title: Integrity of the Human Faecal Microbiota following Long-Term Sample Storage.
abstract: In studies of the human microbiome, faecal samples are frequently used as a non-invasive proxy for the study of the intestinal microbiota. To obtain reliable insights, the need for bacterial DNA of high quality and integrity following appropriate faecal sample collection and preservation steps is paramount. In a study of dietary mineral balance in the context of type 2 diabetes (T2D), faecal samples were collected from healthy and T2D individuals throughout a 13-day residential trial. These samples were freeze-dried, then stored mostly at -20°C from the trial date in 2000/2001 until the current research in 2014. Given the relative antiquity of these samples (~14 years), we sought to evaluate DNA quality and comparability to freshly collected human faecal samples. Following the extraction of bacterial DNA, gel electrophoresis indicated that our DNA extracts were more sheared than extracts made from freshly collected faecal samples, but still of sufficiently high molecular weight to support amplicon-based studies. Likewise, spectrophotometric assessment of extracts revealed that they were of high quality and quantity. A subset of bacterial 16S rRNA gene amplicons were sequenced using Illumina MiSeq and compared against publicly available sequence data representing a similar cohort analysed by the American Gut Project (AGP). Notably, our bacterial community profiles were highly consistent with those from the AGP data. Our results suggest that when faecal specimens are stored appropriately, the microbial profiles are preserved and robust to extended storage periods.
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors.forename: Elahe
authors.initials: E
authors.lastname: Kia
authors.affiliation: Department of Surgery, University of Auckland, Auckland, New Zealand.
authors.forename: Brett
authors.initials: B
authors.lastname: Wagner Mackenzie
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors.forename: Danielle
authors.initials: D
authors.lastname: Middleton
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors.forename: Anna
authors.initials: A
authors.lastname: Lau
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors.forename: David W
authors.initials: DW
authors.lastname: Waite
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors.forename: Gillian
authors.initials: G
authors.lastname: Lewis
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.|Human Nutrition Unit, University of Auckland, Auckland, New Zealand.
authors.forename: Yih-Kai
authors.initials: YK
authors.lastname: Chan
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.|Human Nutrition Unit, University of Auckland, Auckland, New Zealand.
authors.forename: Marta
authors.initials: M
authors.lastname: Silvestre
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors.forename: Garth J S
authors.initials: GJ
authors.lastname: Cooper
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.|Human Nutrition Unit, University of Auckland, Auckland, New Zealand.
authors.forename: Sally D
authors.initials: SD
authors.lastname: Poppitt
authors.affiliation: School of Biological Sciences, University of Auckland, Auckland, New Zealand.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Taylor
mesh_terms: D044822:Biodiversity; D004269:DNA, Bacterial; D005243:Feces / Q000382:microbiology*; D006801:Humans; D054892:Metagenome; D056186:Metagenomics; D050296:Microbial Viability; D064307:Microbiota; D011309:Preservation, Biological; D012336:RNA, Ribosomal, 16S; D013997:Time Factors
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S