Longitudinal gut microbiome study in CKD patients, France
343 samples from adult patients with chronic kidney disease in France, part of a longitudinal study examining gut microbiome composition, uraemic toxins, and CKD severity/progression. machine-written summary
343 samples · 3,541 runs · FR · Adult · 2025 · 3.16 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,372 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 686 sample values (health condition, health condition detail) · PMC12505076 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 343 sample values (antibiotic exposure) · from BugSigDB |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
103 of 240 people sampled more than once (206 samples; median 2, up to 2 per person) · follow-up median 2.9 y (max 3.8 y) · median interval between samples 2.9 y (time from collection dates). Schedule stated by the source: “baseline (T0) and follow-up (T1) ~2.8 years later in 103 of 240 patients” (time origin: baseline); stated follow-up 2.8 y.
Each row is one person (36 shown of 103); 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 | 343 | 100% | ||||
| country | 343 | 100% | 343 | |||
| health_condition | 343 | 100% | 343 | |||
| subject_id | 343 | 100% | 343 | |||
| antibiotic_exposure | 343 | 100% | 343 | |||
| collection_date | 343 | 100% | 343 | |||
| health_condition_detail | 343 | 100% | 343 | |||
| timepoint_label | 343 | 100% | 343 |
- Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study. 2025 PMID 40461059 PMC12505076 own_data
Archive description
Toxic microbiome and progression of chronic kidney disease. Insight of the longitudinal study-CKD-Microbiome
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 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 |
|---|---|---|---|---|---|---|
| SAMEA117579995 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 3 months |
| SAMEA117579995 | collection_date | 2016-12-19 | R1 | 0.90 | biosample.attribute:collection_date | 2016-12-19 |
| SAMEA117579995 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA117579995 | health_condition | kidney_disease | R3 | 0.70 | paper.fulltext.abstract | non-dialysis-dependent patients with chronic kidney disease |
| SAMEA117579995 | health_condition_detail | non-dialysis-dependent CKD stages 2-5 | R3 | 0.70 | paper.fulltext.abstract | non-dialysis-dependent patients with chronic kidney disease |
| SAMEA117579995 | subject_id | ID150 | R1 | 0.85 | biosample.attribute:id_ind | ID150 |
| SAMEA117579995 | timepoint_label | T0 | R1 | 0.85 | sample.attr.timepoint | T0 |
Sequencing
3,541 runs over 343 samples · mean 0.31 Gbp per run (median 0.26 Gbp, total 1,104.39 Gbp; 3,541 runs with a base count) · layout SINGLE 3,541 · platform ION_TORRENT 3,541 · models Ion Torrent Proton (2,689), Ion Torrent S5 (852) · 0% of runs with a Sandpiper profile · first public 2025-01-14
Authors (24)
Laiola M first · Koppe L · Larabi A · Thirion F · Lange C · Quinquis B · David A · Le Chatelier E · Benoit B · Sequino G · Chanon S · Vieille-Marchiset A · Herpe YE · Alvarez JC · Glorieux G · Krukowski H · Huys GR · Raes J · Fouque D · Massy ZA · Ehrlich SD · Stengel B · Wagner S · CKD-REIN Study collaborators last
Downloads
PRJEB81434.csv.gz (11.2 KB) · parquet (85.2 KB) — all 343 samples, every field with route and confidence · PRJEB81434_determinations.csv.gz (16.6 KB) — 2,401 evidence rows