Comparative Genomics Analysis Combined with Homologous Overexpression Reveals the Mechanism of Species-Specific Acid Stress Resistance in Bifidobacterium animalis.

Most Bifidobacterium species exhibit poor stress tolerance, which greatly limits their stability and industrial application. In contrast, Bifidobacterium animalis shows remarkable tolerance and distinct species-specific characteristics. Here, the survival rate of 17 strains from six Bifidobacterium species was evaluated under pH 2.5 for 2 h. All strains of B. animalis maintained survival rates above 60%, whereas other species fell below the detection limit. Comparative genomic analysis among B. animalis, B. breve, B. longum, and B. bifidum revealed 328 unique genes that were conserved across B. animalis strains but absent in the other species. Transcriptomic analysis of the B. animalis subsp. lactis A6 strain under acid stress identified ten genes that were significantly upregulated at both early and late stages of exposure. Homologous overexpression confirmed that four of these genes markedly enhanced survival under acid stress. Among them, BAA6_RS00480, encoding a GlsB/YeaQ/YmgE family stress response membrane protein, increased the survival rate by more than 22-fold. These findings provide new insight into the species-specific genetic mechanisms underlying the exceptional acid tolerance of B. animalis.