For a study, it was determined that Fecal microbiota transplantation (FMT) was a highly efficient treatment for recalcitrant and recurring Clostridium difficile infection (CDI). In a recent trial, the oral distribution of encapsulated, freeze-dried donor material resulted in cure rates comparable to colonoscopic techniques. The fecal bacterial community structure of individuals treated for rCDI with encapsulated donor material was processed here. Before FMT, the variety and number of Firmicutes and Bacteroidetes inpatient feces had decreased, whereas Proteobacteria, notably Enterobacteriaceae, had increased. Furthermore, individuals who had a relapse of CDI within the two-month clinical follow-up had higher levels of Enterobacteriaceae and did not have their dysbioses resolved. Even though rCDI was decided after oral delivery of encapsulated fecal microbiota, community composition took a long time to revert to a donor-like assemblage. Post-FMT taxa within the Firmicutes showed rapid increases in relative abundance that did not change much over time. Bacteroidetes taxa, on the other hand, only demonstrated significant increases in quantity after 1-month post-FMT, corresponding to considerable increases in the donor community. Days, weeks, and months after the FMT, changes in the associations among dominating OTUs were found, implying that community dynamics may be linked to the timing of increases in abundance of specific taxa. The use of encapsulated, freeze-dried fecal microbiota in rCDI patients resulted in bacterial diversity restoration and dysbiosis resolution. Changes in the fecal microbiome, on the other hand, were gradual rather than abrupt and may have been triggered by changes in community dynamics in response to changes in the host environment.