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A wipe-based stool collection and preservation kit for microbiome community profiling

Hui Hua, Cem Meydan, Evan E. Afshin, Loukia Lili, Christopher R. D’Adamo, Joel Dudley, Nathan D. Price, Bodi Zhang, View ORCID ProfileChristopher E. Mason
doi: https://doi.org/10.1101/2021.12.03.471072
Hui Hua
1Thorne HealthTech, 152 W 57th, New York, NY 10019, USA
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  • For correspondence: hui.hua@oxfordalumni.org cmason@onegevity.com
Cem Meydan
1Thorne HealthTech, 152 W 57th, New York, NY 10019, USA
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Evan E. Afshin
1Thorne HealthTech, 152 W 57th, New York, NY 10019, USA
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Loukia Lili
1Thorne HealthTech, 152 W 57th, New York, NY 10019, USA
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Christopher R. D’Adamo
2Department of Family and Community Medicine, University of Maryland School of Medicine, 520 W. Lombard Street, Baltimore, MD 21201, USA
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Joel Dudley
1Thorne HealthTech, 152 W 57th, New York, NY 10019, USA
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Nathan D. Price
1Thorne HealthTech, 152 W 57th, New York, NY 10019, USA
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Bodi Zhang
1Thorne HealthTech, 152 W 57th, New York, NY 10019, USA
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Christopher E. Mason
1Thorne HealthTech, 152 W 57th, New York, NY 10019, USA
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  • ORCID record for Christopher E. Mason
  • For correspondence: hui.hua@oxfordalumni.org cmason@onegevity.com
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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 DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, 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. Future studies will be needed to further explore sample processing options and their applications in non-healthy subjects, particularly patients with irritable bowel syndrome, inflammatory bowel disease, and colorectal cancer, but these data suggest the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.

Competing Interest Statement

All authors except for CRD are employees of Thorne HealthTech and the Onegevity Health platform.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted December 03, 2021.
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A wipe-based stool collection and preservation kit for microbiome community profiling
Hui Hua, Cem Meydan, Evan E. Afshin, Loukia Lili, Christopher R. D’Adamo, Joel Dudley, Nathan D. Price, Bodi Zhang, Christopher E. Mason
bioRxiv 2021.12.03.471072; doi: https://doi.org/10.1101/2021.12.03.471072
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A wipe-based stool collection and preservation kit for microbiome community profiling
Hui Hua, Cem Meydan, Evan E. Afshin, Loukia Lili, Christopher R. D’Adamo, Joel Dudley, Nathan D. Price, Bodi Zhang, Christopher E. Mason
bioRxiv 2021.12.03.471072; doi: https://doi.org/10.1101/2021.12.03.471072

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