Fig. 4
From: Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
Detection of 13C content of labeled E. coli within a mock community of 32 microorganisms developed by [23]. In each experiment, half of the E. coli cells were labeled using 13C1-6-Glucose, corresponding to one generation of labeling, with glucose containing 0, 1, 5, and 10% 13C on top of natural abundance 13C (three replicate samples were generated for each labeling percentage and measured separately). Label in E. coli (orange circles in a), but not in other organisms (blue circles shown for five organisms in b–e), was clearly detectable and reproducible. Yellow box plots show the measured 13C content of sets of E. coli peptides, obtained by downsampling of the results in a, mimicking the spectral intensities of the peptides collected for each unlabeled organism in panels b–e, i.e., only E. coli peptides that corresponded in intensity to peptides of the analyzed organism were used. The percentage in parentheses indicates the relative abundance of the organism in the mock community based on its proteinaceous biomass and the “n = ” indicates the average number of peptides passing the filters in Calis-p for SIP value calculation for the organism in each experiment, which also corresponds to the number of E. coli peptides used in downsampling. These results show label incorporation can be estimated, even for relatively rare species. Supplementary Table S5 shows results for each species