Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of Probiotic Limosilactobacillus reuteri KUB-AC5

SIMPLE SUMMARY: Considerable attention has been given to the species Limosilactobacillus reuteri regarding its probiotic potential. Here, the genome-scale metabolic model (GSMM) of L. reuteri KUB-AC5, namely iTN656 was developed and exploited to evaluate the metabolic capability of L. reuteri KUB-AC5 under various carbon sources. The simulated growth behaviors of iTN656 under single and double omission analysis promisingly identified 14 essential single nutrients and 2 essential double nutrients (pairwise glutamine-glutamate and asparagine-aspartate) for L. reuteri KUB-AC5 growth. Moreover, the integrated transcriptomic analysis using iTN656 allowed to probe the potential metabolic routes for enhancing growth of L. reuteri KUB-AC5 involved in sucrose uptake, nucleotide biosynthesis, urea cycle, and glutamine transporter. Overall, iTN656 provides a powerful systems biology platform for gaining insights into cell metabolism of lactic acid bacteria and guiding the rational development of synthetic media design for scale-up of probiotic production in industrial scale. ABSTRACT: Limosilactobacillus reuteri KUB-AC5 displays the hallmark features of probiotic properties for food and feed industries. Optimization of cultivation condition for the industrial production is important to reach cell concentration and cost reduction. Considering the strain-specific growth physiology, metabolic capability, and essential nutrients of L. reuteri KUB-AC5, the genome-scale metabolic model (GSMM) of L. reuteri KUB-AC5 was developed. Hereby, the GSMM of iTN656 was successfully constructed which contained 656 genes, 831 metabolites, and 953 metabolic reactions. The iTN656 model could show a metabolic capability under various carbon sources and guide potentially 14 essential single nutrients (e.g., vitamin B complex and amino acids) and 2 essential double nutrients (pairwise glutamine-glutamate and asparagine-aspartate) for L. reuteri KUB-AC5 growth through single and double omission analysis. Promisingly, the iTN656 model was further integrated with transcriptome data suggesting that putative metabolic routes as preferable paths e.g., sucrose uptake, nucleotide biosynthesis, urea cycle, and glutamine transporter for L. reuteri KUB-AC5 growth. The developed GSMM offers a powerful tool for multi-level omics analysis, enabling probiotic strain optimization for biomass overproduction on an industrial scale.