Extended Data Fig. 3: Quantitative flow cytometry.

(a) Ratio of abundance of C. difficile in co- versus mono-culture with 5 selected partner species obtained via main proteomics experiment (x-axis, subset of data shown in Fig. 1j) and quantitative flow cytometry (y-axis). Flow cytometry was performed on n = 3 biological replicates, errorbars indicate the standard deviation. This independent measurement confirms that the absolute abundance of C. difficile increases in co-culture with the selected Bacteroidetes but decreases in co-culture with E. coli, as indicated in the main proteomics experiment. (b) Representative plots illustrating the gating strategy used for relative quantification of species via stain which distinguishes gram-positive/negative cells (vancomycin-biodipy conjugate). (c) Representative plot illustrating the gating strategy used for absolute quantification of bacterial cells via bead spike in.