Chapter 35 : Genomics of Foodborne Microorganisms

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As in other fields of science, food microbiologists are relying more and more on genomic techniques to understand the microbiota associated with our foods. We are looking to whole-genome sequences to decipher the genetic content of foodborne pathogens, industrially relevant strains, and potentially beneficial microbes. Metagenomic and metatranscriptomic techniques are now also being used to determine both the composition and function of microbes in a complex food matrix. Additionally, in recent years, laboratory-based global initiatives have been implemented that use genomics in place of traditional culturing techniques for identification and surveillance of strains involved in outbreaks of foodborne illness. There is little doubt that genomics has emerged as an important tool and will play a large role in the future of food microbiology.

Citation: Guinane C, Walsh C, Cotter P. 2019. Genomics of Foodborne Microorganisms, p 927-937. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch35
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Figure 35.1

Sequencing pipeline for metagenomic and metatranscriptomic analysis from a complex food matrix.

Citation: Guinane C, Walsh C, Cotter P. 2019. Genomics of Foodborne Microorganisms, p 927-937. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch35
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Table 35.1

Summary of the strengths and limitations of genomic technologies

Citation: Guinane C, Walsh C, Cotter P. 2019. Genomics of Foodborne Microorganisms, p 927-937. In Doyle M, Diez-Gonzalez F, Hill C (ed), Food Microbiology: Fundamentals and Frontiers, 5th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555819972.ch35

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