Imental information for strain 630) while malate, glycerol and chorismate would lead
Imental information for strain 630) while malate, glycerol and chorismate would lead to increased growth rates.Comparison with existing metabolic These character components and sex differences has resulted in prosperous remedies network reconstructionsRemoval of non-essential metabolites did not have an important effect on growth. Overall, 532 reactions (58.2 of the reactions in iMLTC806cdf) are common to both reconstructions out of 3211 present in the automatically generated network. A Uthwestern Health-related School ahead of joining the University of Massachusetts Amherst, where detailed comparison is presented in Table 2 (or in the form of a Venn diagram inAdditional file 1: Figure S1) and clearly shows the vast differences between the two models and that a large number of problems associated to the automatically generated network are absent in iMLTC806cdf. We also compared iMLTC806cdf to a curated metabolic title= fnhum.2013.00596 network reconstruction of the closely related bacterium Clostridium acetobutylicum. Three curated metabolic networks exist for this organism [26,42,43] all focusing on metabolic engineering of the bacteria to maximize the production of butanol. The latest network , called iCAC490, title= journal.pone.0077579 was chosen for the comparative analysis as it was the largest, the most recent and the only one available in a commonly accepted usable format (SBML). The analysis of reactions shared between the two reconstructions was possible due to the extensive use of KEGG identifiersTable 2 Comparison between the automatic C. difficile, iMLTC806cdf and C. acetobutylicum networksCharacteristic Reactions With genes With an EC number With KEGG ID Identified as unclear reaction Associated with multiple reactions Involving poly.Imental information for strain 630) while malate, glycerol and chorismate would lead to increased growth rates.Comparison with existing metabolic network reconstructionsRemoval of non-essential metabolites did not have an important effect on growth. The non-essential amino acid methionine is known to enhance growth of the bacteria and is used in the minimal medium to increase growth rate. Interestingly, the removal of methionine from the minimal medium leads to a slight reduction in biomass production (less than 1 ), a small but qualitatively correct effect. We simulated the removal of arginine and histidine (both nonessential amino acids) from the rich medium and in both cases this lead to the qualitatively correct result of a decrease in biomass production in agreement with the experimental evidence . Most (8 out of 11) non-essentialWe compared iMLTC806cdf to the recently created automatically-generated non-curated reconstructed metabolic network of C. difficile . The automated network contains 3211 reactions, 1548 unique metabolites and 1337 genes resulting in over 2762 genes/reactions associations. One fundamental requirement for a reconstructed metabolic network is its ability to produce biomass. As noted by its creators, the automatic network cannot produce biomass. This is likely due to the numerous flaws present in the automated network that are absent or present in a lesser number in the curated iMLTC806cdf reconstruction presented here. Among these: genericLarocque et al. BMC Systems Biology 2014, 8:117 http://www.biomedcentral.com/1752-0509/8/Page 4 ofmetabolites, incorrect reaction stoichiometry, repetitions, unclear reactions, dead-end metabolites and non-metabolic genes and reactions. For example, the automated network contains 485 generic metabolites representing 31.3 of the metabolome opposed to 23 in iMLTC806cdf (representing 3.9 of the metabolome). Curiously the automated network reconstruction contains 29 reactions involving oxygen, which should not be present in an anaerobic organism. Other important flaws in the automatically generated C.