Sample storage conditions induce post-collection biases in microbiome profiles.
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ABSTRACT: Background
Here we investigated the influence of different stabilization and storage strategies on the quality and composition of the fecal microbial community. Namely, same-day isolated murine DNA was compared to samples stored for 1 month in air at ambient temperature, with or without preservative buffers (i.e. EDTA and lysis buffer), different temperatures (i.e. 4?°C, -?20?°C, and?-?80?°C), and hypoxic conditions.Results
Only storage in lysis buffer significantly reduced DNA content, yet without integrity loss. Storage in EDTA affected alpha diversity the most, which was also reflected in cluster separation. Distinct changes were also seen in the phyla and bacterial species abundance per storage strategy. Metabolic function analysis showed 22 pathways not significantly affected by storage conditions, whereas the tyrosine metabolism pathway was significantly changed in all strategies except by EDTA.Conclusion
Each long-term storage strategy introduced a unique post-collection bias, which is important to take into account when interpreting data.
SUBMITTER: Jenkins SV
PROVIDER: S-EPMC6307155 | biostudies-literature | 2018 Dec
REPOSITORIES: biostudies-literature
Publications
Sample storage conditions induce post-collection biases in microbiome profiles.
Jenkins Samir V SV Vang Kieng B KB Gies Allen A Griffin Robert J RJ Jun Se-Ran SR Nookaew Intawat I Dings Ruud P M RPM
BMC microbiology 20181227 1
<h4>Background</h4>Here we investigated the influence of different stabilization and storage strategies on the quality and composition of the fecal microbial community. Namely, same-day isolated murine DNA was compared to samples stored for 1 month in air at ambient temperature, with or without preservative buffers (i.e. EDTA and lysis buffer), different temperatures (i.e. 4 °C, - 20 °C, and - 80 °C), and hypoxic conditions.<h4>Results</h4>Only storage in lysis buffer significantly reduced DNA c ...[more]
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