Bacterial communities from subjects treated for recurrent Clostridium difficile 
infection (rCDI) by fecal microbiota transplantation (FMT), using either 
heterologous donor stool samples or autologous stool samples, were characterized 
by Illumina next-generation sequencing. As previously reported, the success of 
heterologous FMT (90%) was superior to that of autologous FMT (43%) (P = 0.019), 
and post-FMT intestinal bacterial communities differed significantly between 
treatment arms (P < 0.001). Subjects cured by autologous FMT typically had 
greater abundances of the Clostridium XIVa clade and Holdemania bacteria prior 
to treatment, and the relative abundances of these groups increased 
significantly after FMT compared to heterologous FMT and pre-FMT samples. The 
typical shift to post-FMT, donor-like assemblages, featuring high relative 
abundances of genera within the Bacteroidetes and Firmicutes phyla, was not 
observed in the autologous FMT subjects. Autologous FMT patient bacterial 
communities were significantly different in composition than those for 
heterologous FMT patients and donors (P < 0.001). The SourceTracker program, 
which employs a Bayesian algorithm to determine source contributions to sink 
communities, showed that patients initially treated by heterologous FMT had 
significantly higher percentages of engraftment (i.e., similarity to donor 
communities, mean value of 74%) compared to those who suffered recurrence 
following autologous FMT (1%) (P ≤ 0.013). The findings of this study suggest 
that complete donor engraftment may be not necessary if functionally critical 
taxa are present in subjects following antibiotic therapy.
IMPORTANCE: This study provides a detailed characterization of fecal bacterial 
communities in subjects who participated in a previously published randomized 
clinical trial to treat recurrent C. difficile infection (rCDI). Bacterial 
communities were characterized to determine differences between subjects who 
received fecal bacteria either from healthy donor stool samples or their own 
stool samples as "placebo" in order to determine which groups of bacteria were 
most important in achieving a cure. The results of this study suggested that 
bacteria associated with secondary bile acid metabolism could potentially 
provide resistance to infection and that complete transfer of healthy donor 
microorganisms was not necessary to resolve CDI following unsuccessful 
antibiotic treatment.