title: Species and genus level resolution analysis of gut microbiota in Clostridium difficile patients following fecal microbiota transplantation.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Col. Glenn Hwy, Dayton, OH 45435, USA.
authors.forename: Vijay
authors.initials: V
authors.lastname: Shankar
authors.affiliation: Department of Soil, Water, and Climate, Biotechnology Institute, and Microbial Plant and Genomics Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, St. Paul, MN 55108, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Hamilton
authors.affiliation: Division of Gastroenterology; Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Khoruts
authors.affiliation: Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Col. Glenn Hwy, Dayton, OH 45435, USA.
authors.forename: Amanda
authors.initials: A
authors.lastname: Kilburn
authors.affiliation: Department of Soil, Water, and Climate, Biotechnology Institute, and Microbial Plant and Genomics Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, St. Paul, MN 55108, USA.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Unno
authors.affiliation: Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, 3640 Col. Glenn Hwy, Dayton, OH 45435, USA.
authors.forename: Oleg
authors.initials: O
authors.lastname: Paliy
authors.affiliation: Department of Soil, Water, and Climate, Biotechnology Institute, and Microbial Plant and Genomics Institute, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, St. Paul, MN 55108, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sadowsky
keywords: Clostridium difficile; Fecal microbiota transplantation; Microbiota; Microbiota Array; Microflora