Desiccation-based microbial sample preservation in remote regions

University Of Oregon Eugene, Eugene OR

Investigators

Abstract

An award is made to the University of Oregon to develop and evaluate non-cryogenic methods for microbial sample preservation in the field based on heat-assisted desiccation, a promising approach that presents several practical and economical advantages over existing sample preservation methods. The methods explored will be designed to have low risk and cost, result in low sample weight, and be practical in remote and less developed regions (e.g., requiring only a vehicle's auxiliary power outlet). The insights gained will enable researchers around the world to survey a substantially broader range of locations with reduced logistical challenges. In addition, because dried material is typically safer, lighter and does not require a cold chain, it is also easier to transport and ship between countries, thus facilitating international collaborations. The portable and economical desiccation methods explored here would greatly facilitate surveys of potentially contaminated water bodies and feces during disease outbreaks, as well as the proactive archival of collected material for future analyses, thus contributing to improved disease management and prevention. In addition, desiccated sample material can be archived over prolonged periods of time at room temperatures, and can thus serve as a cheaper alternative to energy-hungry cryopreservation or as a safety backup in the case of freezer failures. The project will also provide research opportunities to one or more undergraduate students. Modern sequencing methods are revolutionizing microbiome research. However, sample preservation in the field and during transport remains a frequent bottleneck that entails substantial logistical challenges, particularly in remote areas or underdeveloped countries. Indeed, the golden standard in sample preservation, flash-freezing at liquid nitrogen temperatures and subsequent storage in a freezer, is often impractical or outright impossible. While alternative non-cryogenic sample preservation methods exist, each of them comes with a set of limitations. Heat-assisted desiccation is a promising simple and economical approach that has so far received little attention. This project will examine multiple alternative protocols of heat-assisted desiccation in a factorial manner. The project will focus on the ability of the explored methods to yield suitable DNA for 16S rRNA marker gene sequencing and metagenomics (two of the most important techniques in microbiome research), after short-term and long-term sample storage at room temperature. The project will thus provide the first systematic evaluation of heat-assisted sample desiccation in terms of DNA yield, DNA integrity, taxonomic biases and suitability for 16S rRNA and genome-resolved metagenomic sequencing. The project would also serve as an important milestone for the future development of commercial miniaturized heat-based dehydrators optimized for biological research in remote regions. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.