Reconstruction and analysis of the genome-scale metabolic model of Lactobacillus casei LC2W

• We build the first genome-scale metabolic model for L. casei LC2W.
• The iJL846 model was experimentally validated by cell growth on 15 carbohydrates.
• 10 amino acids and 7 vitamins were identified to be essential for L. casei LC2W.
• Biosynthetic potential of 4 typical metabolites was explored on the iJL846 model.

Lactobacillus casei LC2W is a recently isolated probiotic lactic acid bacterial strain, which is widely used in the dairy and pharmaceutical industries and in clinical medicine. The first genome-scale metabolic model for L. casei, composed of 846 genes, 969 metabolic reactions, and 785 metabolites, was reconstructed using both manual genome annotation and an automatic SEED model. Then, the iJL846 model was validated by simulating cell growth on 15 reported carbon sources. The iJL846 model explored the metabolism of L. casei on a genome scale: (1) explanation of the genetic codes—metabolic functions of 342 genes were reannotated in this model; (2) characterization of the physiology—10 amino acids and 7 vitamins were identified to be essential nutrients for L. casei LC2W growth; (3) analyses of metabolic pathways—the transport and metabolism of the 17 essential nutrients and exopolysaccharide (EPS) biosynthesis—were performed; (4) exploration of metabolic capacity was conducted—for lactate, the importance of genes in its biosynthetic pathways was evaluated, and the requirements of amino acids were predicted for mixed acid fermentation; for flavor compounds, the effects of oxygen were analyzed, and three new knockout targets were selected for acetoin production; for EPS, 11 types of nutrients in the rich medium and important reactions in the biosynthetic pathway were identified that enhanced EPS production. In conclusion, the iJL846 model serves as a useful tool for understanding and engineering the metabolism of this probiotic strain.