Metagenomic analysis is ubiquitous in the study of diverse environmental ecosystems, but has until recently not been widely used for microbial analysis of foods because of the presumed low diversity and well-established traditional culture-dependent methods. Spontaneously fermented foods, due to the method of their preparation, contain a diverse microbial community which contributes to the sensory and functional properties of such foods and can at the same time pose a potential safety risk. Numerous metagenomic analyses of spontaneously fermented foods have revealed the diversity of the microbial community present in food. It has been shown that different types of lactic acid bacteria often predominate in microbial communities and often apply selective pressure on other present microorganisms with produced fermentation products. Metagenomic analytical techniques can be successfully used to evaluate food safety and investigate the diversity of the present microbial community and its metabolic potential. Metagenomic techniques in reviewed studies have often been accompanied by other omic approaches to acquire additional information as metagenomics alone does not provide necessary information to evaluate food quality, safety and functionality.
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