Sample storage conditions significantly influence faecal microbiome profiles

Jocelyn Choo, Lex Leong, Geraint Rogers

Research output: Contribution to journalArticlepeer-review

165 Citations (Scopus)

Abstract

Sequencing-based studies of the human faecal microbiota are increasingly common. Appropriate storage of sample material is essential to avoid the introduction of post-collection bias in microbial community composition. Rapid freezing to 80 °C is commonly considered to be best-practice. However, this is not feasible in many studies, particularly those involving sample collection in participants homes. We determined the extent to which a range of stabilisation and storage strategies maintained the composition of faecal microbial community structure relative to freezing to 80 °C. Refrigeration at 4 °C, storage at ambient temperature, and the use of several common preservative buffers (RNAlater, OMNIgene.GUT, Tris-EDTA) were assessed relative to freezing. Following 72 hours of storage, faecal microbial composition was assessed by 16 S rRNA amplicon sequencing. Refrigeration was associated with no significant alteration in faecal microbiota diversity or composition. However, samples stored using other conditions showed substantial divergence compared to 80 °C control samples. Aside from refrigeration, the use of OMNIgene.GUT resulted in the least alteration, while the greatest change was seen in samples stored in Tris-EDTA buffer. The commercially available OMNIgene.GUT kit may provide an important alternative where refrigeration and cold chain transportation is not available.

Original languageEnglish
Article number16350
Number of pages10
JournalScientific Reports
Volume5
DOIs
Publication statusPublished - 2015

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