Gut metagenomes in Crohn's disease & spondyloarthritis, US
85 fecal samples from adults (mostly), elderly, and one infant in Colorado, USA, comparing Crohn's disease and autoimmune inflammatory conditions (including axial spondyloarthritis) to healthy controls; case-control design. machine-written summary
85 samples · 85 runs · US · Adult · 2022 · 1.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 904 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 170 sample values (antibiotic exposure, location site) · PMC7966505 |
| – 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 |
age: two sequence archives disagree for 1 sample (e.g. 33.0 vs 12184.7) — withheld.
The sources disagree on 1 sample. 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 (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN17208818 | age | 33.0 (sequence archive) | 12184.7 (sequence archive) | withheld: neither value published |
Genera, mean relative abundance over 59 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 | 85 | 100% | ||||
| country | 85 | 100% | 85 | |||
| health_condition | 85 | 100% | 85 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 85 | 100% | 85 | |||
| collection_date | 85 | 100% | 85 | |||
| detailed_location | 85 | 100% | ||||
| health_condition_detail | 85 | 100% | 85 | |||
| latitude | 85 | 100% | 85 | |||
| location_region | 85 | 100% | 85 | |||
| location_site | 85 | 100% | 85 | |||
| longitude | 85 | 100% | 85 | |||
| sex | 85 | 100% | 85 | |||
| age_at_collection_days | 84 | 99% | 84 | |||
| bmi | 82 | 96% | 82 | |||
| medication | 58 | 68% | 58 |
- Multi 'Omics Analysis of Intestinal Tissue in Ankylosing Spondylitis Identifies Alterations in the Tryptophan Metabolism Pathway. 2021 PMID 33746944 PMC7966505 own_data
Archive description
Fecal samples from controls (HC), subjects with axial spondyloarhtritis (axSpA), Crohn's disease (CD), and those with both axSpA and CD (CD-axSpA) underwent shotgun metagenomics.
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 · “Fecal samples from controls”
- 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 |
|---|---|---|---|---|---|---|
| SAMN17208796 | age_at_collection_days | 11821.0 | R1 | 0.85 | sample.attr.host_age | 32.4 |
| SAMN17208796 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods | use of antibiotics in the two weeks prior to study entry |
| SAMN17208796 | bmi | 25.27 | R1 | 0.90 | sample.attr.host_body_mass_index | 25.27 |
| SAMN17208796 | collection_date | 2017-12-07 | R1 | 0.90 | biosample.attribute:collection_date | 2017-12-07 |
| SAMN17208796 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Colorado |
| SAMN17208796 | health_condition | autoimmune_inflammatory | R1 | 0.90 | biosample_attr | Spondylarthritis |
| SAMN17208819 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:title | HC |
| SAMN17208796 | health_condition_detail | Spondylarthritis | R1 | 0.90 | sample.attr.host_disease | Spondylarthritis |
| SAMN17208819 | health_condition_detail | HC | R1 | 0.85 | biosample.attribute:title | HC |
| SAMN17208796 | latitude | 39.7420 | R1 | 0.90 | biosample.attribute:lat_lon | 39.742 N 104.842 W |
| SAMN17208796 | location_region | Colorado | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Colorado |
| SAMN17208796 | location_site | University of Colorado Hospital | R3 | 0.70 | paper.body.methods | recruited at the University of Colorado Hospital between November 2017 and November 2018 |
| SAMN17208796 | longitude | -104.8420 | R1 | 0.90 | biosample.attribute:lat_lon | 39.742 N 104.842 W |
| SAMN17208796 | medication | immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:misc_param | TNF inhibitor use |
| SAMN17208796 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
Sequencing
85 runs over 85 samples · mean 2.32 Gbp per run (median 1.43 Gbp, total 197.39 Gbp; 85 runs with a base count) · layout PAIRED 85 · platform ILLUMINA 85 · models Illumina NovaSeq 6000 (85) · 88% of runs with a Sandpiper profile · first public 2022-01-02
Authors (0)
No author record.
Downloads
PRJNA689476.csv.gz (4.3 KB) · parquet (76.7 KB) — all 85 samples, every field with route and confidence · PRJNA689476_determinations.csv.gz (9.4 KB) — 1,074 evidence rows