Game Changer-Next Generation Sequencing and Its Impact on Food Microbiology

Front Cover
Jennifer Ronholm, Sabah Bidawid, Sandra Torriani
Frontiers Media SA, Apr 26, 2018

 Advances in next-generation sequencing technologies (NGS) are revolutionizing the field of food microbiology. Microbial whole genome sequencing (WGS) can provide identification, characterization, and subtyping of pathogens for epidemiological investigations at a level of precision previously not possible. This allows for connections and source attribution to be inferred between related isolates that may be overlooked by traditional techniques. The archiving and global sharing of genome sequences allow for retrospective analysis of virulence genes, antimicrobial resistance markers, mobile genetic elements and other novel genes. The advent of high-throughput 16S rRNA amplicon sequencing, in combination with the advantages offered by massively parallel second-generation sequencing for metagenomics, enable intensive studies on the microbiomes of food products and the impact of foods on the human microbiome. These studies may one day lead to the development of reliable culture-independent methods for food monitoring and surveillance. 


Similarly, RNA-seq has provided insights into the transcriptomes and hence the behaviour of bacterial pathogens in food, food processing environments, and in interaction with the host at a resolution previously not achieved through the use of microarrays and/or RT-PCR. The vast un-tapped potential applications of NGS along with its rapidly declining costs, give this technology the ability to contribute significantly to consumer protection, global trade facilitation, and increased food safety and security. Despite the rapid advances, challenges remain. How will NGS data be incorporated into our existing global food safety infrastructure? How will massive NGS data be stored and shared globally? What bioinformatics solutions will be used to analyse and optimise these large data sets? 

This Research Topic discusses recent advances in the field of food microbiology made possible through the use of NGS.
 

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Contents

Game Changer Next Generation Sequencing and Its Impact on Food Microbiology
7
Genomic Characterization of Dairy Associated Leuconostoc Species and Diversity of Leuconostocs in Undefined Mixed Mesophilic Starter Cultures
10
Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium
24
Genetic Characterization of the Exceptionally High Heat Resistance of the Nontoxic Surrogate Clostridium sporogenes PA 3679
38
Genotypes Associated with Listeria monocytogenes Isolates Displaying Impaired or Enhanced Tolerances to Cold Salt Acid or Desiccation Stress
49
A GenomeWide Association Study to Identify Diagnostic Markers for Human Pathogenic Campylobacter jejuni Strains
69
Evolution and Diversity of Listeria monocytogenes from Clinical and Food Samples in Shanghai China
78
Genome Sequence of Vibrio parahaemolyticus VP152 Strain Isolated from Penaeus indicus in Malaysia
87
Metagenomic Sequencing for Surveillance of Food and Waterborne Viral Diseases
168
Characterization of the Genomic Diversity of Norovirus in Linked Patients Using a Metagenomic Deep Sequencing Approach
179
Insights from HighThroughput Amplicon Sequencing
193
Microbiome Approximations to Explain the terroir Concept
208
A Perspective Study of Koumiss Microbiome by Metagenomics Analysis Based on SingleCell Amplification Technique
220
Genotyping by PCR and HighThroughput Sequencing of Commercial Probiotic Products Reveals Composition Biases
231
Characterization of Gut Microbiome Dynamics in Developing Pekin Ducks and Impact of Management System
242
The Importance of Bacterial Culture to Food Microbiology in the Age of Genomics
257

A SystOMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis
91
The Validation and Implications of Using Whole Genome Sequencing as a Replacement for Traditional Serotyping for a National Salmonella Refere...
99
Pangenome Analyses of the Species Salmonella enterica and Identification of Genomic Markers Predictive for Species Subspecies and Serovar
108
Prophage Integrase Typing Is a Useful Indicator of Genomic Diversity in Salmonella enterica
124
Temporal Genomic Phylogeny Reconstruction Indicates a Geospatial Transmission Path of Salmonella Cerro in the United States and a CladeSpecific ...
135
The Next CultureIndependent Game Changer
147
Harmonization of Critical Food Microbiology Descriptors and Metadata for Improved Food Safety and Surveillance
263
Food Safety in the Age of Next Generation Sequencing Bioinformatics and Open Data Access
274
The Public Health Impact of a Publically Available Environmental Database of Microbial Genomes
284
A Comparative Analysis of the LyveSET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens
288
Back Cover
301
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