Fecal Microbial Transplantation for C. Difficile and/or Ulcerative Colitis or Indeterminate Colitis

Fecal Microbiota Transplantation will be offered to eligible C. difficile patients (does not require Investigational New Drug designation) and to eligible ulcerative colitis or indeterminate colitis patients as Investigational New Drug treatment

The following hypothesis will be tested in this study: 1. Fecal microbiota transplantation is a safe, tolerable, and efficacious procedure for C. difficile patients and is a safe and tolerable procedure for ulcerative colitis and indeterminate colitis patients. 2. The fecal microbial diversity, composition and function in stool recipients after fecal transplantation will change to a similar microbial diversity, composition and functionality as found in donor stool. Primary objectives: 1\. To determine the short term safety and tolerability of fecal microbiota transplantation in patients with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis up to 12 weeks post-transplant. Secondary objectives: 1a. To determine the long term safety and tolerability of fecal microbiota transplantation up to 1 year post-transplant in patients with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 1b. To determine the efficacy of fecal microbiota transplantation in patients with recurrent or refractory Clostridium difficile defined as no recurrence of C. difficile within one year. 2\. To compare microbial diversity in healthy donor stools compared to pre-FMT recipient stools collected from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 3\. To compare microbial composition in healthy donor stools compared to pre-FMT recipient stools from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 4\. To compare microbial function in healthy donor stools compared to pre-FMT recipient stools from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 5\. To compare microbial diversity in healthy donor stools and pre-FMT recipient stools with 1 week post-transplant recipient stool samples collected from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 6\. To compare microbial composition in healthy donor stools and pre-FMT recipient stools with 1 week post-transplant recipient stool samples collected from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 7\. To compare microbial function in healthy donor stools and pre-FMT recipient stools with 1 week post-transplant recipient stool samples collected from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 8\. To compare microbial diversity in healthy donor stools and pre-FMT recipient stools with 12 week post transplant recipient stool samples collected from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 9\. To compare microbial composition in healthy donor stools and pre-FMT recipient stools with 12 week post transplant recipient stool samples collected from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 10\. To compare microbial function in healthy donor stools and pre-FMT recipient stools with 12 week post transplant recipient stool samples collected from patients (recipients) with recurrent or refractory Clostridium difficile and medication refractory Ulcerative colitis or indeterminate colitis. 11\. Stool calprotectin levels will be measured in the recipient at baseline pre-FMT, 1 week and 12 weeks post FMT to determine if FMT causes a statistically significant change.