As microbiome research has steadily grown throughout the past decade, so too has the desire to maximize the diversity of microbial samples by moving collection work outside of the laboratory and into remote environments. This has presented unique challenges in sample storage, as there is no established protocol for microbiome preservation. Additionally, the expansion of research into developing countries has driven the necessity for cost-effective and readily available preservation solutions to help collect specimens from locations and populations that are traditionally underrepresented in microbial studies.
To address this growing need for practical sample storage solutions, a team of researchers with the Center for Microbiome Innovation (CMI) at the University of California San Diego (UC San Diego), led by Clarisse Marotz and Kellen J. Cavagnero, set out to evaluate the efficacy of 95% ethanol as a biospecimen preservation material. The study’s results were published by mSystems in an article entitled “Evaluation of the effect of storage methods on fecal, saliva, and skin microbiome composition” on April 27, 2021.
The research began by re-analyzing 16S rRNA gene amplicon sequencing data from a 2016 study, which revealed that microbial composition was well-maintained over time at various temperatures when samples were stored in 95% ethanol. Next, the group performed shallow shotgun metagenomic sequencing on archived DNA from the aforementioned study, which confirmed that 95% ethanol effectively preserved fecal microbial samples. Lastly, they built upon this work by investigating the ideal sample collection and storage protocols for fecal, saliva, and skin samples.
“The most exciting impact of the research is being able to expand microbiome sciences to places where it’s difficult to maintain the cold chain, such as remote villages or destinations,” Marotz remarked. “Combined with the decrease in material costs, this will allow for much more diverse samples.”
The findings have already proven invaluable in real-world applications, as they have allowed rapid expansion of The Microsetta Initiative (TMI), a citizen science project whose mission is to collect microbiome samples spanning the world’s population.
“These results provide rationale for an accessible, non-toxic, cost-effective solution that will enable crowdsourcing microbiome studies, such as The Microsetta Initiative, and lower the barrier for collecting diverse samples,” co-author Daniel McDonald, Scientific Director of TMI, noted while discussing the importance of the study’s conclusions.
Building upon this paper, the team at the CMI will be working with the Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence at UC San Diego and other research groups to explore the viability of preserving various samples with readily available materials. “We’re planning to perform similar studies on other biospecimens — including urine, vaginal swabs, and breast milk — to extend the types of samples that can be collected at home or in the field,” according to corresponding author Rob Knight, professor and director of the CMI. “These efforts have a particular focus on extending research into women’s and infant health, which are often understudied.”
Additional co-authors include Se Jin Song, Stephen Wandro, Greg Humphrey, MacKenzie Bryant, Gail Ackermann, and Edgar Diaz, all at UC San Diego.
The Center for Microbiome Innovation is proud to include Se Jin Song and Rob Knight on its leadership team.
This piece was written by CMI’s contributing editor Cassidy Symons