Clostridium difficile infection is one of the most common health care-associated 
infections, and up to 40% of patients suffer from recurrence of disease 
following standard antibiotic therapy. Recently, fecal microbiota 
transplantation (FMT) has been successfully used to treat recurrent C. difficile 
infection. It is hypothesized that FMT aids in recovery of a microbiota capable 
of colonization resistance to C. difficile. However, it is not fully understood 
how this occurs. Here we investigated changes in the fecal microbiota structure 
following FMT in patients with recurrent C. difficile infection, and imputed a 
hypothetical functional profile based on the 16S rRNA profile using a predictive 
metagenomic tool. Increased relative abundance of Bacteroidetes and decreased 
abundance of Proteobacteria were observed following FMT. The fecal microbiota of 
recipients following transplantation was more diverse and more similar to the 
donor profile than the microbiota prior to transplantation. Additionally, we 
observed differences in the imputed metagenomic profile. In particular, amino 
acid transport systems were overrepresented in samples collected prior to 
transplantation. These results suggest that functional changes accompany 
microbial structural changes following this therapy. Further identification of 
the specific community members and functions that promote colonization 
resistance may aid in the development of improved treatment methods for C. 
difficile infection.
IMPORTANCE: Within the last decade, Clostridium difficile infection has 
surpassed other bacterial infections to become the leading cause of nosocomial 
infections. Antibiotic use, which disrupts the gut microbiota and its capability 
in providing colonization resistance against C. difficile, is a known risk 
factor in C. difficile infection. In particular, recurrent C. difficile remains 
difficult to treat with standard antibiotic therapy. Fecal microbiota 
transplantation (FMT) has provided a successful treatment method for some 
patients with recurrent C. difficile infection, but its mechanism and long-term 
effects remain unknown. Our results provide insight into the structural and 
potential metabolic changes that occur following FMT, which may aid in the 
development of new treatment methods for C. difficile infection.