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

Vijay Shankar, Matthew J. Hamilton, Alexander Khoruts, Amanda Kilburn, Tatsuya Unno, Oleg Paliy, Michael J. Sadowsky

Research output: Contribution to journalArticlepeer-review

77 Scopus citations


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.

Original languageEnglish (US)
Article number13
Issue number1
StatePublished - Apr 21 2014

Bibliographical note

Funding Information:
The work described in this manuscript was supported by the National Institutes of Health grants AT003423 to OP and AI091907 to AlK and MJS.

Publisher Copyright:
© 2014 Shankar et al.


  • Clostridium difficile
  • Fecal microbiota transplantation
  • Microbiota
  • Microbiota Array
  • Microflora


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