Figure 2.

Cell density and encapsulation. Bacterial density based on flow cytometry measurements and microscopy images of emulsions

(A) Number of Syto BC-stained cells counted per volume of stool sample before dilution, and two overnight culture aliquots of bacterial cultures Bacillus subtilis (B.s.) and Bacteroides vulgatus (B.v.), here shown increased by a factor of 50 to visualize them despite the lower cell densities compared with stool. Measurements were performed in triplicates and the mean and standard deviation are shown for each sample.

(B and C) Microscopy images of droplet emulsion containing diluted B. subtilis culture post droplet PCR. The images are overlays of the microscope's fluorescence and brightfield channel as well as the contours of positive fluorescent areas, as returned from the droplet analysis tool described in the STAR Methods section. The scale bars correspond to 100 μm.