Collection of 40 genomes isolated from fermented vegetables
This study investigates bacterial isolates associated with traditional fermented vegetables through whole-genome sequencing and comprehensive genomic analysis. A total of 40 bacterial isolates were obtained from fermented carrot, sauerkraut, white cabbage kimchi, and fermented kohlrabi. The isolates were collected at different fermentation stages to characterise the cultivable bacterial community present throughout the fermentation process.  The isolation strategy was specifically designed to maximise the recovery of taxonomic and strain-level diversity of lactic acid bacteria present in these fermentations. Samples were plated on MRS agar supplemented with bromocresol green (25 mg/L), allowing visual differentiation of colonies based on morphological characteristics. Colonies displaying distinct morphologies were selected, resulting in more than 600 primary isolates.  Species-level identification of the isolates was carried out using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Representative isolates from each identified species were further characterised using API® 50 CH biochemical profiling and (GTG)5 repetitive sequence-based PCR fingerprinting to evaluate intraspecies diversity. By integrating species identification with strain-level differentiation, 40 isolates were strategically selected to represent the observed diversity and subjected to whole-genome sequencing.  Whole-genome sequencing enabled high-resolution taxonomic confirmation and comparative genomic analyses, providing insights into the genetic composition, functional potential, and ecological roles of the isolates during fermentation.  These genomes were isolated and sequenced in the context of Horizon Europe DOMINO project 101060218.