Gut microbiota in FMF, CAPS, and MKD patients, France
103 fecal shotgun metagenomic samples from France in a case-control study comparing gut microbiota among patients with FMF, CAPS, and MKD autoinflammatory diseases. machine-written summary
103 samples · 103 runs · FR · Adult · 2026 · 15.78 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 823 sample values (age, collection date, country, health condition, health condition detail, latitude, location region, longitude) |
| – Abstract / description | no abstract or project description |
| – Full text | no open-access full text linked |
| – 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. 19.0 vs 7042.0) — 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 |
|---|---|---|---|---|
| SAMEA123172793 | age | 19.0 (sequence archive) | 7042.0 (sequence archive) | withheld: neither value published |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 103 | 100% | ||||
| country | 103 | 100% | 103 | |||
| health_condition | 103 | 100% | 103 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 103 | 100% | 103 | |||
| detailed_location | 103 | 100% | ||||
| health_condition_detail | 103 | 100% | 103 | |||
| latitude | 103 | 100% | 103 | |||
| location_region | 103 | 100% | 103 | |||
| longitude | 103 | 100% | 103 | |||
| age_at_collection_days | 102 | 99% | 102 |
Archive description
Introduction: Familial Mediterranean fever (FMF), cryopyrinopathies (CAPS) and mevalonate deficiency (MKD) are autoinflammatory diseases with gastrointestinal involvement. Dysbiosis has been suggested with 16S rRNA sequencing in FMF. Objective: to describe gut microbiota in FMF, CAPS, and MKD using shotgun sequencing. Methods: 88 FMF, 13 CAPS, and 5 MKD adult patients underwent fecal shotgun metagenomic sequencing and metabolomic profiling. Results: FMF patients exhibited gut dysbiosis: reduced diversity, depletion of SCFA-producing bacteria and bacteriophages. No dysbiosis was detected in CAPS or MKD. Conclusion: Gut dysbiosis in FMF may contribute to inflammation. The absence of dysbiosis in CAPS and MKD suggests different mechanisms.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly 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 · “Gut microbiota analysis in”
- body site study.description · “autoinflammatory diseases with gastrointestinal involvement. Dysbiosis has”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “and 5 MKD adult patients underwent fecal”
- life stage sample.attr.host_age · “64 (n=16/103)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA123172763 | age_at_collection_days | 18993.0 | R1 | 0.85 | sample.attr.host_age | 52 |
| SAMEA123172763 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMEA123172763 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA123172763 | health_condition | autoimmune_inflammatory | R1 | 0.85 | biosample.attribute:description | Gut metagenome of FMF patient |
| SAMEA123172763 | health_condition_detail | Gut metagenome of FMF patient | R1 | 0.85 | biosample.attribute:description | Gut metagenome of FMF patient |
| SAMEA123172763 | latitude | 48.8500 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.85 2.35 |
| SAMEA123172763 | location_region | Ile-de-France | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.85 2.35 |
| SAMEA123172763 | longitude | 2.3500 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.85 2.35 |
Sequencing
103 runs over 103 samples · mean 14.67 Gbp per run (median 15.78 Gbp, total 1,510.50 Gbp; 103 runs with a base count) · layout PAIRED 103 · platform DNBSEQ 103 · models DNBSEQ-T7 (103) · 0% of runs with a Sandpiper profile · first public 2026-07-30 – 2026-08-13
Authors (0)
No author record.
Downloads
PRJEB115114.csv.gz (4.0 KB) · parquet (74.9 KB) — all 103 samples, every field with route and confidence · PRJEB115114_determinations.csv.gz (6.6 KB) — 823 evidence rows