Storage and handling of human faecal samples affect the gut microbiome composition: A feasibility study

Title
Storage and handling of human faecal samples affect the gut microbiome composition: A feasibility study
Publication Date
2019-09
Author(s)
Ezzy, Alan C
Hagstrom, Amanda D
( author )
OrcID: https://orcid.org/0000-0002-8036-9216
Email: ahagstro@une.edu.au
UNE Id une-id:ahagstro
George, Chris
Hamlin, Adam S
( author )
OrcID: https://orcid.org/0000-0003-0495-1973
Email: ahamlin@une.edu.au
UNE Id une-id:ahamlin
Pereg, Lily
Murphy, Aron J
Winter, Gal
( author )
OrcID: https://orcid.org/0000-0003-3789-395X
Email: gwinterz@une.edu.au
UNE Id une-id:gwinterz
Type of document
Journal Article
Language
en
Entity Type
Publication
Publisher
Elsevier BV
Place of publication
Netherlands
DOI
10.1016/j.mimet.2019.105668
UNE publication id
une:1959.11/28862
Abstract
Human gut microbiome analysis through faecal sampling typically involves five stages: sample collection, storage, DNA extraction, next generation sequencing and bioinformatics analysis. Of these, the first three are considered irreversible. This feasibility study describes an assessment of methodologies used for faecal DNA extraction and sample handling, using the parameters DNA yield, purity and resultant microbial profile. Six DNA extraction techniques, including commercially available kits and manual protocols were compared on human faecal samples (n = 3). Different extraction techniques produced significant variance in DNA yield (range 2.7-164 ng/mg faeces) and microbial diversity profiles, with considerable variation in phyla dominance (Firmicutes (P < 0.001), Bacteroidetes (P = 0.003), Actinobacteria (P = 0.003), One-way ANOVA). The most effective method, with the highest DNA yield, was a simple and inexpensive extraction technique named MetaHIT. Using this method, DNA was extracted from separate faecal samples (n = 3) and had been aliquoted to seven storage conditions including three stabilizing buffers and three temperature conditions, for a period of 120-h, with storage at -80 °C as a control treatment. DNA yield and purity was not statistically different between the control and remaining treatments. 16S rDNA-based diversity profile was largely comparable across the treatments with only minor differences in genera between samples stored at room temperature in air and - 80 °C control. Overall these results suggest that the choice of DNA extraction method has a greater influence on the resultant microbial diversity profile than the short-term storage method.
Link
Citation
Journal of Microbiological Methods, v.164, p. 1-9
ISSN
1872-8359
0167-7012
Pubmed ID
31302202
Start page
1
End page
9

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