Pediatric Crohn's disease fecal bile acids, Canada
57 stool samples from pediatric Crohn's disease patients in Canada undergoing diet-based induction therapy, examining the relationship between fecal bile acid composition and microbiome structure; case-control design. machine-written summary
57 samples · 57 runs · CA · Child · 2019 · 0.31 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 342 sample values (collection date, country, health condition, health condition detail, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 · Nutritional therapy to induce remission in pediatric Crohn's disease
“undergoing nutritional therapy to induce disease remission” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
13 of 17 people sampled more than once (53 samples; median 4, up to 6 per person) · follow-up median 8 mo (max 10 mo) · median interval between samples 3 mo (time from timepoint labels). Schedule stated by the source: “stool at baseline, week 4, 8, 12, 24, 36, 48” (time origin: intervention_start).
Each row is one person (5 shown of 13); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 44 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| 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 | |||
| collection_date | 57 | 100% | 57 | |||
| health_condition_detail | 57 | 100% | 57 | |||
| timepoint_label | 57 | 100% | 57 |
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991 unsure
Archive description
Gut microbiome community structure is associated with Crohn’s disease (CD) development and response to therapy. Bile acids (BAs) play a central role in modulating intestinal immune responses, and changes in gut bacterial communities can profoundly alter the intestinal BA pool. We investigated the relationship between the gut microbiome and the fecal BA pool in stool samples obtained from a well-characterized cohort of pediatric CD patients undergoing nutritional therapy to induce disease remission. We found that fecal BA composition was altered in a sub-group of CD patients who did not sustain remission. The microbial community structures associated with priBA and secBA-dominant profiles were distinct.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids 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 · “The Relationship between Fecal Bile Acids and”
- body site study.description · “Gut microbiome community structure”
- body site study.title · “Relationship between Fecal Bile Acids and Microbiome”
- body site study.description · “response to therapy. Bile acids (BAs) play”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.title · “Community Structure in Pediatric Crohn’s Disease”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA6258727 | collection_date | 2014 | R1 | 0.90 | biosample.attribute:collection_date | 2014 |
| SAMEA6258727 | country | CA | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Canada |
| SAMEA6258727 | health_condition | crohns_disease | R1 | 0.85 | biosample.attribute:description | description: gut metagenome samples from Pediatric Crohn's disease patients |
| SAMEA6258727 | health_condition_detail | gut metagenome samples from Pediatric Crohn's disease patients | R1 | 0.85 | biosample.attribute:description | description: gut metagenome samples from Pediatric Crohn's disease patients |
| SAMEA6258727 | subject_id | NR01 | R1 | 0.70 | sample.name_rule:alias | alias: NR01-BSL_metag |
| SAMEA6258727 | timepoint_label | BSL | R1 | 0.70 | sample.name_rule:alias | alias: NR01-BSL_metag |
Sequencing
57 runs over 57 samples · mean 0.32 Gbp per run (median 0.31 Gbp, total 18.47 Gbp; 57 runs with a base count) · layout SINGLE 57 · platform ILLUMINA 57 · models NextSeq 500 (57) · 77% of runs with a Sandpiper profile · first public 2019-12-04
Authors (11)
Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last
Downloads
PRJEB35587.csv.gz (2.4 KB) · parquet (71.6 KB) — all 57 samples, every field with route and confidence · PRJEB35587_determinations.csv.gz (3.3 KB) — 342 evidence rows