Fermenting food is an ancient form of preservation ingrained many in human societies around the world. Westernized diets have moved away from such practices, but even in these cultures, fermented foods are seeing a resurgent interested due to their believed health benefits. Here, we analyze the microbiome and metabolome of organically fermented vegetables, using a salt brine, which is a common ‘at-home’ method of food fermentation. We found that the natural microbial fermentation had a strong effect on the food metabolites, where all four foods (beet, carrot, peppers and radishes) changed through time, with a peak in molecular diversity after 2–3 days and a decrease in diversity during the final stages of the 4-day process. The microbiome of all foods showed a stark transition from one that resembled a soil community to one dominated by Enterobacteriaceae, such as Erwinia
spp., within a single day of fermentation and increasing amounts of Lactobacillales through the fermentation process. With particular attention to plant natural products, we observed significant transformations of polyphenols, triterpenoids and anthocyanins, but the degree of this metabolism depended on the food type. Beets, radishes and peppers saw an increase in the abundance of these compounds as the fermentation proceeded, but carrots saw a decrease through time. This study showed that organically fermenting vegetables markedly changed their chemistry and microbiology but resulted in high abundance of Enterobacteriaceae which are not normally considered as probiotics. The release of beneficial plant specialized metabolites was observed, but this depended on the fermented vegetable.
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