Table 1. Animal studies of the gut microbiota and C. difficile infection.

Host	Antibiotics (route/dose)	Microbiome analysis	Structural changes to the gut microbiota	Strain of C. difficile	Reference
Female CF-1 mice	Subcutaneous injections saline, tigecycline (0.05 mg/day), clindamycin (1.4 mg/day), or piperacillin-tazobactam (8 mg/day) for 4 d.	Culture based: plating onto brucella agar and Bacteroides bile-esculin agar	•      Tigecycline did not suppress total anaerobes or Bacteroides spp. in comparison to saline controls and did not allow for C. difficile colonization. •      Clindamycin and piperacillin-tazobactam did suppress Bacteroides spp.and allowed for C. difficile colonization.	ATCC 43593 VA 17 VA 11	86
Male and female C57BL/6 mice	-Antibiotic cocktail in drinking water: kanamycin (0.4 mg/ml), gentamicin (0.035 mg/ml), colistin (850 U/ml), metronidazole (0.215 mg/ml), vancomycin (0.045 mg/ml) for 5 d followed by clindamycin (10 mg/Kg) intraperitoneal injection. -Cefoperazone (0.5 mg/ml) in drinking water for 10 d.	Non-culture based: 16S rRNA-encoding gene clone libraries	•      Increased abundance of the Proteobacteria phylum (Enterobacteriaceae family) and decreased abundance of the Firmicutes phylum (Lachnospiraceae family) was associated with C. difficile colonization. •      Increased abundance of the Firmicutes and Proteobacteria phyla specifically members of the Lactobacillaceae and Pseudomonadaceae family were also associated with C. difficile colonization.	VPI 10463	83
Female C57BL/6 mice	Single dose of clindamycin (200 ug) by intraperitoneal injection.	Non-culture based: Roche-454 pyrosequencing (V1-V3 primers)	•      Loss of Lachnospiraceae family members and Barnesiella populations and expansion of the Enterobacteriaceae species was associated with C. difficile colonization.	VPI 10463	84
Female C57BL/6, C57BL/6 p402/2, C3H/HeN and C3H/HeJ mice	Clindamycin (250 mg/L) in drinking water for 1 wk.	Non-culture based: 16S rRNA-encoding gene clone libraries	•      Increased abundance of facultative anaerobes including members of the Enterobacteriaceae family and Enterococci was associated with C. difficile colonization. •      Supershedder microbiota contained 16S rRNA gene clones derived from Blautia producta and included 16S rRNA gene sequences of Klebsiella pneumoniae, Escherichia coli, Proteus mirabilis, Parabacteroides distasonis and Enterococcus faecalis.	BI-7 M68 630	85
Male golden syrian hamsters	Single dose of clindamycin (50 mg/Kg) by subcutaneous injection.	Non-culture based: Roche-454 pyrosequencing (V1-V2 primers)	•      Reduction in the abundance of Bacteroidetes and Firmicutes and increase in Proteobacteria was associated with C. difficile colonization. •      Temporary suppression of Bacteroidales and the fungus Saccinobaculus was also associated with C. difficile colonization. •      Inoculation with C. difficile was associated with increases in Clostridiales on days 1 and 2 with a smaller increase in Burkholderiales and Pasteurellales species.	ATCC 43596	87