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Background   Clostridium difficile  is an opportunistic human intestinal pathogen, and  C. difficile  infection (CDI) is one of the main causes of antibiotic-induced diarrhea and colitis. One successful approach to combat CDI, particularly recurrent form of CDI, is through transplantation of fecal microbiota from a healthy donor to the infected patient. In this study we investigated the distal gut microbial communities of three CDI patients before and after fecal microbiota transplantation, and we compared these communities to the composition of the donor’s fecal microbiota. We utilized phylogenetic Microbiota Array, high-throughput Illumina sequencing, and fluorescent  in situ  hybridization to profile microbiota composition down to the genus and species level resolution.    Results  The original patients’ microbiota had low diversity, was dominated by members of Gammaproteobacteria and Bacilli, and had low numbers of Clostridia and Bacteroidia. At the genus level, fecal samples of CDI patients were rich in members of the  Lactobacillus ,  Streptococcus , and  Enterobacter  genera. In comparison, the donor community was dominated by Clostridia and had significantly higher diversity and evenness. The patients’ distal gut communities were completely transformed within 3 days following fecal transplantation, and these communities remained stable in each patient for at least 4 months. Despite compositional differences among recipients’ pre-treatment gut microbiota, the transplanted gut communities were highly similar among recipients post-transplantation, were indistinguishable from that of the donor, and were rich in members of  Blautia ,  Coprococcus , and  Faecalibacterium . In each case, the gut microbiota restoration led to a complete patient recovery and symptom alleviation.    Conclusion  We conclude that  C. difficile  infection can be successfully treated by fecal microbiota transplantation and that this leads to stable transformation of the distal gut microbial community from the one abundant in aerotolerant species to that dominated by members of the Clostridia.

Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation