Unearthing microbial genome sequences yields genetic determinants of the probiotic potential in Lacticaseibacillus paracasei strains E-25 and E-49 isolated from the vagina of cows kept on an organic farm

Study of the genomes and functional properties of autochthonous bacterial strains isolated from the bovine reproductive tract may provide a basis for assessing their probiotic potential and for developing new treatments for genital tract microbiome disorders. This study aimed to analyze the characteristics of whole genomes, primarily relevant to probiotic potential, of two Lacticaseibacillus paracasei strains (E-25 and E-49) isolated from the vaginas of cows kept at the Valaam Monastery organic farm (Republic of Karelia, Russia), following preliminary selection using in vitro tests. Whole-genome sequencing (WGS) of these strains was performed using the Illumina MiSeq platform. In vitro analysis revealed zones of inhibition against Clostridium perfringens with diameters of 32.0 ± 1.1 and 38.0 ± 1.0 mm for strains E-25 and E-49, respectively. The inhibitory effect against Streptococcus agalactiae was 16 ± 0.7 mm for strain E-25, and 32 ± 1.9 mm for strain E-49 against Enterococcus faecalis. Both strains exhibited antifungal activity against Aspergillus spp. (22 ± 0.6 and 20 ± 0.9 mm for E-25 and E-49, respectively). WGS revealed that the genome sizes of strains E-25 and E-49 were 2,913,242 and 3,050,973 bp, respectively, with GC contents of ~46%. In silico analysis revealed the presence of the EnlA and cbnCP52 bacteriocin genes in strain E-25, while strain E-49 harbored a gene cluster homologous to the sactipeptide and ribosomally synthesized and post-translationally modified peptide (RiPP) groups. The genomes of both strains contained a spectrum of genes responsible for heteroenzymatic lactic acid fermentation, the biosynthesis of vitamins B2, B6, and B7, adhesion systems, and oxidative stress resistance determinants. Comparative analysis revealed that the proportion of genes associated with carbohydrate metabolism and phosphotransferase systems in the E-49 genome is 10.0%, higher than that in strain E-25 (2.9%). The identified genetic features and phenotypic characteristics suggest that strains E-25 and E-49 are candidates for the development of targeted probiotic preparations.