title: Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences.
abstract: BACKGROUND
  We conducted a pilot study of reproducibility and associations of microbial diversity and composition in faecal microbial DNA.
  
  
  RESULTS
  Participants (25 men and 26 women, aged 17-65 years) provided questionnaire data and multiple samples of one stool collected with two Polymedco and two Sarstedt devices preloaded with RNAlater. 16S rRNA genes in each faecal DNA aliquot were amplified, sequenced (Roche/454 Life Sciences) and assigned to taxa. Devices were compared for ease of use and reproducibility [intraclass correlation coefficient (ICC)] between duplicate aliquots on diversity and taxonomic assignment. Associations were tested by linear regression. Both collection devices were easy to use. Both alpha diversity (Shannon index) and beta diversity (UniFrac) were higher between than within duplicates (P ≤ 10(-8) ) and did not differ significantly by device (P ≥ 0·62). Reproducibility was good (ICC≥0·77) for alpha diversity and taxonomic assignment to the most abundant phyla, Firmicutes and Bacteroidetes (71·5% and 25·0% of sequences, respectively), but reproducibility was low (ICC≤0·48) for less abundant taxa. Alpha diversity was lower with nonantibiotic prescription medication (P = 0·02), with younger age (P = 0·03) and marginally with higher body mass index (P = 0·08).
  
  
  CONCLUSIONS
  With sampling from various parts of a stool, both devices provided good reproducibility on overall microbial diversity and classification for the major phyla, but not for minor phyla. Implementation of these methods should provide insights into how broad microbial parameters, but not necessarily rare microbes, affect risk of various conditions.
authors.affiliation: Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
authors.forename: Roberto
authors.initials: R
authors.lastname: Flores
authors.forename: Jianxin
authors.initials: J
authors.lastname: Shi
authors.forename: Mitchell H
authors.initials: MH
authors.lastname: Gail
authors.forename: Pawel
authors.initials: P
authors.lastname: Gajer
authors.forename: Jacques
authors.initials: J
authors.lastname: Ravel
authors.forename: James J
authors.initials: JJ
authors.lastname: Goedert
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D005243:Feces / Q000382:microbiology*; D005260:Female; D020459:Genes, rRNA / Q000235:genetics; D006801:Humans; D008297:Male; D054892:Metagenome; D008875:Middle Aged; D010802:Phylogeny; D010865:Pilot Projects; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012044:Regression Analysis; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA; D011795:Surveys and Questionnaires; D055815:Young Adult
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S