Swedish adult gut microbiome longitudinal cohort (S3WP)
177 gut metagenome samples from healthy adults in the Swedish S3WP cohort, collected longitudinally, used to study microbiota species stability over time. machine-written summary
177 samples · 178 runs · Adult · 2024 · 10.93 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 531 sample values (health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table |
| – 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 |
country: sequence archive and GMrepo disagree for 177 samples (e.g. SE vs GB) — withheld.
The sources disagree on 177 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 177)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA14107055 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107056 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107057 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107058 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107059 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107060 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107061 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107062 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107063 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107064 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107065 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107066 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107067 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107068 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107069 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107070 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107071 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107072 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107073 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107074 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107075 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107076 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107077 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107078 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107079 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107080 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107081 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107082 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107083 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107084 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107085 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107086 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107087 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107088 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107089 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107090 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107091 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107092 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107093 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
| SAMEA14107094 | country | SE (sequence archive) | GB (GMrepo) | withheld: neither value published |
longitudinal — not resolved
81 of 96 people sampled more than once (162 samples; median 2, up to 2 per person). Schedule stated by the source: “Two time points three months apart (visit 5 and visit 6)”; stated follow-up 3 mo.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 177 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 177 | 100% | 177 | |||
| subject_id | 177 | 100% | 177 | |||
| health_condition_detail | 177 | 100% | 177 |
- Transient colonizing microbes promote gut dysbiosis and functional impairment. 2024 PMID 39245657 PMC11381545 unsure
Archive description
Human gut shotgun metagenomics study was conducted on healthy swedish population from S3WP cohort to investigate the dynamics of microbiota changes. To this end, healthy individuals with no clinical evidence of diseases were enrolled and followed two time points by every three months (visit 5 and visit6). our analysis identified two different populations of microbial species, inflow and outflowspecies, associated with health and disease.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.description · “Human gut shotgun metagenomics study”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA14107055 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:DESCRIPTION | healthy swedish at v5 from s3wp |
| SAMEA14107055 | health_condition_detail | healthy swedish at v5 from s3wp | R1 | 0.85 | biosample.attribute:DESCRIPTION | healthy swedish at v5 from s3wp |
| SAMEA14107055 | subject_id | 2809 | R1 | 0.70 | sample.name_rule:TITLE | healthy swedish, W001(2809_v5) |
Sequencing
178 runs over 177 samples · mean 13.52 Gbp per run (median 10.94 Gbp, total 2,405.74 Gbp; 178 runs with a base count) · layout PAIRED 178 · platform DNBSEQ 178 · models DNBSEQ-T7 (178) · 0% of runs with a Sandpiper profile · first public 2024-08-05
Authors (24)
Lee S first · Meslier V · Bidkhori G · Garcia-Guevara F · Etienne-Mesmin L · Clasen F · Park J · Plaza Oñate F · Cai H · Le Chatelier E · Pons N · Pereira M · Seifert M · Boulund F · Engstrand L · Lee D · Proctor G · Mardinoglu A · Blanquet-Diot S · Moyes D · Almeida M · Ehrlich SD · Uhlen M · Shoaie S last
Downloads
PRJEB52380.csv.gz (5.1 KB) · parquet (75.7 KB) — all 177 samples, every field with route and confidence · PRJEB52380_determinations.csv.gz (5.9 KB) — 531 evidence rows