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||Bacteria Escherichia coli
||Monk JM et al., Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A. 2013 Dec 10110(50):20338-43. doi: 10.1073/pnas.1307797110. p.20341 table 1PubMed ID24277855
||Abstract: "Genome-scale models (GEMs) of metabolism were constructed for 55 fully sequenced Escherichia coli and Shigella strains." P.20343 right column bottom paragraph: "Materials and Methods: The strain-specific model reconstruction procedure, gap filling algorithms, and in silico growth simulation conditions are described in SI Materials and Methods. Heatmap and phylogenetic tree and decision tree construction are described in SI Materials and Methods Carbon source and growth testing protocols are described in SI Materials and Methods. Eleven strains of E. coli and one strain of S. flexneri were tested as part of this study. The 11 E. coli strains are SMS 3–5, CFT073, HS, DH1, UMN 026, K011, Sakai, ATCC 8739, 042, EDL933, and K-12 MG1655. The S. flexneri strain was 2457T. E. coli 042 was a gift from Ian Henderson (Birmingham University, Birmingham, UK). All other strains were purchased from ATCC."
||P.20339 right column 4th paragraph: "Set of Substrates Differentiate Pathogenic Strains from Commensal (Nonpathogenic) Strains: Based on simulated growth phenotypes, [investigators] observed a general separation of commensal strains from both extraintestinal pathogenic E. coli (ExPec) and intestinal pathogenic E. coli (InPec) strains of E. coli, suggesting that a classification schema of strains based on metabolic capabilities is possible (Fig. 3). Common laboratory strains of E. coli such as E. coli K-12 MG1655 are nonpathogenic, commensal strains. As a first step toward establishing such a schema, the separation between ExPec and commensal strain models was examined. A Fisher’s exact test was used to establish that models of ExPec strains exhibited a statistically significant capability to catabolize four unique compounds with P < 0.05 (Table 1). Most models of strains widely regarded as safe laboratory strains such as K-12 strains, BW2952, and DH1 were unable to grow on a unique subset of nutrients. Notably, N-acetyl-d-galactosamine supported growth in 100% of ExPec strain models compared with 67% of commensal strain models (P = 3.9 × 10^−2). Additionally, several commensal strain models exhibited a statistically significant overrepresentation of catabolic pathways for 13 nutrient sources (Table 1)." See caption beneath table