Ingestible device sampling of human gut regions, USA
302 samples (fecal, oral, and small intestinal) collected from healthy adult and elderly subjects in Stanford, California, USA, using an ingestible sampling device; cross-sectional design comparing intestinal regions versus stool. machine-written summary
302 samples · 302 runs · US · Adult · 2023 · 4.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,718 sample values (age, collection date, country, latitude, location region, location site, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 488 sample values (health condition, health condition detail) · PMC10191855, PMC10229427, PMC11459740 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 116 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
15 of 15 people sampled more than once (273 samples; median 18, up to 45 per person) · follow-up median 4 d (max 12 mo) · median interval between samples 1 d (time from collection dates).
Each row is one person (15 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 252 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 | 302 | 100% | ||||
| country | 302 | 100% | 302 | |||
| health_condition | 302 | 100% | 58 | 244 | ||
| subject_id | 302 | 100% | 302 | |||
| age_at_collection_days | 302 | 100% | 302 | |||
| collection_date | 302 | 100% | 302 | |||
| detailed_location | 302 | 100% | ||||
| health_condition_detail | 302 | 100% | 58 | 244 | ||
| latitude | 302 | 100% | 302 | |||
| location_region | 302 | 100% | 302 | |||
| location_site | 302 | 100% | 302 | |||
| longitude | 302 | 100% | 302 | |||
| sex | 302 | 100% | 302 |
- Human metabolome variation along the upper intestinal tract. 2023 PMID 37165176 PMC10229427 own_data
- Profiling the human intestinal environment under physiological conditions. 2023 PMID 37165188 PMC10191855 own_data
- Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition. 2024 PMID 39679619 PMC11459740 unsure
Archive description
Fecal, oral and small intestinal samples collected from 15 healthy subjects. Small intestine samples were collected using a safe, ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Most of the samples from this study are small intestinal samples (>200), 58 are stool, and 29 are saliva.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Fecal, oral and small intestinal samples”
- body site study.description · “58 are stool, and 29 are saliva”
- life stage sample.attr.host_age · “55 (n=223/302)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN27256204 | age_at_collection_days | 20088.8 | R1 | 0.70 | sample.attr.host_age | 55 |
| SAMN27256204 | collection_date | 2020-06-25 | R1 | 0.90 | biosample.attribute:collection_date | 2020-06-25T00:00:00Z |
| SAMN27256204 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Stanford, California |
| SAMN27256247 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN27256204 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Fifteen healthy individuals were enrolled in this study |
| SAMN27256247 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN27256204 | health_condition_detail | Healthy volunteers excluding clinically detectable gastrointestinal conditions or diseases | R3 | 0.70 | paper.fulltext.methods | Fifteen healthy individuals were enrolled in this study |
| SAMN27256204 | latitude | 37.4241 | R1 | 0.90 | biosample.attribute:lat_lon | 37.4241 N 122.1661 W |
| SAMN27256204 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Stanford, California |
| SAMN27256204 | location_site | Stanford | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Stanford, California |
| SAMN27256204 | longitude | -122.1661 | R1 | 0.90 | biosample.attribute:lat_lon | 37.4241 N 122.1661 W |
| SAMN27256204 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN27256204 | subject_id | 1 | R1 | 0.85 | sample.attr.subject_id | 1 |
Sequencing
302 runs over 302 samples · mean 4.62 Gbp per run (median 4.59 Gbp, total 1,395.83 Gbp; 302 runs with a base count) · layout PAIRED 302 · platform ILLUMINA 302 · models Illumina NovaSeq 6000 (302) · 92% of runs with a Sandpiper profile · first public 2023-01-17
Authors (49)
Folz J first · Culver RN · Morales JM · Grembi J · Triadafilopoulos G · Relman DA · Huang KC · Shalon D · Fiehn O last · Grembi JA · Treit PV · Shi H · Rosenberger FA · Dethlefsen L · Meng X · Yaffe E · Aranda-Díaz A · Geyer PE · Mueller-Reif JB · Spencer S · Patterson AD · Holmes SP · Mann M · Steinbach E first · Belda E · Alili R · Adriouch S · Dauriat CJG · Donatelli G · Dumont JL · Pacini F · Tuszynski T · Pelloux V · Jacques F · Creusot L · Coles E · Taillandier P · Vazquez Gomez M · Masi D · Mateo V · André S · Kordahi M · Rouault C · Zucker JD · Sokol H · Genser L · Chassaing B · Le Roy T · Clément K last
Downloads
PRJNA822660.csv.gz (8.3 KB) · parquet (81.9 KB) — all 302 samples, every field with route and confidence · PRJNA822660_determinations.csv.gz (20.7 KB) — 3,322 evidence rows