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dc.contributor.authorCaoYu
dc.contributor.authorFanning, Seamus
dc.contributor.authorProos, Sinead
dc.contributor.authorJordan, Kieran
dc.contributor.authorSrikumar, Shabarinath
dc.date.accessioned2018-01-10T11:39:31Z
dc.date.available2018-01-10T11:39:31Z
dc.date.issued2017
dc.identifier.citationCao Y, Fanning S, Proos S, Jordan K and Srikumar S (2017) A Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studies.Front. Microbiol. 8:1829. doi: 10.3389/fmicb.2017.01829en_GB
dc.identifier.urihttp://hdl.handle.net/11019/1526
dc.descriptionpeer-revieweden_GB
dc.description.abstractThe development of next generation sequencing (NGS) techniques has enabled researchers to study and understand the world of microorganisms from broader and deeper perspectives. The contemporary advances in DNA sequencing technologies have not only enabled finer characterization of bacterial genomes but also provided deeper taxonomic identification of complex microbiomes which in its genomic essence is the combined genetic material of the microorganisms inhabiting an environment, whether the environment be a particular body econiche (e.g., human intestinal contents) or a food manufacturing facility econiche (e.g., floor drain). To date, 16S rDNA sequencing, metagenomics and metatranscriptomics are the three basic sequencing strategies used in the taxonomic identification and characterization of food-related microbiomes. These sequencing strategies have used different NGS platforms for DNA and RNA sequence identification. Traditionally, 16S rDNA sequencing has played a key role in understanding the taxonomic composition of a food-related microbiome. Recently, metagenomic approaches have resulted in improved understanding of a microbiome by providing a species-level/strain-level characterization. Further, metatranscriptomic approaches have contributed to the functional characterization of the complex interactions between different microbial communities within a single microbiome. Many studies have highlighted the use of NGS techniques in investigating the microbiome of fermented foods. However, the utilization of NGS techniques in studying the microbiome of non-fermented foods are limited. This review provides a brief overview of the advances in DNA sequencing chemistries as the technology progressed from first, next and third generations and highlights how NGS provided a deeper understanding of food-related microbiomes with special focus on non-fermented foods.en_GB
dc.description.sponsorshipWe gratefully acknowledge the Department of Agriculture, Food and Marine (DAFM) (SMART-PIF; 13/F/423) and Enterprise Ireland (IP 2015 0380) for funding YC and SS, respectively.en_GB
dc.language.isoenen_GB
dc.publisherFrontiersen_GB
dc.relation.ispartofseriesFrontiers in Microbiology;
dc.subjectNext Generation Sequencingen_GB
dc.subjectfood microbiome,en_GB
dc.subject16S rDNA,en_GB
dc.subjectmetagenomics,en_GB
dc.subjectmetatranscriptomicsen_GB
dc.titleA Review on the Applications of Next Generation Sequencing Technologies as Applied to Food-Related Microbiome Studiesen_GB
dc.typeArticleen_GB
dc.identifier.doihttp://dx.doi.org/10.3389/fmicb.2017.01829
dc.contributor.sponsorDepartment of Agriculture, Food and the Marine
dc.contributor.sponsorGrantNumberSMART-PIF; 13/F/423
refterms.dateFOA2018-01-12T09:01:00Z


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