biostudies-literatureZhao LScience and Technology Project of the Shanghai Municipal Market Supervision AdministrationScience and Technology Project of the Shanghai Institute of Quality Inspection and Technical Research2282https://www.ebi.ac.uk/biostudies/studies/S-EPMC9367767biostudies-literatureUnknown11(15)Probiotics are universally recognized for their health benefits, despite the fact that their effects depend on the strain. Identification and enumeration of probiotic strains are required prior to evaluating their effectiveness. <i>Lacticaseibacillus rhamnosus</i> X253 is a potential probiotic strain with antioxidant capacity. Comparative genomics and single nucleotide polymorphisms (SNPs) were used to identify a strain-specific locus within the <i>holA</i> gene for strain X253 that was distinct in 30 different <i>L. rhamnosus</i> strains. Using quantitative PCR, the primers and probe designed for the locus were able to distinguish <i>L. rhamnosus</i> X253 from the other 20 probiotic strains. The chosen locus remained stable over 19 generations. The sensitivity of the assay was 0.2 pg genoFoods (Basel, Switzerland)Quantitative PCR Assays for the Strain-Specific Identification and Enumeration of Probiotic Strain <i>Lacticaseibacillus rhamnosus</i> X253.PMC9367767KY-2021-1-SP2022-49Liu YZhao LZhang DJiang QYWang SJXu QMeng DQZhang YNZhong JZhao YfalseQuantitative PCR Assays for the Strain-Specific Identification and Enumeration of Probiotic Strain <i>Lacticaseibacillus rhamnosus</i> X253.Probiotics are universally recognized for their health benefits, despite the fact that their effects depend on the strain. Identification and enumeration of probiotic strains are required prior to evaluating their effectiveness. <i>Lacticaseibacillus rhamnosus</i> X253 is a potential probiotic strain with antioxidant capacity. Comparative genomics and single nucleotide polymorphisms (SNPs) were used to identify a strain-specific locus within the <i>holA</i> gene for strain X253 that was distinct in 30 different <i>L. rhamnosus</i> strains. Using quantitative PCR, the primers and probe designed for the locus were able to distinguish <i>L. rhamnosus</i> X253 from the other 20 probiotic strains. The chosen locus remained stable over 19 generations. The sensitivity of the assay was 0.2 pg geno2022-01-01T00:00:00Z2022 Jul2026-04-08T09:49:14.324Z2025-04-06T09:27:02.928ZS-EPMC93677673595404810.3390/foods11152282