Abstract
Naturally fermented vegetables may provide specific health benefits as they contain diverse nutrients, complex polysaccharides, probiotic microbes, and metabolites, which are transformed from fresh vegetables. Therefore, the kind of vegetable used to ferment and how they are grown may determine the types of health-promoting properties. To further understand the possible benefits of diverse fermented vegetables under distinct growing conditions, we compared the microbiome and metabolome of three different types of naturally fermented vegetables – carrots, peppers, and radishes, that were grown under conventional or regenerative organic growing systems. We profiled bacterial communities via 16S rRNA short read (V4 region) and long-read sequencing and fungal communities using ITS2 sequencing, in tandem with untargeted metabolomics (LC-MS). Results showed that the microbiome and metabolome of the fermented vegetables under each growing system is unique, highlighting distinctions in amino acid metabolites and potentially probiotic microbes (_P_<0.05). Regardless of the growing system, all fermented vegetables contained high amounts of gamma-aminobutyric acid (GABA), a critical neurotransmitter. However, GABA was found to be in higher abundance in the regenerative organic fermented vegetables, particularly in carrots (_P_<0.01) and peppers (_P_<0.05) and was associated with higher abundances of the typically probiotic _Lactiplantibacillus plantarum_. Our findings indicate that different vegetables grown in similar soils under different farming practices may influence the microbiome and metabolome of a fermented vegetable, with implications for their overall health-promoting potential.