Sample storage

What is the best method to preserve samples? In most cases, samples cannot be processed immediately through DNA extraction. Using a fresh sample as the golden standard, what is the best storage method?  Many papers have tackled this question, studying the effects of temperature, days after collection, and preservation solutions. There is no easy answer, so I just give a list of papers, most recent ones first.

Also see my pages on Extraction and Amplification, and Contamination Issues.

Created July 2016, updated March 2018.

Social media posts that inspired this page

Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? – Jonathan Eisen – – January 2015

Storify: Storing nucleic acids for ~ a week w/o a freezer – Cameron Trash – Storify


Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing – Luisa Hugerth – Frontiers in Microbiology – September 2017

Has a nice comparison of different storage temperatures and buffers: Practical considerations for large-scale gut microbiome studies – Doris Vandeputte – FEMS Microbiology Reviews – June 2017

Optimizing methods and dodging pitfalls in microbiome research – Dorothy Kim – Microbiome – May 2017

Research papers

Methodology challenges in studying human gut microbiota – effects of collection, storage, DNA extraction and next generation sequencing technologies – Marina Panek – Scientific Reports – March 2018

Comparison of commercially-available preservatives for maintaining the integrity of bacterial DNA in human milk – Kimberly Lackey – Journal of Microbiological Methods – October 2017

Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants – Wendy Wong – Microbiome – September 2017

The effect of storage at ambient temperature on the feline fecal microbiota – Moran Tal – BMC Veterinary Research – August 2017

DMSO, PEG, glycerol: Functional amplification and preservation of human gut microbiota – Nadia Gaci – Microbial Ecology in Health and Disease – April 2017

Comparison of stool versus rectal swab samples and storage conditions on bacterial community profiles – Christine Bassis – BMC Microbiology – March 2017

No preservative, but tackling the problem computationally using Deblur: Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping – Amnon Amir – mSystems – March 2017

Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research – Sebastian Menke – Frontiers in Microbiology – January 2017

Testing FOBT, FIT, and ethanol: Comparison of collection methods for fecal samples for discovery metabolomics in epidemiologic studies – Erikka Loftfield – Cancer Epidemiol Biomarkers Prev – November 2016

FTA cards vs. freezingEffects of field conditions on fecal microbiota – Vanessa L. Hale – Journal of Microbiological Methods – September 2016

Effects of Specimen Collection Methodologies and Storage Conditions on the Short-Term Stability of Oral Microbiome Taxonomy – Ting Luo – Applied and Environmental Microbiology – September 2016

DNA Genotek OMNIgene∙Gut kit vs. freezingA robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome – Ericka L. Anderson – Scientific Reports – August 2016

Compares RNAlater, lyophilization, ethanol, and freezing: Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data – Ran Blekhman – Scientific Reports – August 2016

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? – Alexander G Shaw – Microbiome – July 2016

High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy – Yuichiro Nishimoto – Gut – June 2016

Compares FOBT, FIT, and ethanol: Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh – Emily Vogtmann – Applied and Environmental Microbiology – May 2016

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants – Cian J. Hill – Microbiome – May 2016

Compares 95% ethanol, FTA cards and the OMNIgene Gut kit, but cautions against the use of 70% ethanol:  Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems – May 2016

Effect of short-term room temperature storage on the microbial community in infant fecal samples – Yong Guo –  Sci Reports – May 2016

Preservation of Biospecimens at Ambient Temperature: Special Focus on Nucleic Acids and Opportunities for the Biobanking Community – Rolf Muller – Biopreservation and Biobanking – April 2016

Optimized sample handling strategy for metabolic profiling of human feces – Jasmine Gratton – Anal Chem – April 2016

Not a scientific paper, but lots of great information here: Spoiler Alert: How to store microbiome samples without losing or altering diversity –  Wudan Yan – The Scientist – March 2016

Compares 7 different methods:  Collecting fecal samples for microbiome analyses in epidemiology studies – Rashmi Sinha – Cancer Epidemiol Biomarkers Prev – February 2016

