Genome-based assessment of safety characteristics of Lacticaseibacillus paracasei NY1301 and genomic differences in closely related strains marketed as probiotics. Lacticaseibacillus paracasei strain:NY1301

The probiotic attributes of Lacticaseibacillus paracasei NY1301 were comprehensively characterized and a comparison with the closely related LcA (Actimel) and LcY (Yakult) probiotic strains was conducted using genomic tools. All strains exhibited high genetic similarity and likely share a common ancestor; differences were primarily expressed as minor chromosomal re-arrangements, substitutions, insertions, and deletions. Compared to LcY, NY1301 exhibited 125 single-nucleotide polymorphisms. NY1301 lacked virulence factor and antibiotic resistance genes and had a 46-kbp prophage. This prophage is spontaneously induced at low levels and remains in a non-lytic state under standard culture conditions. The observed causal adaptive mutations were likely related to niche adaptation within the respective laboratory or manufacturing processes while maintaining the strains. However, the phenotypic effects of these genomic differences remain unclear. Our open-label trial validated the safety of NY1301, consistent with previous in vivo studies and the long history of risk-free human consumption of the probiotic.