Multi-omics analyses reveal the regulation mechanisms of organic acid biosynthesis in newly isolated lactic acid bacteria with application in corn biomass fermentation

Lactic acid bacteria (LAB) are widely used in industrial fermentation due to their versatile metabolic capabilities. This study investigated the molecular mechanisms underlying organic acid biosynthesis in newly isolated <i>Lactiplantibacillus plantarum</i> YC1-1-4B and <i>Lentilactobacillus buchneri</i> PC-C1 strains at two culture intervals and their applications in corn biomass fermentation. YC1-1-4B exhibited faster growth and higher organic acid production (29.18 ± 2.17 mg/L at 12h) compared to PC-C1. Genomic and transcriptomic analyses revealed significant upregulation of <i>ldh</i> and <i>ackA</i> genes at 12h, enhancing lactate and acetate metabolism. In PC-C1, ribosome and RNA polymerase genes were upregulated at 12h, while YC1-1-4B showed activation of the pentose phosphate pathway at both 6h and 12h. Notably, YC1-1-4B highly expressed genes converting 6-phosphogluconolactone and succinyl CoA to organic acids at 12h. Both strains displayed <i>sucC</i> and <i>sucD</i> gene overlap at 12h, suggesting translational coupling. RNA-seq and RT-qPCR results were strongly correlated. LAB fermentation reduced pH over time, with YC1-1-4B exhibiting a homofermentative profile and PC-C1 maintaining a heterofermentative metabolism, enhancing corn biomass stability through acetic acid production. The combined inoculation (PCYC) shifted fermentation from lactic acid to acetic acid dominance, enhancing corn biomass preservation and LAB proliferation. These findings link genomic regulation to practical fermentation applications.