Stool card vs ethanol metagenome comparison, USA
64 stool samples (paired stool-card and 95% ethanol preserved) from healthy adults in the USA, comparing two machine-written summary
64 samples · 64 runs · US · Age unknown · 2025 · 2.40 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 384 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 64 sample values (location site) |
| ✓ Full text | 256 sample values (antibiotic exposure, health condition, health condition detail, sex) · PMC12316560 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
32 of 32 people sampled more than once (64 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 63 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 | 64 | 100% | ||||
| country | 64 | 100% | 64 | |||
| health_condition | 64 | 100% | 64 | |||
| subject_id | 64 | 100% | 64 | |||
| antibiotic_exposure | 64 | 100% | 64 | |||
| collection_date | 64 | 100% | 64 | |||
| detailed_location | 64 | 100% | ||||
| health_condition_detail | 64 | 100% | 64 | |||
| latitude | 64 | 100% | 64 | |||
| location_region | 64 | 100% | 64 | |||
| location_site | 64 | 100% | 64 | |||
| longitude | 64 | 100% | 64 | |||
| sex | 64 | 100% | 64 |
- Comparing the Metagenomic Performance of Stools Collected from Custom Cards and 95% Ethanol in Epidemiologic Studies. 2025 PMID 40434915 PMC12316560 own_data
Archive description
Biomedical research stool sample collection methods must balance ease of use, sample preservation, and handling simplicity. 95% ethanol is commonly used due to its favorable performance, but can cause issues with shipping and DNA extraction. Collection cards are frequently used in cancer epidemiology to avoid difficulties involving solvents. However, relatively few studies use stool microbiome-specific card methods, and their performance against 95% ethanol is not well established.</p><p>Here, we compared shotgun metagenomic data generated from 32 paired samples from a custom stool card and 95% ethanol-preserved sample. The agreement between methods was evaluated at the whole community and individual species level. Method-biased species were compared to a recently generated list of colorectal cancer-associated species to contextualize card performance. Stool cards generally agreed with 95% ethanol, though some taxa were differentially abundant between methods. Streptococci seem to be underrepresented systematically on cards, and Escherichia coli blooms were occasionally observed. Differences between methods were not enriched within the set of colorectal cancer-associated species.</p><p>Both stool cards or 95% ethanol perform well, but differences should be accounted for, especially when mixing collection methods within a study. Community-level deviations can be regarded similarly to typical batch effects and adjusted as such, while species-level biases may require direct attention depending on phenotype of interest.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “stool metagenomic studies”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN47842508 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | hospitalization, or antibiotic use |
| SAMN47842508 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMN47842508 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN47842508 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | history of major chronic diseases or GI disorders |
| SAMN47842508 | health_condition_detail | excluded major chronic diseases or GI disorders | R3 | 0.60 | paper.fulltext.methods | Exclusion criteria for our study included a history of major chronic diseases |
| SAMN47842508 | latitude | 42.3550 | R1 | 0.90 | biosample.attribute:lat_lon | 42.355 N 71.05 W |
| SAMN47842508 | location_region | Massachusetts | R1 | 0.60 | biosample.attribute:lat_lon | 42.355 N 71.05 W |
| SAMN47842508 | location_site | Nurses' Health Study II | R4 | 0.50 | paper.abstract | in the Nurses' Health Study II |
| SAMN47842508 | longitude | -71.0500 | R1 | 0.90 | biosample.attribute:lat_lon | 42.355 N 71.05 W |
| SAMN47842508 | sex | female | R3 | 0.60 | paper.fulltext.results | All 32 participants were female nurses |
| SAMN47842508 | subject_id | 1 | R1 | 0.85 | biosample.attribute:Subject_Treatment | Subject_Treatment: Person1.Ethanol |
| SAMN47842511 | subject_id | 2 | R1 | 0.70 | sample.name_rule:subject_treatment | Person2.Card |
Sequencing
64 runs over 64 samples · mean 2.64 Gbp per run (median 2.40 Gbp, total 169.06 Gbp; 64 runs with a base count) · layout PAIRED 64 · platform ILLUMINA 64 · models Illumina NovaSeq 6000 (64) · 98% of runs with a Sandpiper profile · first public 2025-04-09
Authors (15)
Kuntz TM first · Liu L · Wang K · Everett C · Eliassen AH · Willett WC · Sinha R · Chan AT · Rimm EB · Garrett WS · Segata N · Piccinno G · Huttenhower C · Morgan X · Song M last
Downloads
PRJNA1248002.csv.gz (2.6 KB) · parquet (73.4 KB) — all 64 samples, every field with route and confidence · PRJNA1248002_determinations.csv.gz (5.4 KB) — 704 evidence rows