Antibiotic-induced C. difficile supershedding state is associated with reduced intestinal microbiota diversity. (a) Average fecal shedding of C. difficile by carrier mice (five mice per cage) treated with clindamycin to induce a transient supershedder state. The error bars indicate standard deviations. DNA was extracted from fresh feces from each mouse at the indicated time points (green arrowheads) to create 16S rRNA gene clone libraries. The detection limit was 103 CFU C. difficile/g feces. (b) Temporal shifts in the intestinal bacterial community after clindamycin treatment of carrier mice as determined by 16S rRNA gene analysis. The levels of predominant bacterial groups are expressed as percentages of the clone libraries using pie charts. On day 23 1,400 clones were included (average, 280 clones/mouse), on day 25 1,202 clones were included (average, 241 clones/mouse), on day 27 1,204 clones were included (average, 241 clones/mouse), on day 29 1,081 clones were included (average, 216 clones/mouse), and on day 33 1,167 clones were included (average, 233 clones/mouse). (c) SDI for each phase of the microbiota community structure determined by 16S rRNA gene phylotypes.