Strain-resolved comparative genomics and functional characterization of culturable lactic acid bacteria from Guizhou sour soup

Abstract Guizhou sour soup is a traditional fermented food and a reservoir of diverse lactic acid bacteria (LAB), yet the strain-resolved genomic architecture and functional heterogeneity of its culturable LAB remain poorly defined. We established a large culture collection and integrated comparative genomics with targeted analyses of bile salt hydrolase (BSH), exopolysaccharide/capsular polysaccharide (EPS/CPS) loci, genomic safety, and in vitro phenotypes to evaluate strain-level diversity and identify traits relevant to functional strain selection. Among 1,741 culturable isolates recovered from red and white sour soups, Lactobacillales accounted for 85.69% and 95.24%, respectively. Whole-genome sequencing of 172 isolates, comprising 92 Lacticaseibacillus paracasei , 30 Lactiplantibacillus plantarum , and 50 Limosilactobacillus fermentum , revealed open pan-genomes with distinct species-level functional architectures. L. paracasei showed the greatest accessory-genome contribution, L. plantarum the highest mean normalized BSH representation, and L. fermentum distinct oxidative-stress- and amino-acid-associated profiles. No antimicrobial resistance or virulence-associated genes were detected at the applied screening thresholds. BSH analyses showed lineage-specific sequence variation but conserved catalytic Cys2 and ligand-proximal architecture, whereas EPS/CPS loci varied among species and strains. Cholesterol removal was strongly strain- and condition-dependent: L. paracasei R1156 reached 71.69 ± 4.84% in standard MRS, while L. plantarum R2345, R2037, R1621, and R203 maintained 56.85–64.32% removal under 0.1% bile salts, exceeding the reference strain Lacticaseibacillus rhamnosus GG (LGG). These findings establish a strain-resolved genomic and phenotypic resource and demonstrate the value of integrating comparative genomics with direct phenotypic screening for rational selection of food-associated LAB for further biotechnological evaluation.