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Review
. 2013 May;79(10):3148-55.
doi: 10.1128/AEM.00256-13. Epub 2013 Mar 8.

High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology

Danilo Ercolini  1
Affiliations
Review

High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology

Danilo Ercolini. Appl Environ Microbiol. 2013 May.

Abstract

Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.

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Figures

Fig 1
Fig 1
Culture-independent HTS applications to study food microbiota and possible outputs in a general workflow.
Fig 2
Fig 2
Advantages and disadvantages of the use of HTS to study food-associated microbial ecology.
Fig 3
Fig 3
Examples of rarefaction curves reporting the number of observed OTUs as a function of the number of sequence reads. Data were retrieved from HTS analyses of samples of mozzarella cheese and production intermediates (20) (A) and fresh and aerobically spoiled pork and beef (D. Ercolini, F. De Filippis, and A. La Storia, unpublished data) (B).
None
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