title: Temporal and technical variability of human gut metagenomes.
abstract: BACKGROUND
  Metagenomics has become a prominent approach for exploring the role of the gut microbiota in human health. However, the temporal variability of the healthy gut microbiome has not yet been studied in depth using metagenomics and little is known about the effects of different sampling and preservation approaches. We performed metagenomic analysis on fecal samples from seven subjects collected over a period of up to two years to investigate temporal variability and assess preservation-induced variation, specifically, fresh frozen compared to RNALater. We also monitored short-term disturbances caused by antibiotic treatment and bowel cleansing in one subject.
  
  
  RESULTS
  We find that the human gut microbiome is temporally stable and highly personalized at both taxonomic and functional levels. Over multiple time points, samples from the same subject clustered together, even in the context of a large dataset of 888 European and American fecal metagenomes. One exception was observed in an antibiotic intervention case where, more than one year after the treatment, samples did not resemble the pre-treatment state. Clustering was not affected by the preservation method. No species differed significantly in abundance, and only 0.36% of gene families were differentially abundant between preservation methods.
  
  
  CONCLUSIONS
  Technical variability is small compared to the temporal variability of an unperturbed gut microbiome, which in turn is much smaller than the observed between-subject variability. Thus, short-term preservation of fecal samples in RNALater is an appropriate and cost-effective alternative to freezing of fecal samples for metagenomic studies.
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. anita.voigt@embl.de.|Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, 69120, Heidelberg, Germany. anita.voigt@embl.de.|Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, 69120, Heidelberg, Germany. anita.voigt@embl.de.
authors.forename: Anita Y
authors.initials: AY
authors.lastname: Voigt
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. costea@embl.de.
authors.forename: Paul I
authors.initials: PI
authors.lastname: Costea
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. kultima@embl.de.
authors.forename: Jens Roat
authors.initials: JR
authors.lastname: Kultima
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. simone.li@embl.de.|School of Biotechnology and Biomolecular Sciences, University of New South Wales, 2052, Sydney, Australia. simone.li@embl.de.
authors.forename: Simone S
authors.initials: SS
authors.lastname: Li
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. zeller@embl.de.
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. sunagawa@embl.de.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Sunagawa
authors.affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany. bork@embl.de.|Molecular Medicine Partnership Unit (MMPU), University of Heidelberg and European Molecular Biology Laboratory, 69120, Heidelberg, Germany. bork@embl.de.|Max Delbrück Centre for Molecular Medicine, 13125, Berlin, Germany. bork@embl.de.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D000328:Adult; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000235:genetics; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000378:metabolism / Q000382:microbiology*; D015894:Genome, Human; D006801:Humans; D008297:Male; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods; D013997:Time Factors
chemical_list: D004269:DNA, Bacterial