The donor source for FMT was fecal pellets from naïve, C57BL/6 mice purchased from Charles River Laboratory and housed under specific pathogen-free conditions. Fecal pellets were collected fresh for each FMT and resuspended at a concentration of 0.2 g/mL of deoxygenated PBS under anaerobic conditions to preserve obligate anaerobe bacteria. FMT inoculum was flash spun to settle food debris and administered to mice via oral gavage (200 μl) and intrarectal instillation (100 μl) into chronically C. difficile-infected mice. Twenty-fours hours following initial FMT, mice receive a second dose of freshly prepared FMT via oral gavage (200 μl). To normalize FMT from experiment to experiment, fecal pellets were collected from the same colony of C57BL/6 mice. Following FMT, unless specified, mice were separated into individually housed cages.
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