Paediatric Crohn's disease gut microbiome, diet therapy
57 gut metagenome samples from children with Crohn's disease in Israel, studying gut microbiome changes during nutritional therapy (CDED+PEN or EEN) in an intervention design. machine-written summary
57 samples · 57 runs · IL · Age unknown · 2018 · 0.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 342 sample values (country, health condition, health condition detail, intervention, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC9880954 |
| ○ 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 |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design non_randomized_controlled · population crohns_disease · CDED+PEN or EEN nutritional therapy for 12 weeks in paediatric CD
“underwent one of two nutritional therapy regimes” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
21 of 21 people sampled more than once (57 samples; median 3, up to 3 per person) · follow-up median 3 mo (max 3 mo) · median interval between samples 42 d (time from timepoint labels). Schedule stated by the source: “Stool samples collected at three time points (Weeks 0, 6, 12) during nutritional therapy (CDED+PEN or EEN) in paediatric Crohn's disease patients.” (time origin: intervention_start); stated follow-up 3 mo.
Each row is one person (21 shown); 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 | 57 | 100% | ||||
| country | 57 | 100% | 57 | |||
| health_condition | 57 | 100% | 57 | |||
| subject_id | 57 | 100% | 57 | |||
| health_condition_detail | 57 | 100% | 57 | |||
| intervention | 57 | 100% | 57 | |||
| timepoint_label | 57 | 100% | 57 |
- Successful Dietary Therapy in Paediatric Crohn's Disease is Associated with Shifts in Bacterial Dysbiosis and Inflammatory Metabotype Towards Healthy Controls. 2023 PMID 36106847 PMC9880954 own_data
Archive description
Crohn's disease patients underwent one of two nutritional therapy regimes and were tracked for changes in their gut microbiome over the course of these treatments.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “changes in the gut microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104655651 | country | IL | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Israel |
| SAMEA104655651 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:TITLE | Gut microbiome of CD patients under nutritional therapy |
| SAMEA104655651 | health_condition_detail | Gut microbiome of CD patients under nutritional therapy | R1 | 0.85 | biosample.attribute:TITLE | Gut microbiome of CD patients under nutritional therapy |
| SAMEA104655651 | intervention | diet_intervention | R1 | 0.85 | biosample.attribute:TITLE | Gut microbiome of CD patients under nutritional therapy |
| SAMEA104655651 | subject_id | C1 | R1 | 0.70 | sample.name_rule:alias | C1-W0 |
| SAMEA104655651 | timepoint_label | W0 | R1 | 0.70 | sample.name_rule:alias | C1-W0 |
Sequencing
57 runs over 57 samples · mean 0.42 Gbp per run (median 0.42 Gbp, total 23.86 Gbp; 57 runs with a base count) · layout SINGLE 57 · platform ILLUMINA 57 · models NextSeq 500 (57) · 0% of runs with a Sandpiper profile · first public 2018-03-05
Authors (17)
Verburgt CM first · Dunn KA · Ghiboub M · Lewis JD · Wine E · Sigall Boneh R · Gerasimidis K · Shamir R · Penny S · Pinto DM · Cohen A · Bjorndahl P · Svolos V · Bielawski JP · Benninga MA · de Jonge WJ · Van Limbergen JE last
Downloads
PRJEB25264.csv.gz (2.3 KB) · parquet (71.4 KB) — all 57 samples, every field with route and confidence · PRJEB25264_determinations.csv.gz (3.1 KB) — 342 evidence rows