Experimental design of the mouse microbiome study. Mice were divided into a control group and two treatment groups. The treatment groups received either vancomycin (van) or a combination of penicillin, streptomycin and gentamicin (PSG). After 7 days, some of the mice were administered a C. albicans challenge. Terminal ileum samples were collected on days 7 and 21 and fecal pellet samples on days 7, 9, 14 and 21. C. albicans colonization level was measured by counting the Colony forming units (CFU) following quantitative culture of the fecal pellets. Cytokine mRNA expression (C mRNA) was measured in the terminal ileum samples. Bacterial 16S and Fungal ITS were amplified from both the terminal ileum sections and the fecal pellets. These amplicons were sequenced with 454 pyrosequencing. The YAP bioinformatic workflow  was used to obtain genus-level taxonomic assignments for the bacterial and fungal sequences.