FIG 3 .

Bacterial and fungal community composition in exacerbation series from six subjects. (A) Serial sputum samples from six individuals with CF were obtained during treatment for pulmonary exacerbation and analyzed by NanoString (data in Table S3C). Microbes present in multiple subjects or abundantly in at least one subject are graphed as total counts normalized to positive controls as a stacked plot in which each segment indicates the number of counts for the indicated taxon. Bacteria and fungi are plotted on the upper and lower y axes, respectively, though the data for bacterial and fungal probe sets were obtained in the same reaction. (B) Exacerbation series E1 showed high levels of Exophiala dermatitidis by plate culture on SDA only after extended incubation.