocus Sequence Typing
Food Science
[SDV.EE.IEO]Life Sciences [q-bio]/Ecology
environment/Symbiosis
Zdroj: Food Microbiology
Food Microbiology, Elsevier, 2018, ⟨10.1016/j.fm.2018.11.005⟩
Food microbiology
ISSN: 0740-0020
1095-9998
DOI: 10.1016/j.fm.2018.11.005⟩
Popis: Next Generation Sequencing (NGS) combined with powerful bioinformatic approaches are revolutionising food microbiology. Whole genome sequencing (WGS) of single isolates allows the most detailed comparison possible hitherto of individual strains. The two principle approaches for strain discrimination, single nucleotide polymorphism (SNP) analysis and genomic multi-locus sequence typing (MLST) are showing concordant results for phylogenetic clustering and are complementary to each other. Metabarcoding and metagenomics, applied to total DNA isolated from either food materials or the production environment, allows the identification of complete microbial populations. Metagenomics identifies the entire gene content and when coupled to transcriptomics or proteomics, allows the identification of functional capacity and biochemical activity of microbial populations. The focus of this review is on the recent use and future potential of NGS in food microbiology and on current challenges. Guidance is provided for new users, such as public health departments and the food industry, on the implementation of NGS and how to critically interpret results and place them in a broader context. The review aims to promote the broader application of NGS technologies within the food industry as well as highlight knowledge gaps and novel applications of NGS with the aim of driving future research and increasing food safety outputs from its wider use. © 2018
Databáze: OpenAIRE
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