Systematic identification of Lactobacillus plantarum auxotrophs for fermented Nham using genome-scale metabolic model

• Published in: Journal of biotechnology 2012-12, Vol.162 (2-3), p.327-335
• Main Authors: Chiewchankaset, Porntip, Srimarut, Yanee, Klanchui, Amornpan, Kurdi, Peter, Plengvidhya, Vethachai, Meechai, Asawin
• Format: Article
• Language: English
• Subjects: Auxotroph; Bioengineering; Computer Simulation; Essential gene; Fermentation; Gene Deletion; Genome, Bacterial; Genome-scale metabolic model; Lactobacillus plantarum; Lactobacillus plantarum - genetics; Lactobacillus plantarum - metabolism; Lactobacillus plantarum - physiology; Meat Products - microbiology; Models, Biological; Phenotype; Phenotypic characteristics; Systems Biology - methods
• ISSN: 0168-1656; 1873-4863
• DOI: 10.1016/j.jbiotec.2012.08.019

► We propose a systematic strategy to identify the auxotrophic starters. ► A genome-scale model is used to study the phenotypic characteristics of Nham. ► We obtained a list of auxotrophic strains and their nutritional supplements. ► A computational platform will facilitate for auxotroph starters development. In this study, a systematic strategy is presented, which identifies auxotrophic starters for the popular Thai fermented sausage product, called Nham, using a genome-scale metabolic model. A published genome-scale model of Lactobacillus plantarum WCFS1 is adopted for studying the L. plantarum BCC9546 characteristics cultured on Simulated Nham Broth. Single gene deletion analysis is performed to determine the genes essential for cell growth. Strains lacking such essential genes are considered potential auxotrophic mutants. Then, metabolite supplement analysis is introduced to determine a list of metabolites supplements for each mutant required to restore its growth. Herein, 9 potential auxotrophs are proposed for use in Nham fermentation, along with their metabolite supplements. Simulation studies showed that the secreted fluxes of organic acids, as well as amino-derived flavor compounds of these auxotrophs, are similar to those of the wild-type, indicating that Nham fermented by these auxotrophs would have similar tastes and flavors as Nham fermented by the wild-type. These proposed auxotrophs and corresponding nutritional supplements will be useful for the design of auxotroph starter culture utilized for Nham production in the laboratory. The systematic strategy presented here will facilitate the analysis and development of auxotroph starters used in the food industry.