Abstract
Lactobacillus casei strains are widely used in industry and the utility of this organism in these industrial applications is strain dependent. Hence, tools capable of predicting strain specific phenotypes would have utility in the selection of strains for specific industrial processes. Genome-scale metabolic models can be utilized to better understand genotype-phenotype relationships and to compare different organisms. To assist in the selection and development of strains with enhanced industrial utility, genome-scale models for L. casei ATCC 334, a well characterized strain, and strain 12A, a corn silage isolate, were constructed. Draft models were generated from RAST genome annotations using the Model SEED database and refined by evaluating ATP generating cycles, mass-and-charge-balances of reactions, and growth phenotypes. After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors. We conclude that the metabolic capabilities of the two networks are highly similar. The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes. The developed L. casei ATCC 334 and 12A metabolic models will enable better understanding of the physiology of these organisms and be valuable tools in the development and selection of strains with enhanced utility in a variety of industrial applications.
Highlights
Lactobacillus casei are Gram positive, non-sporulating, nutritionally fastidious and strictly fermentative bacteria that produce lactic acid as their principal metabolic end product [1]
The number of pseudogenes in 12A is 152, a relatively high number compared to the 82 in L. casei ATCC 334, which could indicate that L. casei 12A has undergone more extensive gene decay
Comparative genome analysis between the strains indicates that they share 2,222 orthologous genes; L. casei 12A has 507 unique genes compared to L. casei ATCC334, whereas L. casei ATCC334 has 423 unique genes compared to L. casei 12A
Summary
Lactobacillus casei are Gram positive, non-sporulating, nutritionally fastidious and strictly fermentative bacteria that produce lactic acid as their principal metabolic end product [1]. The utility of L. casei in all of these applications is strain dependent, due to significant variation in gene content that is present in this species. Comparative genome analysis of seventeen L. casei strains has revealed this species has an average of 2,800 orthologous genes (6151), of which 1,715 are shared by all the strains, and 4,220 non-conserved orthologous genes with an average of 119 unique genes found in each strain [5]. This large variation in gene content allows for the selection of strains with unique and industrially important characteristics. Detailed comparisons of strain specific differences at the genomic and phenotypic level are needed
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