title: Impact of next generation sequencing techniques in food microbiology.
abstract: Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.
authors.affiliation: Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain.
authors.forename: Baltasar
authors.initials: B
authors.lastname: Mayo
authors.affiliation: Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil.
authors.forename: Caio T C C
authors.initials: CT
authors.lastname: Rachid
authors.affiliation: Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain.
authors.forename: Angel
authors.initials: A
authors.lastname: Alegría
authors.affiliation: Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil.
authors.forename: Analy M O
authors.initials: AM
authors.lastname: Leite
authors.affiliation: Instituto de Microbiologia, Departamento de Microbiologia Geral, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, 21941904-Cidade Universitária, Rio de Janeiro, RJ, Brazil.
authors.forename: Raquel S
authors.initials: RS
authors.lastname: Peixoto
authors.affiliation: Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain.
authors.forename: Susana
authors.initials: S
authors.lastname: Delgado
keywords: Food ecology.; Food microbiology; Illumina; Molecular microbial ecology; NGS techniques; Next generation sequencing; Pyrosequencing