Phenotypic and genomic evaluation of the probiotic potential of Lacticaseibacillus paracasei IB1 isolated from herdsmen's yogurt in Qinghai, China

Lacticaseibacillus paracasei IB1 was isolated from herders' homemade yogurt in Qinghai Province, China. A comprehensive safety assessment verified the absence of β-hemolytic activity in this strain, a critical criterion for probiotic safety. In vitro tolerance assays demonstrated robust gastrointestinal adaptability: the survival rate was 73.84 ± 2.86% in simulated gastric juice (pH 3.0), 63.82 ± 0.28% in simulated intestinal juice, and 23.77 ± 0.38% in media supplemented with 0.3% bile salts. The scavenging rates of the DPPH free radical and ABTS free radicals were 36.77 ± 0.39% and 85.99 ± 1.17%, respectively. This indicates that the IB1 strain has excellent antioxidant capacity. The cell-free supernatant of L. paracasei IB1 exhibited broad-spectrum antibacterial activity against 11 pathogens, notably damaging enterotoxigenic Escherichia coli K88 and Shigella baumanii ATCC9207, and it was a proficient producer of short-chain fatty acids (acetic, isovaleric, propionic, and butyric acids), which are metabolites that support gut health. Whole-genome sequencing revealed that L. paracasei IB1 has one chromosome, three plasmids, and 3,193 coding sequences (CDSs). Genomic annotation revealed 2 complete prophage regions, 2 bacteriocin gene clusters (linked to antibacterial activity), and 11 genomic islands (associated with environmental adaptation). Functional prediction revealed enrichment of genes for transcriptional regulation and carbohydrate/amino acid transport/metabolism; CAZyme analysis revealed 124 CAZyme-encoding genes (strong carbohydrate utilization), and GutSMASH annotation revealed 4 specialized metabolic gene clusters (potential bioactive secondary metabolite production). Overall, L. paracasei IB1 has in vitro and in vivo safety, favorable gastrointestinal tolerance (acid and bile resistance), a broad antibacterial spectrum, inoxidizability, and beneficial SCFA-producing ability, strongly supporting its potential as a novel, promising probiotic candidate for future food and nutraceutical applications. Importance: This study's significance lies in identifying and validating a potential probiotic strain, L. paracasei IB1. A comprehensive evaluation confirmed that L. paracasei IB1 has excellent gastrointestinal acid and bile salt tolerance, strong antibacterial activity, and efficient short-chain fatty acid production. These findings underscore the immense value of mining novel probiotics from such traditional fermented foods, offering promising candidates for functional and nutritional health products while emphasizing the importance of preserving local traditional fermented foods for scientific research. • Probiotic Lacticaseibacillus paracasei IB1 exhibits excellent intestinal tolerance. • Strain IB1 shows potent antibacterial activity against 11 specific pathogens. • Genome-wide analysis reveals the potential probiotic characteristics of IB1. • Strain IB1 possesses the ability to produce short-chain fatty acids (SCFAs).