Gut microbiome in pediatric Crohn's disease during EEN therapy
111 fecal samples from children with Crohn's disease, collected before, during, and after exclusive enteral nutrition, in an intervention study of diet's effect on microbiota and metabolome. machine-written summary
111 samples · 111 runs · NL · Child · 2016 · 9.6 Mbp / sample · cohort Cholesterol Metabolism by Uncultured Human Gut Bac
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 154 sample values (sex, timepoint) |
| ✓ Abstract / description | 222 sample values (health condition, health condition detail) |
| ✓ Full text | 333 sample values (antibiotic exposure, collection date, country) · PMC12259524, PMC13284047, PMC7609694 |
| ○ 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 single_arm_before_after · population crohns_disease · Exclusive enteral nutrition (EEN) before/during/after treatment
“Feces of 43 children were collected prior, during and after EEN” — abstract:33144591 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “stool at baseline, during EEN, end of EEN, and follow-up on habitual diet” (time origin: intervention_start).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 111 | 100% | ||||
| country | 111 | 100% | 111 | |||
| health_condition | 111 | 100% | 111 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 111 | 100% | 111 | |||
| collection_date | 111 | 100% | 111 | |||
| health_condition_detail | 111 | 100% | 111 | |||
| sex | 111 | 100% | 111 | |||
| timepoint_label | 43 | 39% | 43 |
- Exclusive enteral nutrition mediates gut microbial and metabolic changes that are associated with remission in children with Crohn's disease. 2020 PMID 33144591 PMC7609694 own_data
- Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation. 2025 PMID 40658318 PMC12259524 unsure
- Baseline gut microbiome features associated with fecal calprotectin response to exclusive enteral nutrition in pediatric Crohn's disease. 2026 PMID 42339293 PMC13284047 unsure
Archive description
In Europe, 1 in 250 individuals have inflammatory bowel disease (IBD) and one in four of these patients is diagnosed during childhood. Paediatric patients with IBD are especially vulnerable to the physical and psychosocial morbidities of this disorder. Side-effects of standard immunosuppressive therapy, such as facial swelling, excessive weight gain, hair growth, and acne, reduce quality of life and will lead to poor compliance. Nutritional regimens using exclusive Enteral Nutrition (EEN) are a first stage therapy that offers fewer side effects than immunosuppressive treatments. However, because no other food intake is allowed with EEN, compliance is low. In addition, a therapy that acts by an unknown mechanism is less likely to be implemented in clinical practice. In this study, we aim to elucidate the mechanism of EEN therapy, which will contribute towards the clinical need for a well-tolerated nutritional therapy with sustained potential to induce remission. We hypothesize that microbiota-associated metabolic changes in paediatric IBD patients mediate the currently observed success of EEN. We will establish the changes in metabolites and microbial composition and determine the signalling molecules that act on epithelial and immune cells to improve IBD.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage study.title · “Paediatric Crohn's disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4008176 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | received antibiotics or probiotics within 3 months prior |
| SAMEA4008176 | collection_date | 2010-01/2014-07 | R3 | 0.70 | paper.fulltext.methods | performed between January 2010 and July 2014 |
| SAMEA4008176 | country | NL | R3 | 0.70 | paper.fulltext.methods | academic hospitals (Amsterdam UMC locations AMC and VUMC) |
| SAMEA4008176 | health_condition | crohns_disease | R4 | 0.50 | paper.abstract | children with Crohn's disease |
| SAMEA4008176 | health_condition_detail | All 43 children had Crohn's disease | R4 | 0.50 | paper.abstract | children with Crohn's disease |
| SAMEA4008176 | sex | female | R1 | 0.90 | sample.attr.arrayexpress_sex | female |
| SAMEA4008176 | timepoint_label | baseline | R1 | 0.70 | sample.name_rule:title | P4_Baseline |
Sequencing
111 runs over 111 samples · mean 9.7 Mbp per run (median 9.6 Mbp, total 1.08 Gbp; 111 runs with a base count) · layout PAIRED 111 · platform ILLUMINA 111 · models Illumina MiSeq (111) · 0% of runs with a Sandpiper profile · first public 2016-09-12
Authors (30)
Diederen K first · Li JV · Donachie GE · de Meij TG · de Waart DR · Hakvoort TBM · Kindermann A · Wagner J · Auyeung V · Te Velde AA · Heinsbroek SEM · Benninga MA · Kinross J · Walker AW · de Jonge WJ · Seppen J last · Yu S first · Li J · Ye Z · Zhang M · Guo X · Wang X · Liu L · Wang Y · Zhou X · Fu W · Zhang MQ · Chen YG last · Zheng H first · Chen W last
Downloads
PRJEB14084.csv.gz (3.1 KB) · parquet (73.9 KB) — all 111 samples, every field with route and confidence · PRJEB14084_determinations.csv.gz (4.3 KB) — 709 evidence rows