title: Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis.
abstract: BACKGROUND
  In recent years, studies on the human intestinal microbiota have attracted tremendous attention. Application of next generation sequencing for mapping of bacterial phylogeny and function has opened new doors to this field of research. However, little attention has been given to the effects of choice of methodology on the output resulting from such studies.
  
  
  RESULTS
  IN THIS STUDY WE CONDUCTED A SYSTEMATIC COMPARISON OF THE DNA EXTRACTION METHODS USED BY THE TWO MAJOR COLLABORATIVE EFFORTS: The European MetaHIT and the American Human Microbiome Project (HMP). Additionally, effects of homogenizing the samples before extraction were addressed. We observed significant differences in distribution of bacterial taxa depending on the method. While eukaryotic DNA was most efficiently extracted by the MetaHIT protocol, DNA from bacteria within the Bacteroidetes phylum was most efficiently extracted by the HMP protocol.
  
  
  CONCLUSIONS
  Whereas it is comforting that the inter-individual variation clearly exceeded the variation resulting from choice of extraction method, our data highlight the challenge of comparing data across studies applying different methodologies.
authors.affiliation: Center for Biological Sequence analysis, Technical University of Denmark, Lyngby DK-2800, Denmark.
authors.forename: Agata
authors.initials: A
authors.lastname: Wesolowska-Andersen
authors.affiliation: National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark.
authors.forename: Martin Iain
authors.initials: MI
authors.lastname: Bahl
authors.affiliation: National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark.
authors.forename: Vera
authors.initials: V
authors.lastname: Carvalho
authors.affiliation: Department of Biology, University of Copenhagen, Copenhagen N DK-2200, Denmark.
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristiansen
authors.affiliation: Center for Biological Sequence analysis, Technical University of Denmark, Lyngby DK-2800, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Pontén
authors.affiliation: Center for Biological Sequence analysis, Technical University of Denmark, Lyngby DK-2800, Denmark.
authors.forename: Ramneek
authors.initials: R
authors.lastname: Gupta
authors.affiliation: National Food Institute, Technical University of Denmark, Søborg DK-2860, Denmark.
authors.forename: Tine Rask
authors.initials: TR
authors.lastname: Licht