Cross-sectional Gut Microbiome Cohort in IBD, France
844 shotgun metagenomic samples from adults (mostly) in France, including Crohn's disease, ulcerative colitis, and healthy controls, in a cross-sectional study of IBD-microbiome associations. machine-written summary
844 samples · 844 runs · FR · Adult · 2026 · 16.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,670 sample values (age, collection date, country, health condition, health condition detail, sex, subject id) |
| ✓ Abstract / description | 844 sample values (location locality) |
| ○ Full text | read; no usable statement or table · PMC13290079 |
| ○ 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 |
age: two sequence archives disagree for 8 samples (e.g. 27.3 vs 9971.0) — withheld.
The sources disagree on 8 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 (8)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA122926834 | age | 27.3 (sequence archive) | 9971.0 (sequence archive) | withheld: neither value published |
| SAMEA122926871 | age | 26.4 (sequence archive) | 9636.0 (sequence archive) | withheld: neither value published |
| SAMEA122926896 | age | 49.2 (sequence archive) | 17967.0 (sequence archive) | withheld: neither value published |
| SAMEA122927005 | age | 38.0 (sequence archive) | 13784.0 (sequence archive) | withheld: neither value published |
| SAMEA122927267 | age | 29.6 (sequence archive) | 10811.0 (sequence archive) | withheld: neither value published |
| SAMEA122927346 | age | 64.0 (sequence archive) | 23407.0 (sequence archive) | withheld: neither value published |
| SAMEA122927603 | age | 37.1 (sequence archive) | 13545.0 (sequence archive) | withheld: neither value published |
| SAMEA122927649 | age | 61.0 (sequence archive) | 22294.0 (sequence archive) | withheld: neither value published |
longitudinal
113 of 588 people sampled more than once (259 samples; median 2, up to 5 per person) · follow-up median 2.7 y (max 10.3 y) · median interval between samples 22 mo (time from age at collection).
Each row is one person (36 shown of 113); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 844 | 100% | ||||
| country | 844 | 100% | 844 | |||
| health_condition | 844 | 100% | 844 | |||
| subject_id | 734 | 87% | 734 | |||
| detailed_location | 844 | 100% | ||||
| health_condition_detail | 844 | 100% | 844 | |||
| location_locality | 844 | 100% | 844 | |||
| sex | 840 | 100% | 840 | |||
| age_at_collection_days | 830 | 98% | 830 | |||
| collection_date | 734 | 87% | 734 |
- Inhibition of Aryl hydrocarbon receptor Interleukin-22 signaling and worsening of intestinal inflammation by <i>Sutterella</i> species. 2026 PMID 42324633 PMC13290079 own_data
Archive description
The human gut microbiome plays a central role in the onset and progression of inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC). However, both conditions are highly heterogeneous across clinical presentation, host biology, and microbial composition, complicating efforts to define consistent microbiome–disease associations. Here, leveraging a cross-sectional cohort of 845 shotgun metagenomic samples with extensive clinical metadata, we perform a fine-grained dissection of microbiome–phenotype relationships in IBD. We found shared and disease- or activity-specific microbial signatures, including a new non-monotonic triphasic signal for some key bacterial taxa. Conventional therapy was associated with worsened IBD dysbiosis, while biologics correlated with partial recovery of disease-depleted commensals. In addition, we built a machine learning model that predicts disease relapse at 1 year. Finally, we assessed IBD-associated strain-level variations, which appeared mainly driven by gene-content diversity. In particular, we identify disease-associated strain-level patterns in Faecalibacterium prausnitzii, well known for its importance in health.
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.title · “IBD Parisian Gut Microbiome Cohorte”
- body site study.description · “The human gut microbiome plays a”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA122926827 | age_at_collection_days | 11566.0 | R1 | 0.70 | sample.attr.host_age | 31.6659822039699 |
| SAMEA122926827 | collection_date | 2015-06-15 | R1 | 0.90 | biosample.attribute:collection_date | 2015-06-15 |
| SAMEA122926827 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA122926827 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | Crohn's disease |
| SAMEA122926827 | health_condition_detail | Crohn's disease | R1 | 0.90 | sample.attr.host_disease_status | Crohn's disease |
| SAMEA122926827 | location_locality | Paris | R4 | 0.40 | ena.study_title | IBD Parisian Gut Microbiome Cohorte |
| SAMEA122926827 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMEA122926827 | subject_id | 5721 | R1 | 0.85 | sample.attr.host_subject_id | 5721 |
Sequencing
844 runs over 844 samples · mean 15.49 Gbp per run (median 16.43 Gbp, total 13,076.49 Gbp; 844 runs with a base count) · layout PAIRED 844 · platform DNBSEQ 844 · models DNBSEQ-T7 (844) · 0% of runs with a Sandpiper profile · first public 2026-06-23
Authors (19)
Dupraz L first · Orianne G · Da Costa G · Gauthier R · Blondeau A · Boinet M · Farfar A · Creusot L · Magniez A · Dubois L · Guarino-Vignon P · Chollet L · Rolhion N · Danne C · Dvořák Z · Seksik P · Berteau O · Sokol H · Michel ML last
Downloads
PRJEB114255.csv.gz (31.6 KB) · parquet (114.5 KB) — all 844 samples, every field with route and confidence · PRJEB114255_determinations.csv.gz (52.9 KB) — 6,514 evidence rows