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

• Published in: Biology (Basel, Switzerland) Vol. 11; no. 2; p. 294
• Main Authors: Namrak, Thanawat, Raethong, Nachon, Jatuponwiphat, Theeraphol, Nitisinprasert, Sunee, Vongsangnak, Wanwipa, Nakphaichit, Massalin
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 11.02.2022; MDPI
• Subjects: Amino acids; Asparagine; Bacteria; Biomass; Biosynthesis; Carbon; Carbon sources; Cell culture; cost effectiveness; Food industry; Gene expression; genome-scale metabolic model; Genomes; Glucose; Glutamine; Laboratories; Lactic acid; Lactic acid bacteria; Lactose; Limosilactobacillus reuteri; Linear programming; Lipids; metabolic capability; Metabolism; Metabolites; Nutrients; Physiology; probiotic strain; Probiotics; Proteins; Salmonella; Simulation; Sucrose; transcriptome; Transcriptomes; Transcriptomics; urea cycle; vitamin B complex; United States > US; Japan; metabolic capability; probiotic strain; Limosilactobacillus reuteri; genome-scale metabolic model; nutrients
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology11020294

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.