Fermented food microbial ecosystem

The evaluation of microbial diversity in fermented food is problematic. It is often difficult to cultivate viable microorganisms using known media, as part of them might not be cultivable in vitro. Some species are outcompeted by numerically more abundant microbial species. Moreover, Fleet (1999) highlighted that adverse conditions in food ecosystem such as nutrient depletion, heat treatments, pH variations, or low temperatures could induce microbial cells in a stressed state characterized by the inability to produce colonies on media even if they are stiU able to perform metabolic activity. They enter in a viable but noncultivable state, which cannot be detected by culture-dependent methods. 

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Currently, advanced molecular methods represent an invaluable tool in the study of food ecosystems and the strains responsible of fermentation processes. At the same time, especially in industrial or applied microbiology, phenotypic tests, which were used widely in the past for microbial identification, are still being considered for the characterization of strain metabolic properties, growth performance, resistance to industrial processes, and shelf life. However, due to their poor reproducibility and low discriminatory power, phenotypic methods have been almost abandoned for identification purposes. Their low taxonomic resolution often leads to differentiation only at the genus level, and they require a labor-intensive approach. On the contrary, genotypic techniques provide a more robust classification and identification, and their costs, over the years, have been decreasing. 

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