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

• NCJ Number: 304248
• Journal: Msystems Dated: 2016
• Author(s): Se Jin Song; Et Al
• Date Published: 2016
• Grant Number(s): 2014-R2-CX-K411; 2014-R2-CX-K011
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical)
• Award: Evaluating the Skin Microbiome as Trace Evidence; Evaluating the Skin Microbiome ad Trace Evidence

Annotation

This study tested five methods for preserving human and dog fecal specimens for periods of up to 8 weeks, under variations that included freeze-thaw cycles and the high temperature fluctuations often encountered under field conditions.

 

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. The current study found that three of the methods—95-percent 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 1 week, allowing meta-analyses of samples collected using various methods when the effect of interest is expected to be larger than inter-individual variation (although use of a single method within a study is strongly recommended to reduce batch effects). For FTA cards, the differences caused by this method were systematic and can be detrended. As in other studies, the researchers caution against the use of 70-percent ethanol. The results, spanning 15 individuals and over 1,200 samples, provide the 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.  (publisher abstract modified)