Comparative genomics of <i>Lacticaseibacillus paracasei</i> strain 69Bis reveals encoded probiotic traits and genomic specificities

This study provides a comprehensive characterization of Lacticaseibacillus paracasei strain 69Bis, isolated from traditional fermented goat milk collected in Biskra (southeast Algeria). Phenotypic investigations revealed robust probiotic traits across all isolates, including NaCl tolerance at 10%, acid resistance at pH 2.0 for 3 h, bile tolerance at 0.3%, and survival in simulated gastrointestinal digestion. Adhesion properties included high auto-aggregation and hydrophobicity. The strain exhibited potent antimicrobial activity, particularly against Pseudomonas aeruginosa. Whole-genome sequencing yielded a genome of 2.9 Mbp, with 46.38% GC and 2,969 protein-coding sequences, enriched in carbohydrate and amino acid metabolism. Functional annotation highlighted genomic features associated with probiotic functions, including adhesion factors (acm, fimA, lapA), stress response pathways, and exopolysaccharide synthesis (eps gene family). Three biosynthetic gene clusters were detected, encoding bacteriocins and terpene synthesis. The absence of known acquired antimicrobial resistance genes and the susceptibility to all tested antibiotics indicate a favourable safety profile. The presence of CRISPR-Cas systems was confirmed, which may contribute to genomic stability and protection against phages. Comparative genomics, through genome-based taxonomy, confirmed the assignment to Lacticaseibacillus paracasei. Pan-genome analysis of 122 genomes from the same species (including 69Bis) revealed an open pan-genome (6,878 genes, 25.76% core), along with several unique and rare determinants linked to probiotic traits in 69Bis. Overall, these results position strain 69Bis as a promising candidate for use in functional foods, particularly in the context of nutrition in arid regions.