Integrated Metabolomics and Transcriptomics Analyses Identify Key Amino Acid Metabolic Mechanisms in Lacticaseibacillus paracasei SMN-LBK

During lactobacillus fermentation, the types of proteins in the fermentation substrate significantly influence the characteristics of the fermented product. Proteins are composed of various amino acids. Consequently, investigating the metabolic mechanisms of key amino acids during lactic acid bacteria fermentation is important for improving their application in the food industry. In this study, the growth of <i>Lacticaseibacillus paracasei</i> SMN-LBK was significantly inhibited following glutamate and arginine deficiency (<i>p</i> < 0.05). Genomic analysis and in vitro addition assays showed that α-ketoglutarate (OXO), as a precursor of glutamate, significantly eliminated growth inhibition of SMN-LBK (<i>p</i> < 0.05). Meanwhile, the inhibition of SMN-LBK growth following arginine deficiency may be linked to glutamate. Metabolomics analysis illustrated that glutamate and arginine deficiencies mainly affected the carbohydrate and amino acid metabolic pathways of SMN-LBK, especially the pentose phosphate pathway, alanine, glutamate and aspartate metabolism, and arginine metabolism. Transcriptomics analysis further identified glutamate and arginine deficiencies affecting carbohydrate and amino acid metabolism, specifically the glutamate metabolism, pentose phosphate pathway, and glycolysis/gluconeogenesis, involving key genes such as pfkA, gapA, ldh, argG, argE, and argH. Elucidating the molecular mechanisms of key amino acids in SMN-LBK will provide a theoretical foundation for understanding the differential fermentation of various proteins by lactic acid bacteria.