Comparative genomic analysis of selected lactic acid bacteria and phenotypic association of the key genes involved in fructan and ribose utilisation

Abstract Lactic acid bacteria (LAB) are valued in the food industry due to their ability to utilise a wide range of compounds, especially carbohydrates, and production of organic acids. A large species diversity and proven safety of LAB have led to the investigation into their potential for innovative industrial application. Owning to their diversity in carbohydrates fermentation, identification of the strain with desired phenotype using traditional experimental methods can be time-consuming and resource intensive while predicting phenotypes solely based on genome analysis is highly dependent on the existing knowledge about genotype–phenotype correlation. This study included the within-species comparative genomics and genotype–phenotype analysis based on carbohydrate metabolism. Genomes of 31 LAB belonging to Lacticaseibacillus paracasei ( L. paracasei ), Lactiplantibacillus plantarum ( L. plantarum ), and Pediococcus pentosaceus ( P. pentosaceus ) were sequenced. Gene-trait matching (GTM) analysis were conducted to identify genes associated with specific carbohydrate utilization phenotypes. The ability of the strains to ferment 23 carbohydrates, including monosaccharides, sugar alcohols, disaccharides, and polysaccharides, was determined and compared to the presence of glycoside hydrolases (GH) on their genomes. The results revealed significant intra- and inter-species diversity in carbohydrate utilization and provided indirect evidence for gene loss and horizontal gene transfer in the evolution of LAB. The GTM enabled the identification of a genetic cluster associated with ribose utilisation in L. paracasei , a novel genetic trait within the species. Furthermore, the GTM revealed the presence of fosABCDXE operon with extracellular fructan-β-fructofuranosidase in the genomes of inulin- and levan-fermenting strains of L. paracasei and P. pentosaceus . This study contributes to the growing knowledge of LAB species establishing a foundation for future genomic and functional investigations aimed at unravelling the intricate connections between their diverse genetic characteristics and specific phenotypes.