The use of next generation sequencing for improving food safety: Translation into practice

Balamurugan Jagadeesan*, Peter Gerner-Smidt, Marc W. Allard, Sébastien Leuillet, Anett Winkler, Yinghua Xiao, Samuel Chaffron, Jos Van Der Vossen, Silin Tang, Mitsuru Katase, Peter McClure, Bon Kimura, Lay Ching Chai, John Chapman, Kathleen Grant

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

121 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)96-115
Number of pages20
JournalFood Microbiology
Publication statusPublished - Jun 2019

Bibliographical note

Funding Information:
This work was conducted by an expert group brought together by the European branch of the International Life Sciences Institute (ILSI Europe), with support from the ILSI North America Food Microbiology Committee, ILSI Japan Next Generation Sequencing Project, and ILSI Southeast Asia Region. The expert group and this publication were coordinated by the ILSI Europe Microbiological Food Safety Task Force. Industry members of this task force are listed on the ILSI Europe website at . Experts were not paid for the time spent on this work; however, the non-industry members within the expert group were offered support for travel and accommodation cost from the ILSI Europe Microbiological Food Safety Task Force, the ILSI North America Food Microbiology Committee, ILSI Japan, and ILSI Southeast Asia Region to attend meetings to discuss the manuscript. The ILSI Europe Microbiological Food Safety Task Force offered to all non-industry members a small compensatory sum (honoraria) with the option to decline. The research reported is the result of a scientific evaluation in line with ILSI Europe's framework to provide a precompetitive setting for public–private partnership. The opinions expressed herein and the conclusions of this publication are those of the authors and do not necessarily represent the views of ILSI Europe nor those of its member companies. For further information about ILSI Europe, please email or call +32 2771 00 14.

Funding Information:
ILSI Europe fosters collaboration among the best scientists from industry, academia and the public sector to provide evidence-based scientific solutions and to pave the way forward in nutrition, food safety, consumer trust and sustainability. To deliver science of the highest quality and integrity, scientists collaborate and share their unique expertise in expert groups, workshops, symposia and resulting publications. ILSI Europe's activities are mainly funded by its member companies. In addition, ILSI Europe receives funding from the European Union-funded projects they partner with and from projects initiated by Member States' national authorities.


  • Data sharing
  • Food safety and quality
  • Implementation
  • Metabarcoding
  • Metagenomics
  • Microbiology
  • Next generation sequencing
  • Whole genome sequencing


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