Fig. 4

Effect of treatment on the gut microbiota diversity and composition. Experimental design is shown on top panel (red line indicates antibiotic cocktail treatment 6 days prior to the C. difficile infection for 3 days, followed by 2 days of water and clindamycin (30 mg per kg) the day prior to C. difficile infection, green line indicates no treatment). Within-sample diversity was estimated using Shannon diversity index (ns denotes not significant, *p value greater than 0.01 but not greater than 0.05, **p value is less than 0.01, unpaired Student t-test) The center line, bounds of box, and whiskers of the boxplot represents median, interquartile, and range of within-sample diversity. Each treatment group is the result of two experimental cages. Each barplot indicates the mean relative abundance of bacterial families with relative abundance >1% from mice in two experimental cages. The Peptostreptococcaceae family of bacteria includes C. difficile and its abundance was consistently below 1% in all experiments and thus is included in others. a Control, NEN, and vancomycin treatment in the absence of C. difficile infection; b control (water with 5% DSMO) and NEN treatment (50 mg per kg); c water with vancomycin and NEN treatment (50 mg per kg); d water with vancomycin and NEN treatment (50 mg per mL) with vancomycin (0.5 mg per mL). First sampling day (day 0) is 4 h after C. difficile infection