title: Sample storage conditions significantly influence faecal microbiome profiles.
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.
authors.affiliation: Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide 5000, SA, Australia.
authors.forename: Jocelyn M
authors.initials: JM
authors.lastname: Choo
authors.affiliation: Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide 5000, SA, Australia.
authors.forename: Lex E X
authors.initials: LE
authors.lastname: Leong
authors.affiliation: Infection and Immunity Theme, South Australia Health and Medical Research Institute, North Terrace, Adelaide 5000, SA, Australia.|School of Medicine, Flinders University, Bedford Park, Adelaide 5042, SA, Australia.
authors.forename: Geraint B
authors.initials: GB
authors.lastname: Rogers
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D002021:Buffers; D005243:Feces / Q000382:microbiology*; D005615:Freezing; D006801:Humans; D064307:Microbiota; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013048:Specimen Handling / Q000592:standards*; D013696:Temperature; D013997:Time Factors
chemical_list: D002021:Buffers; D012336:RNA, Ribosomal, 16S