Utility of a portable desiccant system for preservation of fecal samples for downstream 16S rRNA amplicon sequencing

Abstract

While recent advances in culture-independent sequencing approaches have revitalized the field of microbiology, rapid collection and preservation of microbial DNA in samples like feces is critical to avoid degradation of target DNA via nuclease activity and proliferation of aerotolerant microbes. Common laboratory practices to ameliorate such changes rely on prompt freezing of samples or dispersion in nuclease-inhibiting reagents. As many of the microbial enzymes associated with nuclease activity and bacterial proliferation are hydrolases, prompt desiccation of samples offers an attractive alternative to freezing and liquid reagents for field collection of samples in remote areas. Herein, we evaluated the utility of a portable desiccant chamber with a rechargeable cartridge, for preservation of equine fecal samples for downstream microbial profiling via 16S rRNA amplicon sequencing. Controls included matched samples promptly frozen at −80 °C or left at room temperature for an equivalent period of time. While samples held at room temperature showed a significant reduction in richness and proliferation of several facultative anaerobes, desiccated samples showed minimal change from promptly frozen samples, with the exception of increased abundance of Acinetobacter spp. in desiccated samples relative to frozen samples. The data support the utility of portable desiccant chambers for the preservation of microbial field samples intended for downstream sequencing approaches.