BMC Microbiology · 2018 · 40 citations · 21 references
The study examined how various stabilization and storage methods affect fecal microbiome quality and composition. The authors compared freshly isolated murine DNA to samples stored for one month under diverse conditions—ambient air, with EDTA or lysis buffer, at 4 °C, –20 °C, –80 °C, or hypoxia—to assess effects on DNA and microbial profiles. Lysis buffer lowered DNA yield without compromising integrity, while EDTA most strongly altered alpha diversity and clustering; storage conditions also shifted phyla, species, and most metabolic pathways, with tyrosine metabolism affected by all but EDTA, underscoring that each long‑term strategy introduces a distinct post‑collection bias.
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. 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. Each long-term storage strategy introduced a unique post-collection bias, which is important to take into account when interpreting data.
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Evolution of Mammals and Their Gut Microbes
Ruth E. Ley, Micah Hamady, Catherine Lozupone et al. · Science · 2008 · 3.7K citations · Full text