Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

Se Jin Song; Amnon Amir; Jessica L Metcalf; Katherine R Amato; Zhenjiang Zech Xu; Greg Humphrey; Rob Knight

doi:10.1128/mSystems.00021-16

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

mSystems. 2016 May 3;1(3):e00021-16. doi: 10.1128/mSystems.00021-16. eCollection 2016 May-Jun.

Authors

Se Jin Song¹, Amnon Amir², Jessica L Metcalf¹, Katherine R Amato³, Zhenjiang Zech Xu², Greg Humphrey², Rob Knight⁴

Affiliations

¹ Department of Pediatrics, University of California-San Diego, La Jolla, California, USA; Department of Ecology and Evolutionary Biology, University of Colorado-Boulder, Boulder, Colorado, USA.
² Department of Pediatrics, University of California-San Diego, La Jolla, California, USA.
³ Department of Anthropology, Northwestern University, Evanston, Illinois, USA.
⁴ Department of Pediatrics, University of California-San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, University of California-San Diego, La Jolla, California, USA.

Abstract

Immediate freezing at -20°C or below has been considered the gold standard for microbiome preservation, yet this approach is not feasible for many field studies, ranging from anthropology to wildlife conservation. Here we tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including such types of variation as freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions. We found that three of the methods-95% ethanol, FTA cards, and the OMNIgene Gut kit-can preserve samples sufficiently well at ambient temperatures such that differences at 8 weeks are comparable to differences among technical replicates. However, even the worst methods, including those with no fixative, were able to reveal microbiome differences between species at 8 weeks and between individuals after a week, allowing meta-analyses of samples collected using various methods when the effect of interest is expected to be larger than interindividual variation (although use of a single method within a study is strongly recommended to reduce batch effects). Encouragingly for FTA cards, the differences caused by this method are systematic and can be detrended. As in other studies, we strongly caution against the use of 70% ethanol. The results, spanning 15 individuals and over 1,200 samples, provide our most comprehensive view to date of storage effects on stool and provide a paradigm for the future studies of other sample types that will be required to provide a global view of microbial diversity and its interaction among humans, animals, and the environment. IMPORTANCE Our study, spanning 15 individuals and over 1,200 samples, provides our most comprehensive view to date of storage and stabilization effects on stool. We tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, including the types of variation often encountered under field conditions, such as freeze-thaw cycles and high temperature fluctuations. We show that several cost-effective methods provide excellent microbiome stability out to 8 weeks, opening up a range of field studies with humans and wildlife that would otherwise be cost-prohibitive.

Keywords: DNA stability; fecal microbiome; sample storage.