title: High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.
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.
authors.affiliation: Department of Agriculture, University of Naples Federico II, Portici, Italy. ercolini@unina.it
authors.forename: Danilo
authors.initials: D
authors.lastname: Ercolini
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000254:growth & development; D058448:Biota; D017753:Ecosystem; D005285:Fermentation; D005506:Food Contamination / Q000032:analysis*; D005516:Food Microbiology; D005798:Genes, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota; D012329:RNA, Bacterial / Q000032:analysis; D017423:Sequence Analysis, RNA
chemical_list: D012329:RNA, Bacterial