The HMA mice were housed in positive-pressure individually ventilated cages (IVCs) (ISOcage P; Techniplast, West Chester, PA) in order to prevent cross-contamination and maintain their gnotobiotic status 49 , 50 . All mice were fed a sterilized rodent breeder diet 5013 (LabDiet, St. Louis, MO). 8- to 16-week-old female and male mice were used in all experiments. All animals were handled in accordance with the protocols approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Michigan. To attain robust C. difficile infection in HC-HMA mice, the animals were treated with a cocktail of antibiotics ofr 5 days. The cocktail contains kanamycin (0.4 mg/ml), gentamicin (0.035 mg/ml), colistin (850 U/ml), metronidazole, (0.215 mg/ml), and vancomycin (0.045 mg/ml). Clindamycin (10 mg/kg) was then injected intra-peritoneally at day 5. One day after clindamycin injection, mice were challenged by C. difficile 24 h post-IP injection 17 (link).