title: Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation.
abstract: Culture independent methods first appeared in the food microbiology field at the end of the 90s and since then they have been applied extensively. These methods do not rely on cultivation and target nucleic acids (DNA and RNA) to identify and follow the changes that occur in the main populations present in a specific ecosystem. The method that has most often been used as a culture independent method in food microbiology is denaturing gradient gel electrophoresis (DGGE). The number of papers dealing with DGGE grew exponentially in the late nineties and, by analysing the studies available in the literature, it is possible to describe a trend in the subjects that have been investigated. DGGE was first used as a tool to monitor the ecology of fermented food, such as fermented sausage, cheese and sourdough, and later it also showed its potential in microbial spoilage process. In the last few years, the main application of DGGE has been to study fermented food from Asia, Africa and South America. The information collected using DGGE has made it possible to confirm the existing knowledge on food fermentation and spoilage. However, in some cases, new evidence that helps scientists to fully comprehend a specific microbial ecosystem has emerged. In this review, the roadmap of culture independent methods in food microbiology will be summarized, focusing on the DGGE technique. Examples of how this approach is useful to obtain a better understanding of microbial diversity are reported for several kinds of fermented food, such as fermented sausage, cheese and wine. The future of culture independent methods in food microbiology, with the increasing availability of next generation sequencing techniques, is also discussed.
authors.affiliation: Università di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Via Leonardo da Vinci 44, Grugliasco, 10095 Turin, Italy. Electronic address: lucasimone.cocolin@unito.it.
authors.forename: Luca
authors.initials: L
authors.lastname: Cocolin
authors.forename: Valentina
authors.initials: V
authors.lastname: Alessandria
authors.forename: Paola
authors.initials: P
authors.lastname: Dolci
authors.forename: Roberta
authors.initials: R
authors.lastname: Gorra
authors.forename: Kalliopi
authors.initials: K
authors.lastname: Rantsiou
mesh_terms: D018407:Bacterial Physiological Phenomena; D044822:Biodiversity; D058645:Denaturing Gradient Gel Electrophoresis; D005285:Fermentation; D005516:Food Microbiology / Q000379:methods*; D005658:Fungi / Q000502:physiology; D006801:Humans; D064307:Microbiota / Q000502:physiology*
keywords: Culture independent methods; DGGE; Food fermentation; Food spoilage; Microbial ecology