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A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling
Hui Hua1, Cem Meydan1, Evan E Afshin1
1Thorne HealthTech, New York, NY, United States.
Abstract:
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.
Insights
A novel wipe-based method simplifies fecal sample collection for microbiome analysis. This approach, using DESS solution, offers stable room-temperature storage and transport, comparable to traditional methods.
Area of Science:
- Microbiome Research
- Molecular Biology
- Genomics
Background:
- Traditional stool collection methods are often complex and require specialized handling.
- Standardized and user-friendly fecal sample collection is crucial for accurate microbiome analysis.
Purpose of the Study:
- To introduce and validate a novel, wipe-based method for fecal sample collection and stabilization.
- To assess the efficacy of this new method for metagenomics analysis compared to existing techniques.
Main Methods:
- Collected 72 fecal samples using four preservation methods: freezing, room temperature storage, a commercial kit, and a novel DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) wipe.
- Performed metagenomic sequencing and analyzed taxonomic abundance, bacterial metabolic pathways, and diversity metrics.
Main Results:
- The DESS wipe method demonstrated high correlation (R²=0.96) with frozen samples for species abundance across all kingdoms.
- Shannon diversity (3.1-3.3) and species richness (151-159) were maintained, comparable to frozen samples.
- DESS wipe performance was similar to a commercial preservation kit (R²=0.98), with samples clustering by subject across all methods.
Conclusions:
- The DESS wipe method is a validated, stable approach for room-temperature fecal specimen collection and transport.
- This novel method simplifies sample handling for microbiome studies, enhancing accessibility and potentially improving data consistency.
