Supplementary MaterialsS1 Fig: Impact from the concentration of nitrogen source for the growth in carbon-deficient batch cultures. on AOC (assimilable organic carbon). Four replicate cultures of the MG1655 strain were grown in glass culture tubes containing M9 medium without any supplemented sugar. As determined by an increase in the CFU count per ml of the culture between day 0 and day 1, AOC can support growth of about 1.6 x 106 cells/ml. Error bars present standard error of the mean from 4 biological replicates, 1,5-Anhydrosorbitol with each replicate value averaged over 4 technical samples. The experiment is described in S1 File, section ‘Bacterial growth on AOC’.(TIFF) pgen.1007122.s002.tiff (1.3M) GUID:?F1D4A715-1C7B-4BF5-A809-7BF4C6DE985E S3 Fig: Decreasing fraction of unlabeled sugars in chemostats after switch to media containing labeled sugars. Here we show the decreasing fraction of unlabeled glucose (blue curve) in nitrogen-limited, carbon-excess chemostats. From this curve we calculated the average fraction of unlabeled glucose that a cell experienced during the 3 hour-labeling period in chemostats (red line). This average fraction of unlabeled glucose is the integral of the blue curve during the 3 hour-labeling period, divided by the labeling FNDC3A period.(TIFF) pgen.1007122.s003.tiff (2.3M) GUID:?51D555D4-C5BD-45EF-A2CC-78140F268E2E S4 Fig: Sugar assimilation in the pathogenic strain 55989. The pattern of assimilation of arabinose and glucose in the enteroaggregative (EAEC) pathogenic strain 55989 was similar to the results obtained for the laboratory strain (Fig 1B). The assimilation of both isotopes in EAEC was significantly correlated and positive (Table 1). We did not observe that the level of metabolic specialization in EAEC was more pronounced than in the laboratory strain NN114. Statistical analysis revealed differences between the assimilation of 13C-arabinose and 2H-glucose in the clonal EAEC cells and the NN114 cells (Kolmogorov-Smirnov test: p-value = 0.046 for 2H excess atom fraction, and p-value = 0.001 for 13C excess atom fraction).(TIFF) pgen.1007122.s004.tiff (2.3M) GUID:?05EB32B4-B647-4FFE-BC85-0A769D9C5A5B S5 Fig: Relevant growth characteristics of the EAEC strain 55989. The strains 55989 and MG1655 are 1,5-Anhydrosorbitol phylogenetically closely related . For example, the EAEC (enteroaggregative and in the MG1655 strain (according to the sequences defined in the plasmid library ) are 100% identical with the corresponding EAEC sequences. Furthermore, the gene has 99% identity with the respective sequence in the EAEC strain, has 99% identity, and has 100% identity. Overnight grown cultures were diluted 1 to 100 into 24-well plates, and growth was recorded by a plate reader as A600 (the same setup as used in S1 Fig). (A) We used the plate-reader to show that the EAEC isolate can grow under laboratory conditions, in M9 minimal media with arabinose and/or glucose supplemented. (Error bars present standard deviation between 3 replicates for mixed-carbon, and 4 replicates for solitary carbon source circumstances.) (B) We evaluated whether development characteristics from the EAEC stress are different compared to the NN114 stress (MG1655-derived stress) beneath the same nutrient concentrations as found in carbon-limited chemostats, in press containing 10 M Glc and 10 M Ara. We computed optimum development rate Utmost on 10 M Glc and 10 M Ara for both strains. Utmost was thought as the maximal worth of slopes determined as ln-transformed typical ideals over 3 period factors, i.e. Utmost = 0.575 h-1 for strain NN114 measured between t1 = 5.25 h and t2 = 5.75 h; Utmost = 0.427 h-1 for the EAEC stress measured between t1 = 5 h and t2 = 5.5 h. (Mistake bars present regular deviation between 5 EAEC replicates and 4 replicates of stress NN114.)(TIFF) pgen.1007122.s005.tiff (2.6M) GUID:?6E472806-9F88-43DA-906F-1FACA9047A9E S6 Fig: Estimated growth prices about glucose and arabinose in carbon-limited chemostats. Model ideals for development price on glucose, mean = 0.010 h-1, CV = 0.880; and on arabinose mean = 0.017 h-1, CV = 0.781. Model ideals for total estimated growth rate (Fig 2B), mean = 0.037 h-1, CV = 0.724.(TIFF) pgen.1007122.s006.tiff (2.1M) GUID:?82BD01FF-7B66-458F-9DE4-78DA205E9D4D S7 Fig: Cell-to-cell variation in growth rates in chemostats and batch cultures. We determined coefficients of variation (CVs) in growth rate in 1,5-Anhydrosorbitol mixed-carbon environments. CVs are shown for growth on glucose (6 replicates; average CV = 0.858) and for total estimated growth (growth on glucose, arabinose and AOC) in carbon-limited chemostats (average CV = 0.723), and for growth on glucose in carbon-excess chemostats (nitrogen-limited, 2 replicates; average CV = 0.782) and carbon-excess batch cultures (3 replicates; average CV = 0.221). Error bars show standard error of the mean. Variation in growth rate was more than 3 times lower in the batch cultures than in the chemostats. For the analysis of isotope enrichments and calculations of growth rates in carbon-limited.