title: Translating Omics to Food Microbiology.
abstract: This review examines the applications of omics technologies in food microbiology, with a primary focus on high-throughput sequencing (HTS) technologies. We discuss the different sequencing approaches applicable to the study of food-related microbial isolates and mixed microbial communities in foods, and we provide an overview of the sequencing platforms suitable for each approach. We highlight the potential for genomics, metagenomics, and metatranscriptomics to guide efforts to optimize food fermentations. Additionally, we explore the use of comparative and functional genomics to further our understanding of the mechanisms of probiotic action and we describe the applicability of HTS as a food safety measure. Finally, we consider the use of HTS to investigate the effects that ingested microbes have on the human gut microbiota.
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; email: paul.cotter@teagasc.ie.|APC Microbiome Institute, University College Cork, Cork, Ireland.|School of Microbiology, University College Cork, Cork, Ireland.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Walsh
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; email: paul.cotter@teagasc.ie.
authors.forename: Fiona
authors.initials: F
authors.lastname: Crispie
authors.affiliation: APC Microbiome Institute, University College Cork, Cork, Ireland.|School of Microbiology, University College Cork, Cork, Ireland.
authors.forename: Marcus J
authors.initials: MJ
authors.lastname: Claesson
authors.affiliation: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; email: paul.cotter@teagasc.ie.|APC Microbiome Institute, University College Cork, Cork, Ireland.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Cotter
mesh_terms: D005516:Food Microbiology; D000069196:Gastrointestinal Microbiome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D056186:Metagenomics; D019936:Probiotics; D059467:Transcriptome
keywords: fermentation; food microbiology; foodborne pathogens; gut microbiota; high-throughput sequencing; probiotics