Apr 29, 2019 Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific

Salmonella strains are traditionally classi fi ed into serovars based on their surface antigens. While increasing availability of whole-genome sequences has allowed for more detailed subtyping of strains, links between genotype, serovar, and host remain elusive. Here we reconstruct genome-scale metabolic models for 410 Salmonella strains spanning 64 serovars. Model-predicted growth capabilities in over 530 different environments demonstrate that: (1) the Salmonella accessory metabolic network includes alternative carbon metabolism, and cell wall biosynthesis; (2) metabolic capabilities correspond to each strain ’ s serovar and isolation host; (3) growth predictions agree with 83.1% of experimental outcomes for 12 strains (690 out of 858); (4) 27 strains are auxotrophic for at least one compound, including L -tryptophan, niacin, L -histidine, L -cysteine, and p-aminobenzoate; and (5) the catabolic pathways that are important for fi tness in the gastrointestinal environment are lost amongst extraintestinal serovars. Our results reveal growth differences that may re fl ect adaptation to particular colonization sites. metabolic reconstructions for the species and subspecies of the Salmonella genus using strains with de fi ned serovars and fully sequenced genomes. We selected 410 high-quality, closed-genome sequences of Salmonella 15,16 , spanning both species, three subspecies and 64 different serovars. Choosing genomes that provide a diverse variety of subspecies, serovars, and hosts allowed for a comprehensive comparison of genomic features and metabolic capabilities across the Salmonella genus. Using this set of strain-speci fi c information, we reveal the basis for serovar-speci fi c and host-associated metabolic traits. growth could not be achieved, the model was fl agged for further investigation. Other identi fi cation tests that characterize Salmonella by its inability to produce a certain enzyme or to catabolize certain substrates were not taken into consideration here because they are already embedded in the curated metabolic reconstructions.

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