Pediatric Crohn's disease gut microbiome during EEN, Canada
139 fecal samples from pediatric Crohn's disease patients (age 8-15) in Canada, collected longitudinally up to 96 weeks during exclusive enteral nutrition to study gut microbiome changes linked to treatment remission. machine-written summary
139 samples · 139 runs · CA · Child · 2019 · 24.2 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,272 sample values (collection date, country, health condition, health condition detail, latitude, location region, longitude, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 280 sample values (age, location locality, location site) · PMC7301407 |
| ○ 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 observational_with_procedure · population crohns_disease · Exclusive enteral nutrition (EEN) induction therapy
“treatment with EEN” — abstract:31961432 (study level; per-sample arms are in the intervention column below)
longitudinal
20 of 22 people sampled more than once (137 samples; median 7, up to 10 per person) · follow-up median 20 mo (max 2.0 y) · median interval between samples 3 mo (time from collection dates). Schedule stated by the source: “Fecal samples from same patients at baseline and multiple follow-up points up to 96 weeks” (time origin: treatment_start); stated follow-up 22 mo.
Each row is one person (14 shown of 20); 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 | 139 | 100% | ||||
| country | 139 | 100% | 139 | |||
| health_condition | 139 | 100% | 139 | |||
| subject_id | 139 | 100% | 139 | |||
| detailed_location | 139 | 100% | ||||
| health_condition_detail | 139 | 100% | 139 | |||
| latitude | 139 | 100% | 139 | |||
| location_locality | 139 | 100% | 139 | |||
| location_region | 139 | 100% | 139 | |||
| location_site | 139 | 100% | 139 | |||
| longitude | 139 | 100% | 139 | |||
| sex | 139 | 100% | 139 | |||
| collection_date | 138 | 99% | 138 | |||
| timepoint_label | 22 | 16% | 22 | |||
| age_at_collection_days | 2 | 1% | 2 |
- Bacterial Taxa and Functions Are Predictive of Sustained Remission Following Exclusive Enteral Nutrition in Pediatric Crohn's Disease. 2020 PMID 31961432 PMC7301407 own_data
- 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
Induction of remission in pediatric Crohn’s disease (CD) patients by exclusive enteral nutrition (EEN) extensively involves the gut microbiome. In this follow-up study of pediatric CD patients undergoing treatment with EEN, we employ machine learning models trained on baseline gut microbiome data to distinguish those that achieved sustained remission (SR) and those who relapsed (non-SR) after 24 weeks. We collected robust clinical data from patients at each timepoint. A total of 139 fecal samples were obtained from 22 patients (age 8-15) for up to 96 weeks. Gut microbiome taxonomy was assessed by 16S rRNA gene sequencing and functional capacity was assessed by metagenomic sequencing. We used standard metrics of diversity and taxonomy to quantify differences between SR and non-SR patients, and to associate gut microbial shifts with fecal calprotectin (FCP), and disease severity as quantified by wPCDAI. We used microbial datasets in addition to clinical metadata in random forests (RF) models to classify treatment response and predict FCP levels.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adolescent by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “139 fecal samples were obtained”
- life stage study.description · “22 patients (age 8-15)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5883261 | age_at_collection_days | 2922.0 | R3 | 0.80 | paper.body.TABLE 1.[Age at Baseline] | 8 |
| SAMEA5883198 | collection_date | 2014-10-26 | R1 | 0.90 | biosample.attribute:collection_date | 2014-10-26 |
| SAMEA5883198 | country | CA | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Canada |
| SAMEA5883198 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | Crohn's Disease |
| SAMEA5883198 | health_condition_detail | Crohn's Disease | R1 | 0.90 | sample.attr.gastrointestinal_tract_disorder | Crohn's Disease |
| SAMEA5883198 | latitude | 44.6372 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.63716 -63.584014 |
| SAMEA5883198 | location_locality | Halifax | R3 | 0.70 | paper.fulltext.methods | IWK Health Centre (Halifax, NS, Canada) |
| SAMEA5883198 | location_region | Nova Scotia | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.63716 -63.584014 |
| SAMEA5883198 | location_site | IWK Health Centre | R3 | 0.70 | paper.fulltext.methods | IWK Health Centre (Halifax, NS, Canada) |
| SAMEA5883198 | longitude | -63.5840 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.63716 -63.584014 |
| SAMEA5883198 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMEA5883198 | subject_id | CD001 | R1 | 0.85 | sample.attr.host_subject_id | CD001 |
| SAMEA5883202 | timepoint_label | baseline | R1 | 0.70 | sample.name_rule:alias | CD001-B |
Sequencing
139 runs over 139 samples · mean 22.5 Mbp per run (median 24.2 Mbp, total 3.13 Gbp; 139 runs with a base count) · layout PAIRED 139 · platform ILLUMINA 139 · models NextSeq 550 (139) · 0% of runs with a Sandpiper profile · first public 2019-10-01
Authors (9)
Jones CMA first · Connors J · Dunn KA · Bielawski JP · Comeau AM · Langille MGI · Van Limbergen J last · Zheng H first · Chen W last
Downloads
PRJEB33603.csv.gz (4.8 KB) · parquet (77.5 KB) — all 139 samples, every field with route and confidence · PRJEB33603_determinations.csv.gz (9.8 KB) — 1,552 evidence rows