title: Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.
abstract: BACKGROUND
  Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard antibiotic therapy. Despite its widespread recent use, however, little is known about the stability of the fecal microbiota following FMT.
  
  
  RESULTS
  Here we report on short- and long-term changes and provide kinetic visualization of fecal microbiota composition in patients with multiply recurrent CDI that were refractory to antibiotic therapy and treated using FMT. Fecal samples were collected from four patients before and up to 151 days after FMT, with daily collections until 28 days and weekly collections until 84 days post-FMT. The composition of fecal bacteria was characterized using high throughput 16S rRNA gene sequence analysis, compared to microbiota across body sites in the Human Microbiome Project (HMP) database, and visualized in a movie-like, kinetic format. FMT resulted in rapid normalization of bacterial fecal sample composition from a markedly dysbiotic state to one representative of normal fecal microbiota. While the microbiome appeared most similar to the donor implant material 1 day post-FMT, the composition diverged variably at later time points. The donor microbiota composition also varied over time. However, both post-FMT and donor samples remained within the larger cloud of fecal microbiota characterized as healthy by the HMP.
  
  
  CONCLUSIONS
  Dynamic behavior is an intrinsic property of normal fecal microbiota and should be accounted for in comparing microbial communities among normal individuals and those with disease states. This also suggests that more frequent sample analyses are needed in order to properly assess success of FMT procedures.
authors.affiliation: Department of Soil, Water, and Climate, and Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN USA ; BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA.
authors.forename: Alexa
authors.initials: A
authors.lastname: Weingarden
authors.affiliation: BioFrontiers Institute, University of Colorado, Boulder, CO USA.
authors.forename: Antonio
authors.initials: A
authors.lastname: González
authors.affiliation: Department of Computer Science, University of Colorado, Boulder, CO USA.
authors.forename: Yoshiki
authors.initials: Y
authors.lastname: Vázquez-Baeza
authors.affiliation: Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO USA.
authors.forename: Sophie
authors.initials: S
authors.lastname: Weiss
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, USA.
authors.forename: Gregory
authors.initials: G
authors.lastname: Humphry
authors.affiliation: Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, USA.
authors.forename: Donna
authors.initials: D
authors.lastname: Berg-Lyons
authors.affiliation: Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN USA ; BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Knights
authors.affiliation: BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Unno
authors.affiliation: Division of Gastroenterology, Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN USA.
authors.forename: Aleh
authors.initials: A
authors.lastname: Bobr
authors.affiliation: BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA ; Division of Gastroenterology, Department of Medicine, Center for Immunology, University of Minnesota, Minneapolis, MN USA.
authors.forename: Johnthomas
authors.initials: J
authors.lastname: Kang
authors.affiliation: BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA ; 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: BioFrontiers Institute, University of Colorado, Boulder, CO USA ; Department of Chemistry & Biochemistry, University of Colorado, Boulder, CO USA ; Howard Hughes Medical Institute, Boulder, CO USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.affiliation: Department of Soil, Water, and Climate, and Microbial and Plant Genomics Institute, University of Minnesota, St Paul, MN USA ; BioTechnology Institute, 1479 Gortner Ave, 140 Gortner Labs, St. Paul, MN 55108 USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sadowsky
keywords: Short- and long-term changes in microbiota following FMT
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