Sample storage conditions induce post-collection biases in microbiome profiles.

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PubMed ID: 30591021

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Jenkins SV, Vang KB, Gies A, Griffin RJ, Jun SR, Nookaew I, Dings RPM

BMC Microbiol. Dec 2018. doi: 10.1186/s12866-018-1359-5

COMMENT: In this work the authors determine the effect of different long term storage strategies on the composition of the murine fecal microbial community by 16S ribosomal RNA (rRNA) gene sequencing. 


Here we investigated the influence of different stabilization and storage strategies, i.e. different preservative buffers, temperatures, and oxygen concentrations, on the quality and composition of murine fecal microbiome after being stored for over 1 month.


Storage in commercially available lysis buffer reduced the DNA content the most, yet did not cause loss of DNA integrity.

Long-term storage in EDTA affected the alpha diversity the most. 

Storage under hypoxic conditions favors bacterial strains within the Bacteroidetes and Proteobacteria phyla (...) without significant loss in DNA content or integrity.

The coldest condition, − 80 °C, is preferred when immediate isolation is not possible or practical.


All 7 different strategies introduced a unique post-collection bias. Thus it is important to take this into account during the data interpretation of past, current, or future microbiome profile studies, as well as during therapeutic approaches involving stool-derived treatments (...). Alternatively, this post-collection bias can be used to an advantage if one favors a particu- lar sub-set of phyla or bacteria (e.g. anaerobes), which can be relatively enriched during long-term storage.


Raquel Ruiz-Arroyo