Comparative genomic analysis of hydrogen peroxide and nitric oxide metabolic pathways in Limosilactobacillus fermentum

Limosilactobacillus fermentum strains influence human health through distinct metabolic pathways; however, the genetic basis of these strain-specific functions remains unclear. This study investigated phenotypic divergence between two L. fermentum strains isolated from the human oral microbiome. Despite 98.2% average nucleotide identity, comparative genomics revealed substantial strain-specific gene repertoires (485 and 542 unique genes in DM072 and DM075, respectively). Functional characterization demonstrated that DM072 synthesizes hydrogen peroxide via pyruvate oxidase (EC 1.2.3.3; K00158), conferring strong antimicrobial efficacy against the Streptococcus mutans. Conversely, DM075 lacks this oxidative pathway but exhibits six-fold elevated nitrate reductase activity during the stationary phase. Transcriptomic profiling revealed significant temporal upregulation of glutamate synthase (gltB, p < 0.05) and alkyl hydroperoxide reductase (ahpC, p < 0.05) in DM075, indicating coordinated nitrogen assimilation and oxidative stress responses. Bioinformatic analyses identified strain-specific enzymatic profiles, including differential distributions of glycosyl hydrolases and transferases, alongside disparate acid tolerance (pH 2.5 for DM075 vs. pH 3.0 for DM072). These findings demonstrate functional specialization at the strain level within closely related taxa, highlighting the potential of DM072 as an antimicrobial probiotic for dental caries prophylaxis and DM075 as a potential cardiovascular homeostasis modulator via the nitrate–nitrite–nitric oxide pathway.