High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria

Matthew J. Hamilton, Alexa R. Weingarden, Tatsuya Unno, Alexander Khoruts, Michael J. Sadowsky

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231 Scopus citations


Fecal microbiota transplantation (FMT) is becoming a more widely used technology for treatment of recurrent Clostridum difficile infection (cDI). While previous treatments used fresh fecal slurries as a source of microbiota for FMT, we recently reported the successful use of standardized, partially purified and frozen fecal microbiota to treat cDI. here we report that high-throughput 16s rRNA gene sequencing showed stable engraftment of gut microbiota following FMT using frozen fecal bacteria from a healthy donor. similar bacterial taxa were found in post-transplantation samples obtained from the recipients and donor samples, but the relative abundance varied considerably between patients and time points. post FMT samples from patients showed an increase in the abundance of Firmicutes and Bacteroidetes, representing 75-80% of the total sequence reads. proteobacteria and Actinobacteria were less abundant (< 5%) than that found in patients prior to FMT. post FMT samples from two patients were very similar to donor samples, with the Bacteroidetes phylum represented by a great abundance of members of the families Bacteroidaceae, Rikenellaceae and porphyromonadaceae, and were largely comprised of Bacteroides, Alistipes and Parabacteroides genera. Members of the phylum Firmicutes were represented by Ruminococcaceae, Lachnospiraceae, Verrucomicrobiaceae and unclassified clostridiales and members of the Firmicutes. One patient subsequently received antibiotics for an unrelated infection, resulting in an increase in the number of intestinal proteobacteria, primarily enterobacteriaceae. Our results demonstrate that frozen fecal microbiota from a healthy donor can be used to effectively treat recurrent cDI resulting in restoration of the structure of gut microbiota and clearing of Clostridum difficile.

Original languageEnglish (US)
Pages (from-to)125-135
Number of pages11
JournalGut microbes
Issue number2
StatePublished - Mar 2013

Bibliographical note

Funding Information:
A.K. and M.J.S. received funding from CIPAC LLC to carry-out research on FMT using frozen microbiota. A.K. and M.J.S. have provided consulting services for CIPAC and conflicts of interest are being managed by the University of Minnesota Conflicts of Interest Program.

Funding Information:
We would like to thank the nursing staff, volunteer donor and recipient patients in helping with the work described in this paper. This research was supported, in part, by a grant from the Minnesota Medical Foundation, NIH Grant R21AI091907 and funding provided by CIPAC LLC. M.J.H. was supported by a fellowship from the NIH, NIDCR T32 Institutional Training Grant: Minnesota Craniofacial Research Training (MinnCResT) Program.


  • Bacteroides
  • Clostridium difficile
  • Curing
  • DNA sequence analysis
  • Fecal microbial transplantation
  • Firmicutes
  • Frozen preparations
  • Illumina
  • Microbiota
  • Restoration


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