OMNIgene.gutSample storage conditions significantly influence faecal microbiome profiles – Jocelyn M Choo -Scientific Reports – November 2015

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota – Tobin Hammer – PeerJ – August 2015

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool – Monika A. Gorzelak – PLOS ONE – August 2015

Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation – Michael Reck – BMC Genomics – July 2015

EthanolEffect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks – Vanessa L. Hale – Journal of Microbiological Methods – June 2015

The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects – Danyta I. Tedjo – PLOS ONE – May 2015

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes – Manuel Kleiner – BMC Genomics – January 2015

Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity – Frederiek-Maarten Kerckhof – PLOS ONE – June 2014

Relating the metatranscriptome and metagenome of the human gut –  Eric Franzosa – P Natl Acad Sci USA – June 2014

Comparison of methods for fecal microbiome biospecimen collection – Christine Dominianni – BMC Microbiology – April 2014

Tanzania samples were submerged in 30 ml of 97% ethanol for 2-3 days. Subsequently, the ethanol was poured out and the remaining solid material was transferred to 50 ml tubes containing silica beads before transport. Supplemental methods show that this method yields DNA composition similar to that of frozen samples.  Gut microbiome of the Hadza hunter-gatherersGut microbiome of the Hadza hunter-gatherers – Stephanie L. Schnorr – Nature Communications – April 2014

Differential recovery of bacterial and archaeal 16S rRNA genes from ruminal digesta in response to glycerol as cryoprotectant – Nest McKain – Journal of Microbiological Methods – December 2013

Comparison of DNA preservation methods for environmental bacterial community samples – Gray Michael A. – FEMS Microbiology Ecology – February 2013

Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage – Ian M. Carroll – PLOS ONE – October 2012

Storage conditions of intestinal microbiota matter in metagenomic analysis – Silvia Cardona – BMC Microbiology – July 2012

Comparison of Storage Conditions for Human Vaginal Microbiome Studies – Guoyun Bai – PLOS ONE – May 2012

Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis – Martin Iain Bahl – FEMS Microbiology Letters – April 2012

The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples – Johanna Maukonen – FEMS Microbiology Ecology – March 2012

Examination of Microbial Proteome Preservation Techniques Applicable to Autonomous Environmental Sample Collection – Mak A. Saito – Frontiers in Microbiology – November 2011

Storage of environmental samples for guaranteeing nucleic acid yields for molecular microbiological studies – Antti Juhani Rissanen – Applied Microbiology and Biotechnology – October 2010

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags – Gary D Wu – BMC Microbiology – July 2010

Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples – Christian L. Lauber – FEMS Microbiology Letters – April 2010

Influence of Fecal Sample Storage on Bacterial Community Diversity – Luiz F. W Roesch – Open Microbiology Journal – March 2009

Effect of soil sample preservation, compared to the effect of other environmental variables, on bacterial and eukaryotic diversity – Vesela A. Tzeneva – Research in Microbiology – March 2009

SLB bufferA comparison of methods for total community DNA preservation and extraction from various thermal environments – Kendra R. Mitchell – Journal of Industrial Microbiology & Biotechnology – July 2008

In vitro alterations of intestinal bacterial microbiota in fecal samples during storage – Stephan J. Ott – Diagnostic Microbiology and Infectious Disease – December 2004

Microbial Diversity in Archived Soils – J. Dolfing – Science – October 2004

Ethanol: Soil conservation for DNA preservation for bacterial molecular studies – Myriam Harry – European Journal of Soil Biology – January 2000

Commercial products and news articles

I am not specifically endorsing one, but just a handy list:

Nucleic Acid Extraction—Keeping It Stable and Intact – Josh P. Roberts – Biocompare – June 2016

RNAlater, Stabilize and protect RNA with immediate RNase inactivation – Sigma Aldrig
RNAlater and AllProtect – QIAgen

Omnigene.GUT (contains ethanol) – DNA Genotek

Stool Nucleic Acid Collection and Preservation Tubes (Cat. 45630, 45660) – Norgen Biotek

Whatman FTA Elute Cards and other collection cards