Fig. 5
From: Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
Measurement of 13C label content in individual proteins. Analysis of a subset of the data shown in Fig. 4. E. coli grown in standard LB medium without label (0% added label) was part of a mock community consisting of 32 microorganisms [23]. To this mock community E. coli grown in minimal M9 medium with glucose (5% of total glucose as 13C1-6-Glucose) in air tight bottles under oxygen limiting conditions was added in a 1:1 ratio to the unlabeled LB grown E. coli cells in the mock community. a Detection of increased 13C/12C ratios in individual proteins as a function of the total number of different peptides detected for each protein. Proteins from all species in the unlabeled mock community are compared to the proteins of all unlabeled species in the mock community that contained the 5% labeled E. coli cells, as well as to the proteins from E. coli in the mock community that contained the labeled E. coli cells. The boxes indicate the 25th and 75th percentile, the line the median, the whiskers the 10th and 90th percentile, and the dots the 5th and 95th percentile. b Examples of E. coli proteins that showed no or high label incorporation in 5% 13C glucose grown E. coli in the mock community. Unchanged 13C/12C ratios shown in the table between treatments indicate that proteins were not produced in cells that were grown in M9 medium with labeled glucose, but were present in cells grown in LB. Proteins with high ratio were mostly or exclusively produced by cells grown in M9. 13C/.12C ratios in the table are averages of three replicate samples. Only proteins that were detected in at least two replicates in one of the conditions are shown. The full table is Supplementary Table S6