Figure 5.

Shifts in microbial community structure and composition associated with antibiotic administration and C. difficile infection. The community structure of the gut microbiota was determined by 16s rRNA gene clone library construction. (A) The microbial communities in animals that were treated with the antibiotic cocktail (abx) or with clindamycin alone (clinda) were altered from that seen in untreated controls. The antibiotic cocktail alone resulted in the appearance of significant numbers of lactobacilli, whereas clindamycin administration was associated with an increase in Proteobacteria. (B) The microbial communities in animals that received the combination of the antibiotic cocktail and clindamycin were also dominated by Proteobacteria. Animals that were challenged with C. difficile after antibiotic treatment harbored gut communities that were distinguished by the clinical disease that developed. Proteobacteria dominated sick antibiotic treated animals exposed to C. difficile while the communities of animals that remained well appeared to resemble controls with a predominance of Firmicutes. Dendrograms were constructed using Morisita-Horn community similarities based on >97% sequence similarity while taxonomic assignments were made using the Ribosomal Database Project Classifier. abx-antibiotic cocktail, clinda-clindamycin, C.diff-C. difficile.