Chapter 4 : Automated and Large-Scale Characterization of Microbial Communities in Food Production

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Microbial communities in food and food production establishments have highly versatile structures based on various extrinsic factors. The information gained by large-scale microbial community analysis not only can deepen the understanding of food microbiology in general but also can lead to improvement of food production systems for increased quality and safety and extension of shelf life. This chapter reviews the most recent methods applied to microbial communities, and presents examples of some cutting-edge technologies. Molecular methods have been developing rapidly in recent years both for specific detection of single species and for screening assays that allow the species composition of a given food sample to be unraveled. Examples of those methods are 16S rRNA clone analysis, fingerprinting methods such as terminal restriction fragment length polymorphism (t-RFLP) and denaturing gradient gel electrophoresis (DGGE), tag-encoded pyrosequencing, single-nucleotide primer extension (SNuPE), and microarrays. Furthermore, flow cytometry is also addressed in the chapter, but this technique is based on single-cell analysis whereby a cell suspension is concentrated by nanofluidics and analyzed by laser technology. High-throughput analysis of microbial populations in food products and food processing environments has revealed the existence of a higher complexity in the microbial world than previously expected. The new approaches provide opportunities for further understanding of the microbial developments that are initiated during food production and storage.

Citation: Reynisson E, Rudi K, Marteinsson V, Nakayama J, Sakamoto N, Rasooly A, Hootfar J. 2011. Automated and Large-Scale Characterization of Microbial Communities in Food Production, p 63-79. In Hoorfar J (ed), Rapid Detection, Characterization, and Enumeration of Foodborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555817121.ch4
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Image of FIGURE 1

Growth of the 16S rRNA database since 1996 ( ) (adapted from http://rdp.cme.msu.edu).

Citation: Reynisson E, Rudi K, Marteinsson V, Nakayama J, Sakamoto N, Rasooly A, Hootfar J. 2011. Automated and Large-Scale Characterization of Microbial Communities in Food Production, p 63-79. In Hoorfar J (ed), Rapid Detection, Characterization, and Enumeration of Foodborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555817121.ch4
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Image of FIGURE 2

(Left) The number of reads (closed bar) and unique sequences (open bar) per nukadoko sample. A total of 18,268 valid reads including 6,519 different sequences were obtained. (Right) Circle graph representation of bacterial species composition in a long-aged nukadoko (sample no. 6).

Citation: Reynisson E, Rudi K, Marteinsson V, Nakayama J, Sakamoto N, Rasooly A, Hootfar J. 2011. Automated and Large-Scale Characterization of Microbial Communities in Food Production, p 63-79. In Hoorfar J (ed), Rapid Detection, Characterization, and Enumeration of Foodborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555817121.ch4
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Image of FIGURE 3

Flow sheet of the fundamentals of t-RFLP when used on a mixture of three cultures (species 1, 2, and 3). To start with, they are coamplified with PCR, resulting in a labeled PCR product (indicated by asterisk). The three species contain restriction sites on several locations within their 16S gene (A). Upon restriction, only the terminal fragment is detectable in a DNA fragment analyzer due to the fluorogenic labeling (B and C).

Citation: Reynisson E, Rudi K, Marteinsson V, Nakayama J, Sakamoto N, Rasooly A, Hootfar J. 2011. Automated and Large-Scale Characterization of Microbial Communities in Food Production, p 63-79. In Hoorfar J (ed), Rapid Detection, Characterization, and Enumeration of Foodborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555817121.ch4
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Summary of fast and/or large-scale methods used in microbial community analysis

Citation: Reynisson E, Rudi K, Marteinsson V, Nakayama J, Sakamoto N, Rasooly A, Hootfar J. 2011. Automated and Large-Scale Characterization of Microbial Communities in Food Production, p 63-79. In Hoorfar J (ed), Rapid Detection, Characterization, and Enumeration of Foodborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555817121.ch4

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