Annals of Microbiology

, Volume 63, Issue 1, pp 21–37 | Cite as

Next-generation sequencing and its potential impact on food microbial genomics

  • Lisa Solieri
  • Tikam Chand Dakal
  • Paolo Giudici
Review Article


Recent efforts of researchers to elucidate the molecular mechanisms of biological systems have been revolutionized greatly with the use of high throughput and cost-effective techniques such as next generation sequencing (NGS). Application of NGS to microbial genomics is not just limited to predict the prevalence of microorganisms in food samples but also to elucidate the molecular basis of how microorganisms respond to different food-associated conditions, which in turn offers tremendous opportunities to predict and control the growth and survival of desirable or undesirable microorganisms in food. Concurrently, NGS has facilitated the development of new genome-assisted approaches for correlating genotype and phenotype. The aim of this review is to provide a snapshot of the various possibilities that these new technologies are opening up in area of food microbiology, focusing the discussion mainly on lactic acid bacteria and yeasts associated with fermented food. The contribution of NGS to a system level understanding of food microorganisms is also discussed.


Next generation sequencing Food microbiology Community profiling Metagenomics Genome sequencing 


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Copyright information

© Springer-Verlag and the University of Milan 2012

Authors and Affiliations

  • Lisa Solieri
    • 1
  • Tikam Chand Dakal
    • 1
  • Paolo Giudici
    • 1
  1. 1.Department of Agricultural and Food SciencesUniversity of Modena and Reggio EmiliaReggio EmiliaItaly

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