Analysis of the intestinal microbiome of a recovered Clostridium difficile patient after fecal transplantation

Digestion. 2013;88(4):243-51. doi: 10.1159/000355955. Epub 2013 Dec 5.


Background: Clostridium difficile infections upon antibiotic disruption of the gut microbiota are potentially lethal. Fecal microbiota transplantation (FMT) is a promising treatment option for recurrent C. difficile-associated disease (CDAD). Here, we present a patient with recurrent CDAD that received FMT, leading to full recovery for what has now been 3 years. We performed metagenomic sequencing on stool samples to assess if there are indications for recolonization with C. difficile and changes in the gut microbiota after FMT.

Methods: DNA from the stool of the donor and recipient was subjected to illumina sequencing. Obtained read sets were assembled to contiguous sequences and open reading frames were predicted. Deduced proteins were taxonomically assigned.

Results: We detected complex and apparently healthy microbiomes in the donor's and recipient's intestines after FMT, but no indications for C. difficile colonization.

Conclusions: Metagenomic analysis proved suitable to analyze the intestinal microbiome after FMT. Discussion of our evaluation procedure and data management may be helpful for future studies. We demonstrated restoration of a healthy and diverse gut microbiome with chimeric composition from donor and recipient, and long-lasting clearance of C. difficile. The procedure is simple, cheap, caused no side effects, and was stable over 3 years.

Publication types

  • Case Reports
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Therapy
  • Clostridioides difficile*
  • DNA, Bacterial / analysis*
  • Enterocolitis, Pseudomembranous / therapy*
  • Feces / microbiology*
  • Female
  • Humans
  • Intestines / microbiology*
  • Metagenomics
  • Microbiota*
  • Middle Aged
  • Sequence Analysis, DNA / methods


  • DNA, Bacterial