Genomic characterization of Lacticaseibacillus paracasei strains from Greek fermented olives reveals common and unique characteristics and distinct clades

In this study, we isolated and sequenced the genomes of three lactic acid bacteria derived from Greek fermented table olives. The isolates, OLXI-1, OLXI-6, and OLXI-9, all belonged to the species Lacticaseibacillus paracasei, and a phylogenomic analysis revealed they clustered into three distinct clades. A pangenome analysis was performed with 220 public Lc. paracasei genomes and the three olive isolates. The source (dairy, non-dairy) and the geographical information (Asia, Europe, North America, South America, Africa) of each strain were mapped onto the pan-genome and the phylogeny to inform the possible inter-environmental transmission of Lc. paracasei. Based on the carbohydrate-active enzyme (CAZyme) annotation of the Lc. paracasei genomes, we identified unique gene clusters and CAZymes relevant to their physiological role in fermented foods, as well as traits that may contribute to health benefits. We also compared in silico results with functional in vitro experiments to assess growth on different prebiotic substrates (fructooligosaccharides FOS, XOS, galactooligosaccharides GOS, and inulin), growth in olive pomace, and in the production of inhibitory substances. Notably, consistent with the observed presence of the relevant CAZymes, the olive-derived strain, OLXI-9, grew best on the two fructans, inulin and FOS, with cell densities even higher than glucose.IMPORTANCEFermentation has long been used to preserve and enhance the shelf-life, flavor, texture, and functional properties of food. Table olives, in particular, are well known for their sensory and nutritional properties, and more recently, the microbiota of fermented olives has been suggested to contribute potential benefits in the gastrointestinal tract. In this study, a strain of Lacticaseibacillus paracasei, isolated from Greek fermented table olives, had the genetic and physiological capacity to consume prebiotic substrates. These findings provide a basis for understanding how fermentation-associated microbes grow on prebiotic fibers and potentially contribute to human health.