A 20-year-old female was diagnosed with ulcerative colitis (UC) at age 14 and primary sclerosing cholangitis (PSC) at age 16. The PSC was successfully treated with high doses of oral vancomycin; however, the UC was more difficult to manage. After many drug treatments failed to treat the UC, the patient began following the specific carbohydrate diet (SCD). This report documents fecal microbiome changes resulting from following the SCD for two weeks. The DNA extracted from fecal samples was subjected to 16S rRNA gene sequencing to quantify bacterial species abundance. Not only were substantial changes in the fecal bacterial composition detectable within two weeks, but all UC symptoms were also controlled as early as one week following the start of the diet. The patient's fecal microbiota was dramatically different from those of three healthy control subjects and showed remarkable loss of bacterial diversity in terms of species richness, evenness, and overall diversity measures. Other specific changes in bacterial composition included an increase in Enterobacteriaceae, including Escherichia and Enterobacter species. A two- to three-fold decrease was observed in the prevalence of the most dominant fecal bacterial species, Fusobacterium ulcerans, after two weeks on the SCD. Overall species diversity and evenness increased to levels near the controls, although species richness remained low. These findings provide information on the fecal bacteria from a patient with PSC and UC, following prolonged oral vancomycin treatment, and identifies a potentially specific microbial effect for the SCD.