Pediatric Crohn's disease gut microbiome, USA (case-control)
43 fecal/mucosal samples from children in the USA, comparing Crohn's disease patients (28) to healthy controls (8) in a case-control design. machine-written summary
43 samples · 731 runs · US · Child · 2014 · 8.00 Gbp / sample · cohort Segmented filamentous bacteria are worldwide human
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 43 sample values (country) |
| ✓ Abstract / description | 50 sample values (health condition detail, location region) |
| ○ Full text | read; no usable statement or table · PMC10939037, PMC11650326, PMC12268991, PMC13153320, PMC4059512, PMC5133246, PMC5598433, PMC6759048, PMC6905537, PMC8496832, PMC9685977, PMC9805753, PMC9860194 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 72 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 38 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 | 43 | 100% | ||||
| country | 43 | 100% | 43 | |||
| health_condition | 36 | 84% | 36 | |||
| subject_id | 0 | 0% | ||||
| detailed_location | 43 | 100% | ||||
| health_condition_detail | 43 | 100% | 36 | 7 | ||
| location_region | 43 | 100% | 43 |
- Comparative In silico Analysis of Butyrate Production Pathways in Gut Commensals and Pathogens. 2016 PMID 27994578 PMC5133246 own_data
- Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. 2017 PMID 28924494 PMC5598433 own_data
- Exploring thematic structure and predicted functionality of 16S rRNA amplicon data. 2019 PMID 31825995 PMC6905537 own_data
- Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network. 2021 PMID 34550967 PMC8496832 own_data
- Agr2-associated ER stress promotes adherent-invasive E. coli dysbiosis and triggers CD103+ dendritic cell IL-23-dependent ileocolitis. 2022 PMID 36384110 PMC9805753 own_data
8 more
- Mucosal microbiome is predictive of pediatric Crohn's disease across geographic regions in North America. 2022 PMID 36704050 PMC9860194
- The treatment-naive microbiome in new-onset Crohn's disease. 2014 PMID 24629344 PMC4059512
- Microbial genes and pathways in inflammatory bowel disease. 2019 PMID 31249397 PMC6759048
- Machine learning for data integration in human gut microbiome. 2022 PMID 36419034 PMC9685977
- Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. 2024 PMID 38423015 PMC10939037
- Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease. 2024 PMID 39691780 PMC11650326
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991
- Segmented filamentous bacteria are worldwide human gut commensals. 2026 PMID 41786702 PMC13153320
Archive description
Risk Stratification and Identification of Immunogenetic and Microbial Markers of Rapid Disease Progression in Children with Crohn’s Disease.
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 external_curation.infant_catalog · “body_site_call stool”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.description · “Disease Progression in Children with Crohn’s Disease.”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN02674595 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea_region | USA |
| SAMN02674595 | health_condition | crohns_disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN02674595 | health_condition_detail | Crohn Disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN02674601 | health_condition_detail | mixed_case_control: pediatric Crohn's disease patients vs non-IBD controls | R4 | 0.50 | paper.abstract | pediatric patients with CD and 221 non-inflammatory bowel disease controls |
| SAMN02674595 | location_region | North America | R4 | 0.30 | paper.abstract | controls from across North America |
Sequencing
731 runs over 43 samples · mean 0.48 Gbp per run (median 0.47 Gbp, total 349.73 Gbp; 731 runs with a base count) · layout PAIRED 731 · platform ILLUMINA 731 · models Illumina HiSeq 2000 (731) · 80% of runs with a Sandpiper profile · first public 2014-04-28 – 2015-01-20
Authors (65)
Viladomiu M first · Khounlotham M · Dogan B · Lima SF · Elsaadi A · Cardakli E · Castellanos JG · Ng C · Herzog J · Schoenborn AA · Ellermann M · Liu B · Zhang S · Gulati AS · Sartor RB · Simpson KW · Lipkin SM · Longman RS last · Shah R first · Hoffman K · Denson L · Kugathasan S · Kellermayer R last · Ha SM first · Lee K · Kim GH · Hurych J · Cinek O · Shim JO last · Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last · Kiran S first · Cruz AR · Daniau A · Ma B · Marbouty M · Pipoli Da Fonseca J · Legrand A · Baudry L · Cokelaer T · Bensussan M · Moya-Nilges M · Garneau J · Monot M · Ochieng JB · Antonio M · Tamboura B · de Vos WM · Salonen A · Hossain J · Omore R · Sow SO · Sansonetti PJ · Ravel J · Cerf-Bensussan N · Schnupf P last
Downloads
PRJNA237362.csv.gz (2.1 KB) · parquet (70.8 KB) — all 43 samples, every field with route and confidence · PRJNA237362_determinations.csv.gz (1.8 KB) — 165 evidence rows