Gut microbiota in Crohn's relatives vs healthy controls, children
96 faecal samples from adult relatives of children with Crohn's disease, unrelated healthy adults, and children with Crohn's disease, comparing microbiota composition during exclusive enteral nutrition in a case-control design. machine-written summary
96 samples · 96 runs · GB · Child · 2017 · 1.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2 sample values (country) · PMC11645270, PMC11650326, PMC12781464, PMC13589510, PMC5319678 |
| ✓ Supplementary tables | 312 sample values (age, antibiotic exposure, health condition, health condition detail, subject id, timepoint) |
| ✓ External resources | 368 sample values (age, antibiotic exposure, country, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – 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) in paediatric Crohn's disease
“sequential changes during exclusive enteral nutrition” — study.title (study level; per-sample arms are in the intervention column below)
longitudinalparent–child — not resolved
12 of 52 people sampled more than once (56 samples; median 5, up to 5 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 12 mo (time from age at collection). Schedule stated by the source: “CD children sampled at start of EEN, 15 days on EEN, 30 days on EEN, end of EEN, and after end of EEN on free diet; relatives/healthy controls sampled once.”.
Each row is one person (3 shown of 12); dots are samples at days since that person's first sample.
Adult relatives (mothers/fathers) of CD children sampled alongside their affected children; 16/19 CD children blood-related to relative cohort; unrelated healthy adults/children as controls..
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 96 | 100% | ||||
| country | 96 | 100% | 94 | 2 | ||
| health_condition | 96 | 100% | 96 | |||
| subject_id | 96 | 100% | 96 | |||
| antibiotic_exposure | 96 | 100% | 96 | |||
| health_condition_detail | 96 | 100% | 96 | |||
| timepoint_label | 96 | 100% | 96 | |||
| age_at_collection_days | 95 | 99% | 95 | |||
| sex | 11 | 11% | 11 |
- The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred. 2017 PMID 28222161 PMC5319678 own_data
- Noninvasive, microbiome-based diagnosis of inflammatory bowel disease. 2024 PMID 39367251 PMC11645270 unsure
- Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease. 2024 PMID 39691780 PMC11650326 unsure
- Deciphering the personalized functional redundancy hierarchy in the gut microbiome. 2025 PMID 41345980 PMC12781464 unsure
- Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease. 2026 PMID 42575094 PMC13589510 unsure
Archive description
The study is concerned with 16SrRNA and whole genome shotgun sequencing analysis of gut microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “associations between the gut microbiota and colonic”
- body site study.description · “sequencing analysis of gut microbiome.”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “nutrition (EEN) for children with Crohn's disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA39879418 | age_at_collection_days | 2922.0 | R2 | 0.75 | external.cmd source | age: 8; age_unit: Year; age_group: Child |
| SAMEA40012918 | age_at_collection_days | 16801.5 | R2 | 0.80 | paper.supp.pone.0172605.s005.csv[Age] | 46 |
| SAMEA39879418 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA40012918 | antibiotic_exposure | no | R2 | 0.80 | paper.supp.pone.0172605.s005.csv[Antibiotics] | No |
| SAMEA39879418 | country | GB | R2 | 0.75 | external.cmd source | country: United Kingdom |
| SAMEA40012918 | country | GB | R3 | 0.50 | paper.fulltext.methods | Yorkhill Hospital Research Ethics Committee |
| SAMEA39879418 | health_condition | crohns_disease | R2 | 0.80 | paper.supp.pone.0172605.s005.csv[Type] | CD |
| SAMEA39892168 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA39879418 | health_condition_detail | CD | R2 | 0.80 | paper.supp.pone.0172605.s005.csv[Type] | CD |
| SAMEA39892168 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA39892168 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMEA39879418 | subject_id | 1 | R2 | 0.80 | paper.supp.pone.0172605.s005.csv[New participant code] | 1 |
| SAMEA39879418 | timepoint_label | Crohn's at start of EEN | R2 | 0.80 | paper.supp.pone.0172605.s005.csv[Sample type explained] | Crohn's at start of EEN |
Sequencing
96 runs over 96 samples · mean 1.18 Gbp per run (median 1.10 Gbp, total 112.87 Gbp; 96 runs with a base count) · layout SINGLE 96 · platform ILLUMINA 96 · models Illumina MiSeq (96) · 49% of runs with a Sandpiper profile · first public 2017-01-07
Authors (52)
Ijaz UZ first · Quince C · Hanske L · Loman N · Calus ST · Bertz M · Edwards CA · Gaya DR · Hansen R · McGrogan P · Russell RK · Gerasimidis K last · Zheng J first · Sun Q · Zhang M · Liu C · Su Q · Zhang L · Xu Z · Lu W · Ching J · Tang W · Cheung CP · Hamilton AL · Wilson O'Brien AL · Wei SC · Bernstein CN · Rubin DT · Chang EB · Morrison M · Kamm MA · Chan FKL · Zhang J · Ng SC last · Ha SM first · Lee K · Kim GH · Hurych J · Cinek O · Shim JO last · Jiang Y first · Che L · Li SC last · Zhai J first · Li Y · Liu J · Su X · Cui R · Zheng D · Sun Y · Yu J · Dai C last
Downloads
PRJEB18780.csv.gz (3.8 KB) · parquet (74.6 KB) — all 96 samples, every field with route and confidence · PRJEB18780_determinations.csv.gz (8.0 KB) — 682 evidence rows