Clostridium difficile infection (CDI) following antibiotic therapy is a major public health threat. While antibiotic disruption of the indigenous microbiota underlies the majority of cases of CDI, the early dynamics of infection in the disturbed intestinal ecosystem are poorly characterized. This study defines the dynamics of infection with C. difficile strain VPI 10463 throughout the gastrointestinal (GI) tract using a murine model of infection. After inducing susceptibility to C. difficile colonization via antibiotic administration, we followed the dynamics of spore germination, colonization, sporulation, toxin activity, and disease progression throughout the GI tract. C. difficile spores were able to germinate within 6 h postchallenge, resulting in the establishment of vegetative bacteria in the distal GI tract. Spores and cytotoxin activity were detected by 24 h postchallenge, and histopathologic colitis developed by 30 h. Within 36 h, all infected mice succumbed to infection. We correlated the establishment of infection with changes in the microbiota and bile acid profile of the small and large intestines. Antibiotic administration resulted in significant changes to the microbiota in the small and large intestines, as well as a significant shift in the abundance of primary and secondary bile acids. Ex vivo analysis suggested the small intestine as the site of spore germination. This study provides an integrated understanding of the timing and location of the events surrounding C. difficile colonization and identifies potential targets for the development of new therapeutic strategies.C lostridium difficile infection (CDI) is the most common cause of health care-associated infectious diarrhea and colitis. CDI results in upwards of 14,000 deaths annually and $4.8 billion in excess health care costs in the United States (1). C. difficile is a Gram-positive, anaerobic, spore-forming bacterium that produces toxins that inactivate Rho family GTPases, resulting in a loss of epithelial barrier function, mucosal inflammation, and intestinal damage (2). Individuals infected with C. difficile exhibit clinical manifestations that can range from mild diarrhea to toxic megacolon and death (2).CDI is initiated by transmission of the environmentally stable spore form of the pathogen. To establish infection, the spore must germinate following interactions with small molecule germinants, which are primarily bile acids (3). After germination, a productive infection will result in vegetative growth of the pathogen, which then produces toxin, resulting in colitis. Thus, CDI results when C. difficile spores encounter an intestinal environment that supports all of the aspects of C. difficile physiology. The use of antibiotics is a primary risk factor for developing CDI due to loss of the protective effects of the gut microbiota, deemed colonization resistance (4-6).The loss of colonization resistance against CDI results in an environment that allows for C. difficile germination and growth. How the gut microbiota mediates coloniza...