Sample storage conditions significantly influence faecal microbiome profiles

• Published in: Scientific reports Vol. 5; no. 1; p. 16350
• Main Authors: Choo, Jocelyn M, Leong, Lex EX, Rogers, Geraint B
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 17.11.2015; Nature Publishing Group
• Subjects: 45; 631/158/2452; 631/208/514/2256; Ambient temperature; Bacteria - genetics; Bacteria - isolation & purification; Buffers; Collections; Community composition; Community structure; Edetic acid; Feces - microbiology; Freezing; Humanities and Social Sciences; Humans; Microbiota; multidisciplinary; Preservatives; Refrigeration; RNA, Ribosomal, 16S - chemistry; RNA, Ribosomal, 16S - genetics; RNA, Ribosomal, 16S - metabolism; rRNA; Science; Sequence Analysis, DNA; Specimen Handling - standards; Storage conditions; Temperature; Temperature effects; Time Factors
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep16350

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.