A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling

• Published in: Frontiers in Immunology
• Main Authors: Hui Hua, Cem Meydan, Evan E. Afshin, Loukia N. Lili, Christopher R. D’Adamo, Nate Rickard, Joel T. Dudley, Nathan D. Price, Bodi Zhang, Christopher E. Mason
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2022-05-01
• Subjects: microbiome; wipe; metagenomics; DESS; stool collection
• Online Access: https://www.frontiersin.org/articles/10.3389/fimmu.2022.889702/full

While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.