Stool preservation method comparison in healthy US adults
71 stool samples from healthy adults in the USA compared four preservation methods (freezing, room temperature, a commercial DNA kit, and a DESS-based dissolvable wipe) for microbiome community profiling. machine-written summary
71 samples · 71 runs · US · Age unknown · 2022 · 1.00 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 213 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 142 sample values (health condition, health condition detail) · PMC9196042 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
6 of 6 people sampled more than once (71 samples; median 12, up to 12 per person).
Genera, mean relative abundance over 62 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 71 | 100% | ||||
| country | 71 | 100% | 71 | |||
| health_condition | 71 | 100% | 71 | |||
| subject_id | 71 | 100% | 71 | |||
| collection_date | 71 | 100% | 71 | |||
| health_condition_detail | 71 | 100% | 71 |
- A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling. 2022 PMID 35711426 PMC9196042 own_data
Archive description
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 degree 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.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “stool collection and preservation kit”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN27386862 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN27386862 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN27386862 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | A total of 6 healthy subjects were enrolled |
| SAMN27386862 | health_condition_detail | healthy subjects, no IBD, screened by Bristol Stool Scale | R3 | 0.70 | paper.fulltext.methods | A total of 6 healthy subjects were enrolled |
| SAMN27386862 | subject_id | S1 | R1 | 0.85 | sample.attr.subjectid | S1 |
Sequencing
71 runs over 71 samples · mean 1.32 Gbp per run (median 1.00 Gbp, total 93.46 Gbp; 71 runs with a base count) · layout SINGLE 71 · platform ILLUMINA 71 · models NextSeq 550 (71) · 87% of runs with a Sandpiper profile · first public 2022-05-26
Authors (10)
Hua H first · Meydan C · Afshin EE · Lili LN · D'Adamo CR · Rickard N · Dudley JT · Price ND · Zhang B · Mason CE last
Downloads
PRJNA824068.csv.gz (2.4 KB) · parquet (72.1 KB) — all 71 samples, every field with route and confidence · PRJNA824068_determinations.csv.gz (2.4 KB) — 355 evidence rows